WorldWideScience

Sample records for deep evolutionary origins

  1. Evolutionary origins of Hsp90 chaperones and a deep paralogy in their bacterial ancestors.

    Science.gov (United States)

    Stechmann, Alexandra; Cavalier-Smith, Thomas

    2004-01-01

    The 82-90 kD family of molecular chaperone proteins has homologs in eukaryotes (Hsp90) and many eubacteria (HtpG) but not in Archaebacteria. We used representatives of all four different eukaryotic paralogs (cytosolic, endoplasmic reticulum (ER), chloroplast, mitochondrial) together with numerous eubacterial HtpG proteins for phylogenetic analyses to investigate their evolutionary origins. Our trees confirm that none of the organellar Hsp90s derives from the endosymbionts of early eukaryotes. Contrary to previous suggestions of distant origins through lateral gene transfer (LGT) all eukaryote Hsp90s are related to Gram-positive eubacterial HtpG proteins. The nucleocytosolic, ER and chloroplast Hsp90 paralogs are clearly mutually related. The origin of mitochondrial Hsp90 is more obscure, as these sequences are deeply nested within eubacteria. Our trees also reveal a deep split within eubacteria into a group of mainly long-branching sequences (including the eukaryote mitochondrial Hsp90s) and another group comprising exclusively short-branching HtpG proteins, from which the cytosolic/ER versions probably arose. Both versions are present in several eubacterial phyla, suggesting gene duplication very early in eubacterial evolution and multiple independent losses thereafter. We identified one probable case of LGT within eubacteria. However, multiple losses can simply explain the evolutionary pattern of the eubacterial HtpG paralogs and predominate over LGT. We suggest that the actinobacterial ancestor of eukaryotes harbored genes for both eubacterial HtpG paralogs, as the actinobacterium Streptomyces coelicolor still does; one could have given rise to the mitochondrial Hsp90 and the other, following another duplication event in the ancestral eukaryote, to the cytosolic and ER Hsp90 homologs.

  2. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    Ellen Clarke

    2014-04-01

    An `evolutionary transition in individuality’ or `major transition’ is a transformation in the hierarchical level at which natural selection operates on a population. In this article I give an abstract (i.e. level-neutral and substrate-neutral) articulation of the transition process in order to precisely understand how such processes can happen, especially how they can get started.

  3. Evolutionary origins of membrane proteins

    Science.gov (United States)

    Mulkidjanian, Armen Y.; Galperin, Michael Y.

    Although the genes that encode membrane proteins make about 30% of the sequenced genomes, the evolution of membrane proteins and their origins are still poorly understood. Here we address this topic by taking a closer look at those membrane proteins the ancestors of which were present in the Last Universal Common Ancestor, and in particular, the F/V-type rotating ATPases. Reconstruction of their evolutionary history provides hints for understanding not only the origin of membrane proteins, but also of membranes themselves. We argue that the evolution of biological membranes could occur as a process of coevolution of lipid bilayers and membrane proteins, where the increase in the ion-tightness of the membrane bilayer may have been accompanied by a transition from amphiphilic, pore-forming membrane proteins to highly hydrophobic integral membrane complexes.

  4. Evolutionary process of deep-sea bathymodiolus mussels.

    Directory of Open Access Journals (Sweden)

    Jun-Ichi Miyazaki

    Full Text Available BACKGROUND: Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. METHODOLOGY/PRINCIPAL FINDING: We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI and NADH dehydrogenase subunit 4 (ND4 genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. CONCLUSIONS/SIGNIFICANCE: The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of

  5. The Evolutionary Origins of Hierarchy.

    Science.gov (United States)

    Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

    2016-06-01

    Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  6. The Evolutionary Origins of Hierarchy.

    Directory of Open Access Journals (Sweden)

    Henok Mengistu

    2016-06-01

    Full Text Available Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments. Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  7. The Evolutionary Origins of Hierarchy.

    Directory of Open Access Journals (Sweden)

    Henok Mengistu

    2016-06-01

    Full Text Available Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments. Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  8. Evolutionary origins of leadership and followership.

    Science.gov (United States)

    Van Vugt, Mark

    2006-01-01

    Drawing upon evolutionary logic, leadership is reconceptualized in terms of the outcome of strategic interactions among individuals who are following different, yet complementary, decision rules to solve recurrent coordination problems. This article uses the vast psychological literature on leadership as a database to test several evolutionary hypotheses about the origins of leadership and followership in humans. As expected, leadership correlates with initiative taking, trait measures of intelligence, specific task competencies, and several indicators of generosity. The review finds no link between leadership and dominance. The evolutionary analysis accounts for reliable age, health, and sex differences in leadership emergence. In general, evolutionary theory provides a useful, integrative framework for studying leader-follower relationships and generates various novel research hypotheses.

  9. The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals

    Directory of Open Access Journals (Sweden)

    Stolarski Jarosław

    2011-10-01

    Full Text Available Abstract Background Scleractinian corals are currently a focus of major interest because of their ecological importance and the uncertain fate of coral reefs in the face of increasing anthropogenic pressure. Despite this, remarkably little is known about the evolutionary origins of corals. The Scleractinia suddenly appear in the fossil record about 240 Ma, but the range of morphological variation seen in these Middle Triassic fossils is comparable to that of modern scleractinians, implying much earlier origins that have so far remained elusive. A significant weakness in reconstruction(s of early coral evolution is that deep-sea corals have been poorly represented in molecular phylogenetic analyses. Results By adding new data from a large and representative range of deep-water species to existing molecular datasets and applying a relaxed molecular clock, we show that two exclusively deep-sea families, the Gardineriidae and Micrabaciidae, diverged prior to the Complexa/Robusta coral split around 425 Ma, thereby pushing the evolutionary origin of scleractinian corals deep into the Paleozoic. Conclusions The early divergence and distinctive morphologies of the extant gardineriid and micrabaciid corals suggest a link with Ordovician "scleractiniamorph" fossils that were previously assumed to represent extinct anthozoan skeletonized lineages. Therefore, scleractinian corals most likely evolved from Paleozoic soft-bodied ancestors. Modern shallow-water Scleractinia, which are dependent on symbionts, appear to have had several independent origins from solitary, non-symbiotic precursors. The Scleractinia have survived periods of massive climate change in the past, suggesting that as a lineage they may be less vulnerable to future changes than often assumed.

  10. Evolutionary origin of rhizobium Nod factor signaling.

    Science.gov (United States)

    Streng, Arend; op den Camp, Rik; Bisseling, Ton; Geurts, René

    2011-10-01

    For over two decades now, it is known that the nodule symbiosis between legume plants and nitrogen fixing rhizobium bacteria is set in motion by the bacterial signal molecule named nodulation (Nod) factor. Upon Nod factor perception a signaling cascade is activated that is also essential for endomycorrhizal symbiosis (Fig. 1). This suggests that rhizobium co-opted the evolutionary far more ancient mycorrhizal signaling pathway in order to establish an endosymbiotic interaction with legumes. As arbuscular mycorrhizal fungi of the Glomeromycota phylum can establish a symbiosis with the fast majority of land plants, it is most probable that this signaling cascade is wide spread in plant kingdom. However, Nod factor perception generally is considered to be unique to legumes. Two recent breakthroughs on the evolutionary origin of Rhizobium Nod factor signaling demonstrate that this is not the case. The purification of Nod factor-like molecules excreted by the mycorrhizal fungus Glomus intraradices and the role of the LysM-type Nod factor receptor PaNFP in the non-legume Parasponia andersonii provide novel understanding on the evolution of rhizobial Nod factor signaling.

  11. Evolutionary origin of the turtle skull.

    Science.gov (United States)

    Bever, G S; Lyson, Tyler R; Field, Daniel J; Bhullar, Bhart-Anjan S

    2015-09-10

    Transitional fossils informing the origin of turtles are among the most sought-after discoveries in palaeontology. Despite strong genomic evidence indicating that turtles evolved from within the diapsid radiation (which includes all other living reptiles), evidence of the inferred transformation between an ancestral turtle with an open, diapsid skull to the closed, anapsid condition of modern turtles remains elusive. Here we use high-resolution computed tomography and a novel character/taxon matrix to study the skull of Eunotosaurus africanus, a 260-million-year-old fossil reptile from the Karoo Basin of South Africa, whose distinctive postcranial skeleton shares many unique features with the shelled body plan of turtles. Scepticism regarding the status of Eunotosaurus as the earliest stem turtle arises from the possibility that these shell-related features are the products of evolutionary convergence. Our phylogenetic analyses indicate strong cranial support for Eunotosaurus as a critical transitional form in turtle evolution, thus fortifying a 40-million-year extension to the turtle stem and moving the ecological context of its origin back onto land. Furthermore, we find unexpected evidence that Eunotosaurus is a diapsid reptile in the process of becoming secondarily anapsid. This is important because categorizing the skull based on the number of openings in the complex of dermal bone covering the adductor chamber has long held sway in amniote systematics, and still represents a common organizational scheme for teaching the evolutionary history of the group. These discoveries allow us to articulate a detailed and testable hypothesis of fenestral closure along the turtle stem. Our results suggest that Eunotosaurus represents a crucially important link in a chain that will eventually lead to consilience in reptile systematics, paving the way for synthetic studies of amniote evolution and development.

  12. Probing the evolutionary origins of music perception.

    Science.gov (United States)

    McDermott, Josh; Hauser, Marc D

    2005-12-01

    Empirical data have recently begun to inform debates on the evolutionary origins of music. In this paper we discuss some of our recent findings and related theoretical issues. We claim that theories of the origins of music will be usefully constrained if we can determine which aspects of music perception are innate, and, of those, which are uniquely human and specific to music. Comparative research in nonhuman animals, particularly nonhuman primates, is thus critical to the debate. In this paper we focus on the preferences that characterize most humans' experience of music, testing whether similar preferences exist in nonhuman primates. Our research suggests that many rudimentary acoustic preferences, such as those for consonant over dissonant intervals, may be unique to humans. If these preferences prove to be innate in humans, they may be candidates for music-specific adaptations. To establish whether such preferences are innate in humans, one important avenue for future research will be the collection of data from different cultures. This may be facilitated by studies conducted over the internet.

  13. Evolutionary origins of animal skeletal biomineralization.

    Science.gov (United States)

    Murdock, Duncan J E; Donoghue, Philip C J

    2011-01-01

    The evolutionary history of biomineralization in animals is crucial to our understanding of modern mineralized tissues. Traditional methods of unravelling this history have aimed to derive a theory of the development of biomineralization through evolution by the comparison of mineralized systems in model organisms. This has led to the recognition of the 'biomineralization toolkit' and raised the question of the homology of mineralized tissues versus convergent or parallel evolution. The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. In addition, the fossil record of the earliest mineralized skeletons presents a rapid proliferation of biomineralization across a range of animal phyla with fossil representatives of many modern biomineralizing phyla. A synthesis of molecular, developmental, phylogenetic and fossil evidence demonstrates the convergent or parallel evolution of biomineralization in animals at the phylum level. The fossil record of the Cambrian explosion not only provides vital evidence for the evolution of animal mineralized tissues but also suggests a mechanism for its rapid and synchronous convergent origin. Copyright © 2011 S. Karger AG, Basel.

  14. On The Evolutionary Origin of Symbolic Communication

    Science.gov (United States)

    Grouchy, Paul; D’Eleuterio, Gabriele M. T.; Christiansen, Morten H.; Lipson, Hod

    2016-10-01

    The emergence of symbolic communication is often cited as a critical step in the evolution of Homo sapiens, language, and human-level cognition. It is a widely held assumption that humans are the only species that possess natural symbolic communication schemes, although a variety of other species can be taught to use symbols. The origin of symbolic communication remains a controversial open problem, obfuscated by the lack of a fossil record. Here we demonstrate an unbroken evolutionary pathway from a population of initially noncommunicating robots to the spontaneous emergence of symbolic communication. Robots evolve in a simulated world and are supplied with only a single channel of communication. When their ability to reproduce is motivated by the need to find a mate, robots evolve indexical communication schemes from initially noncommunicating populations in 99% of all experiments. Furthermore, 9% of the populations evolve a symbolic communication scheme allowing pairs of robots to exchange information about two independent spatial dimensions over a one-dimensional channel, thereby increasing their chance of reproduction. These results suggest that the ability for symbolic communication could have emerged spontaneously under natural selection, without requiring cognitive preadaptations or preexisting iconic communication schemes as previously conjectured.

  15. On The Evolutionary Origin of Symbolic Communication

    Science.gov (United States)

    Grouchy, Paul; D’Eleuterio, Gabriele M. T.; Christiansen, Morten H.; Lipson, Hod

    2016-01-01

    The emergence of symbolic communication is often cited as a critical step in the evolution of Homo sapiens, language, and human-level cognition. It is a widely held assumption that humans are the only species that possess natural symbolic communication schemes, although a variety of other species can be taught to use symbols. The origin of symbolic communication remains a controversial open problem, obfuscated by the lack of a fossil record. Here we demonstrate an unbroken evolutionary pathway from a population of initially noncommunicating robots to the spontaneous emergence of symbolic communication. Robots evolve in a simulated world and are supplied with only a single channel of communication. When their ability to reproduce is motivated by the need to find a mate, robots evolve indexical communication schemes from initially noncommunicating populations in 99% of all experiments. Furthermore, 9% of the populations evolve a symbolic communication scheme allowing pairs of robots to exchange information about two independent spatial dimensions over a one-dimensional channel, thereby increasing their chance of reproduction. These results suggest that the ability for symbolic communication could have emerged spontaneously under natural selection, without requiring cognitive preadaptations or preexisting iconic communication schemes as previously conjectured. PMID:27721422

  16. Ernst Haeckel's concept of an evolutionary origin of life.

    Science.gov (United States)

    Dose, K

    1981-01-01

    In 1865/66 E. Haeckel for the first time suggested an evolutionary sequence in order to explain the origin of the first living cell. Haeckel's concept is compared with modern theories of the origin of life. It is evident that Haeckel has not as yet received the credit that he deserves for his evolutionary concept.

  17. A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

    Science.gov (United States)

    Werner, Gijsbert D. A.; Cornwell, William K.; Sprent, Janet I.; Kattge, Jens; Kiers, E. Toby

    2014-01-01

    Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. PMID:24912610

  18. Evolutionary cell biology: two origins, one objective.

    Science.gov (United States)

    Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

    2014-12-02

    All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

  19. Hot, deep origin of petroleum: deep basin evidence and application

    Science.gov (United States)

    Price, Leigh C.

    1978-01-01

    Use of the model of a hot deep origin of oil places rigid constraints on the migration and entrapment of crude oil. Specifically, oil originating from depth migrates vertically up faults and is emplaced in traps at shallower depths. Review of petroleum-producing basins worldwide shows oil occurrence in these basins conforms to the restraints of and therefore supports the hypothesis. Most of the world's oil is found in the very deepest sedimentary basins, and production over or adjacent to the deep basin is cut by or directly updip from faults dipping into the basin deep. Generally the greater the fault throw the greater the reserves. Fault-block highs next to deep sedimentary troughs are the best target areas by the present concept. Traps along major basin-forming faults are quite prospective. The structural style of a basin governs the distribution, types, and amounts of hydrocarbons expected and hence the exploration strategy. Production in delta depocenters (Niger) is in structures cut by or updip from major growth faults, and structures not associated with such faults are barren. Production in block fault basins is on horsts next to deep sedimentary troughs (Sirte, North Sea). In basins whose sediment thickness, structure and geologic history are known to a moderate degree, the main oil occurrences can be specifically predicted by analysis of fault systems and possible hydrocarbon migration routes. Use of the concept permits the identification of significant targets which have either been downgraded or ignored in the past, such as production in or just updip from thrust belts, stratigraphic traps over the deep basin associated with major faulting, production over the basin deep, and regional stratigraphic trapping updip from established production along major fault zones.

  20. The human dark side: evolutionary psychology and original sin.

    Science.gov (United States)

    Lee, Joseph; Theol, M

    2014-04-01

    Human nature has a dark side, something important to religions. Evolutionary psychology has been used to illuminate the human shadow side, although as a discipline it has attracted criticism. This article seeks to examine the evolutionary psychology's understanding of human nature and to propose an unexpected dialog with an enduring account of human evil known as original sin. Two cases are briefly considered: murder and rape. To further the exchange, numerous theoretical and methodological criticisms and replies of evolutionary psychology are explored jointly with original sin. Evolutionary psychology can partner with original sin since they share some theoretical likenesses and together they offer insights into the nature of what it means to be human.

  1. The Evolutionary Origins of Human Generosity

    NARCIS (Netherlands)

    Komter, Aafke

    2010-01-01

    This article examines how altruism and self-interest are linked in human generosity, and what social scientists can learn from this linkage. The origins of generosity are explored by combining biological, psychological, anthropological and sociological evidence. Kinship altruism, reciprocal

  2. The evolutionary origin and significance of Menopause

    Science.gov (United States)

    Pollycove, Ricki; Naftolin, Frederick; Simon, James A.

    2010-01-01

    Contemporary human females have long life expectancy (81y US), especially relative to age at menopause (51y US). Menopause is a consequence of reproductive aging and follicular depletion (ovarian failure), yielding very low circulating estrogen* serum concentrations and biologically disadvantageous metabolic alterations. Stated in terms of antagonistic pleiotropy, the ongoing hypoestrogenic endocrine environment, beneficial during lactation, results in acceleration of several age-related health conditions following menopause (i.e. late postmenopausal osteoporosis, cardiovascular disease and cognitive decline). In contrast, the complex hypoestrogenic hormonal milieu present during postpartum lactation provides biologic advantages to both mother and newborn. The lactational hormonal milieu causes symptoms similar to those of the late perimenopause and early postmenopause, prompting theories for their biologic selective advantage. The precepts of evolutionary medicine encourage a reassessment of hormone therapy. Based on data presented, the authors propose additional opportunities for disease prevention and morbidity reduction in postmenopausal women. PMID:21252729

  3. The Evolutionary Origins of Human Generosity

    NARCIS (Netherlands)

    Komter, Aafke

    2010-01-01

    This article examines how altruism and self-interest are linked in human generosity, and what social scientists can learn from this linkage. The origins of generosity are explored by combining biological, psychological, anthropological and sociological evidence. Kinship altruism, reciprocal altruism

  4. Evolutionary origin of the turtle shell.

    Science.gov (United States)

    Lyson, Tyler R; Bever, Gabe S; Scheyer, Torsten M; Hsiang, Allison Y; Gauthier, Jacques A

    2013-06-17

    The origin of the turtle shell has perplexed biologists for more than two centuries. It was not until Odontochelys semitestacea was discovered, however, that the fossil and developmental data could be synthesized into a model of shell assembly that makes predictions for the as-yet unestablished history of the turtle stem group. We build on this model by integrating novel data for Eunotosaurus africanus-a Late Guadalupian (∼260 mya) Permian reptile inferred to be an early stem turtle. Eunotosaurus expresses a number of relevant characters, including a reduced number of elongate trunk vertebrae (nine), nine pairs of T-shaped ribs, inferred loss of intercostal muscles, reorganization of respiratory muscles to the ventral side of the ribs, (sub)dermal outgrowth of bone from the developing perichondral collar of the ribs, and paired gastralia that lack both lateral and median elements. These features conform to the predicted sequence of character acquisition and provide further support that E. africanus, O. semitestacea, and Proganochelys quenstedti represent successive divergences from the turtle stem lineage. The initial transformations of the model thus occurred by the Middle Permian, which is congruent with molecular-based divergence estimates for the lineage, and remain viable whether turtles originated inside or outside crown Diapsida. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Science.gov (United States)

    Blackstone, Neil W.

    2016-01-01

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

  6. An Evolutionary Framework for Understanding the Origin of Eukaryotes.

    Science.gov (United States)

    Blackstone, Neil W

    2016-04-27

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  7. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Directory of Open Access Journals (Sweden)

    Neil W. Blackstone

    2016-04-01

    Full Text Available Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  8. The origins of variation: evolutionary insights from developmental science.

    Science.gov (United States)

    Lickliter, Robert

    2013-01-01

    Evidence from contemporary epigenetic research indicates that it is not biologically meaningful to discuss genes without reference to the molecular, cellular, organismal, and environmental context within which they are activated and expressed. Genetic and nongenetic factors, including those beyond the organism, constitute a dynamic relational developmental system. This insight highlights the importance of bringing together genetics, development, and ecology into one explanatory framework for a more complete understanding of the emergence and maintenance of phenotypic stability and variability. In this Chapter, I review some examples of this integrative effort and explore its implications for developmental and evolutionary science, with a particular emphasis on the origins of phenotypic novelty. I argue that developmental science is critical to this integrative effort, in that evolutionary explanation cannot be complete without developmental explanation. This is the case because the process of development generates the phenotypic variation on which natural selection can act.

  9. Evolutionary origins and early development of number processing

    CERN Document Server

    Geary, David C; Mann Koepke, Kathleen

    2014-01-01

    The first volume in this ground-breaking series focuses on the origins and early development of numerical cognition in non-human primates, lower vertebrates, human infants, and preschool children. The text will help readers understand the nature and complexity of these foundational quantitative concepts and skills along with evolutionary precursors and early developmental trajectories. Brings together and focuses the efforts and research of multiple disciplines working in math cognition.The contributors bring vast knowledge and experience to bear on resolving extant

  10. Charles Darwin and the origins of plant evolutionary developmental biology.

    Science.gov (United States)

    Friedman, William E; Diggle, Pamela K

    2011-04-01

    Much has been written of the early history of comparative embryology and its influence on the emergence of an evolutionary developmental perspective. However, this literature, which dates back nearly a century, has been focused on metazoans, without acknowledgment of the contributions of comparative plant morphologists to the creation of a developmental view of biodiversity. We trace the origin of comparative plant developmental morphology from its inception in the eighteenth century works of Wolff and Goethe, through the mid nineteenth century discoveries of the general principles of leaf and floral organ morphogenesis. Much like the stimulus that von Baer provided as a nonevolutionary comparative embryologist to the creation of an evolutionary developmental view of animals, the comparative developmental studies of plant morphologists were the basis for the first articulation of the concept that plant (namely floral) evolution results from successive modifications of ontogeny. Perhaps most surprisingly, we show that the first person to carefully read and internalize the remarkable advances in the understanding of plant morphogenesis in the 1840s and 1850s is none other than Charles Darwin, whose notebooks, correspondence, and (then) unpublished manuscripts clearly demonstrate that he had discovered the developmental basis for the evolutionary transformation of plant form.

  11. Evolutionary origins of human handedness: evaluating contrasting hypotheses.

    Science.gov (United States)

    Cochet, Hélène; Byrne, Richard W

    2013-07-01

    Variation in methods and measures, resulting in past dispute over the existence of population handedness in nonhuman great apes, has impeded progress into the origins of human right-handedness and how it relates to the human hallmark of language. Pooling evidence from behavioral studies, neuroimaging and neuroanatomy, we evaluate data on manual and cerebral laterality in humans and other apes engaged in a range of manipulative tasks and in gestural communication. A simplistic human/animal partition is no longer tenable, and we review four (nonexclusive) possible drivers for the origin of population-level right-handedness: skilled manipulative activity, as in tool use; communicative gestures; organizational complexity of action, in particular hierarchical structure; and the role of intentionality in goal-directed action. Fully testing these hypotheses will require developmental and evolutionary evidence as well as modern neuroimaging data.

  12. Origin and evolutionary process of the genetic code.

    Science.gov (United States)

    Ikehara, Kenji; Niihara, Yuka

    2007-01-01

    The genetic code plots the relationship between a triplet base sequence on RNA and an amino acid that corresponds to a protein associated with a required function in organisms. Accurate knowledge about the genetic code, including its origin and evolutionary process, would be helpful for determining the causes of genetic disorders and discovering new medical treatments, as well as for understanding the origin of life. This review begins with discussion of several well-known theories on the origin of the genetic code. Then, a GNC-SNS primitive genetic code hypothesis, which we originally proposed, is explained in relation to the weak points of other theories. S and N denote G or C and any of the four bases, respectively. We also introduce our hypothesis of the GADV-protein world hypothesis on the origin of life, where GADV stands for the four amino acids, Gly[G], Ala[A], Asp[D] and Val[V]. Next, we discuss the reason why genetic disorders, which should be triggered by base replacements, are repressed at a low level under the universal genetic code. Finally, we explain the current difficulties we faced in treating genetic disorders, suggesting a prospect for a new type of treatments of these disorders.

  13. Evolutionary origins of hepatitis A virus in small mammals.

    Science.gov (United States)

    Drexler, Jan Felix; Corman, Victor M; Lukashev, Alexander N; van den Brand, Judith M A; Gmyl, Anatoly P; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G; Lemon, Stanley M; Drosten, Christian

    2015-12-08

    Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

  14. Evolutionary origin of insect-Wolbachia nutritional mutualism.

    Science.gov (United States)

    Nikoh, Naruo; Hosokawa, Takahiro; Moriyama, Minoru; Oshima, Kenshiro; Hattori, Masahira; Fukatsu, Takema

    2014-07-15

    Obligate insect-bacterium nutritional mutualism is among the most sophisticated forms of symbiosis, wherein the host and the symbiont are integrated into a coherent biological entity and unable to survive without the partnership. Originally, however, such obligate symbiotic bacteria must have been derived from free-living bacteria. How highly specialized obligate mutualisms have arisen from less specialized associations is of interest. Here we address this evolutionary issue by focusing on an exceptional insect-Wolbachia nutritional mutualism. Although Wolbachia endosymbionts are ubiquitously found in diverse insects and generally regarded as facultative/parasitic associates for their insect hosts, a Wolbachia strain associated with the bedbug Cimex lectularius, designated as wCle, was shown to be essential for host's growth and reproduction via provisioning of B vitamins. We determined the 1,250,060-bp genome of wCle, which was generally similar to the genomes of insect-associated facultative Wolbachia strains, except for the presence of an operon encoding the complete biotin synthetic pathway that was acquired via lateral gene transfer presumably from a coinfecting endosymbiont Cardinium or Rickettsia. Nutritional and physiological experiments, in which wCle-infected and wCle-cured bedbugs of the same genetic background were fed on B-vitamin-manipulated blood meals via an artificial feeding system, demonstrated that wCle certainly synthesizes biotin, and the wCle-provisioned biotin significantly contributes to the host fitness. These findings strongly suggest that acquisition of a single gene cluster consisting of biotin synthesis genes underlies the bedbug-Wolbachia nutritional mutualism, uncovering an evolutionary transition from facultative symbiosis to obligate mutualism facilitated by lateral gene transfer in an endosymbiont lineage.

  15. Genomic insights into the evolutionary origin of Myxozoa within Cnidaria.

    Science.gov (United States)

    Chang, E Sally; Neuhof, Moran; Rubinstein, Nimrod D; Diamant, Arik; Philippe, Hervé; Huchon, Dorothée; Cartwright, Paulyn

    2015-12-01

    The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell-cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content.

  16. Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

    Science.gov (United States)

    Chang, E. Sally; Neuhof, Moran; Rubinstein, Nimrod D.; Diamant, Arik; Philippe, Hervé; Huchon, Dorothée; Cartwright, Paulyn

    2015-01-01

    The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell–cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content. PMID:26627241

  17. Origin and evolution of deep brain stimulation

    Directory of Open Access Journals (Sweden)

    Vittorio Alessandro eSironi

    2011-08-01

    Full Text Available This paper briefly describes how the electrical stimulation, used since antiquity to modulate the nervous system, has been a fundamental tool of neurophysiologic investigation in the second half of the 18th century and was subsequently used by the early 20th century, even for therapeutic purposes. In mid-20th century the advent of stereotactic procedures has allowed the drift from lesional to stimulating technique of deep nuclei of the brain for therapeutic purposes. In this way, DBS was born, that, over the last two decades, has led to positive results for the treatment of medically refractory Parkinson's disease, essential tremor and dystonia. In recent years, the indications for therapeutic use of DBS have been extended to epilepsy, Tourette's syndrome, psychiatric diseases (depression, obsessive-compulsive disorder, some kinds of headache, eating disorders and the minimally conscious state. The potentials of the DBS for therapeutic use are fascinating, but there are still many unresolved technical and ethical problems, concerning the identification of the targets for each disease, the selection of the patients and the evaluation of the results.

  18. The evolutionary origin of jaw yaw in mammals.

    Science.gov (United States)

    Grossnickle, David M

    2017-03-21

    Theria comprises all but three living mammalian genera and is one of the most ecologically pervasive clades on Earth. Yet, the origin and early history of therians and their close relatives (i.e., cladotherians) remains surprisingly enigmatic. A critical biological function that can be compared among early mammal groups is mastication. Morphometrics and modeling analyses of the jaws of Mesozoic mammals indicate that cladotherians evolved musculoskeletal anatomies that increase mechanical advantage during jaw rotation around a dorsoventrally-oriented axis (i.e., yaw) while decreasing the mechanical advantage of jaw rotation around a mediolaterally-oriented axis (i.e., pitch). These changes parallel molar transformations in early cladotherians that indicate their chewing cycles included significant transverse movement, likely produced via yaw rotation. Thus, I hypothesize that cladotherian molar morphologies and musculoskeletal jaw anatomies evolved concurrently with increased yaw rotation of the jaw during chewing cycles. The increased transverse movement resulting from yaw rotation may have been a crucial evolutionary prerequisite for the functionally versatile tribosphenic molar morphology, which underlies the molars of all therians and is retained by many extant clades.

  19. Ontogenetic data and the evolutionary origin of the mammalian scapula

    Science.gov (United States)

    Sánchez-Villagra, Marcelo; Maier, Wolfgang

    2002-09-01

    One of the most useful diagnostic therian features is the division of the lateral surface of the scapula into two fossae separated by a scapular spine. A new model to describe this evolutionary innovation based on ontogenetic data is provided, consistent with information provided by recent fossil discoveries. The development of the scapula in three didelphid and one dasyurid marsupials using histological sections was studied. Only the ventral, acromial portion of the scapular spine, which originates from the anterior margin of the scapular blade, is preformed in cartilage. The major dorsal portion is formed at a later stage by appositional bone, which expands from the perichondral ossification of the scapula into an intermuscular aponeurosis between the supra-and infraspinatus muscles. This intermuscular aponeurosis inserts more or less in the middle of the lateral surface of the developing scapula. Thus, the floor of the supraspinous fossa is already present at the beginning of scapular development, simultaneous with the infraspinous fossa. The portion of the scapular spine that is situated dorsal to the acromial process is hypothesized to be a neomorphic structure of therians. The dorsal portion of the scapular spine evolved as additional attachment for powerful supraspinatus and infraspinatus muscles meeting near the middle of the lateral scapula.

  20. Ancient evolutionary origins of epigenetic regulation associated with posttraumatic stress disorder

    Directory of Open Access Journals (Sweden)

    Levent eSipahi

    2014-05-01

    Full Text Available Epigenetic marks, including DNA methylation, are modifiable molecular factors that may underlie mental disorders, especially responses to trauma, including the development of and resilience to posttraumatic stress disorder (PTSD. Previous work has identified differential DNA methylation at CpG dinucleotide sites genomewide between trauma exposed individuals with and without PTSD, suggesting a role for epigenetic potential – the capacity to epigenetically regulate behavior and physiology in response to lived experiences. The human species is characterized by an increased period of adaptive plasticity during brain development. The evolutionary history of epigenetic potential in relation to adaptive plasticity is currently unknown. Using phylogenetic methods and functional annotation analyses, we trace the evolution of over 7,000 CpG dinucleotides, including 203 associated with PTSD, during the descent of humans in during mammalian evolution and characterize the biological significance of this evolution. We demonstrate that few (7% PTSD-associated CpG sites are unique to humans, while the vast majority of sites have deep evolutionary origins: 73% and 93% were unambiguously present in the last common ancestor of humans/orangutans and humans/chimpanzees, respectively. Genes proximal to evolved PTSD-associated CpG sites revealed significant enrichment for immune function during recent human evolution and regulation of gene expression during more ancient periods of human evolution. Additionally, 765 putative transcription factor binding sites (TFBS were identified that overlap with PTSD-associated CpG sites. Elucidation of the evolutionary history of PTSD-associated CpG sites may provide insights into the function and origin of epigenetic potential in trauma responses, generally, and PTSD, specifically. The human capacity to respond to trauma with stable physiologic and behavioral changes may be due to epigenetic potentials that are shared among many

  1. The evolutionary origin and population history of the grauer gorilla.

    Science.gov (United States)

    Tocheri, Matthew W; Dommain, René; McFarlin, Shannon C; Burnett, Scott E; Troy Case, D; Orr, Caley M; Roach, Neil T; Villmoare, Brian; Eriksen, Amandine B; Kalthoff, Daniela C; Senck, Sascha; Assefa, Zelalem; Groves, Colin P; Jungers, William L

    2016-01-01

    Gorillas living in western central Africa (Gorilla gorilla) are morphologically and genetically distinguishable from those living in eastern central Africa (Gorilla beringei). Genomic analyses show eastern gorillas experienced a significant reduction in population size during the Pleistocene subsequent to geographical isolation from their western counterparts. However, how these results relate more specifically to the recent biogeographical and evolutionary history of eastern gorillas remains poorly understood. Here we show that two rare morphological traits are present in the hands and feet of both eastern gorilla subspecies at strikingly high frequencies (>60% in G. b. graueri; ∼28% in G. b. beringei) in comparison with western gorillas (gorillas after diverging from their western relatives during the early to middle Pleistocene. The extremely high frequencies observed among grauer gorillas-which currently occupy a geographic range more than ten times the size of that of mountain gorillas-imply that grauers originated relatively recently from a small founding population of eastern gorillas. Current paleoenvironmental, geological, and biogeographical evidence supports the hypothesis that a small group of eastern gorillas likely dispersed westward from the Virungas into present-day grauer range in the highlands just north of Lake Kivu, either immediately before or directly after the Younger Dryas interval. We propose that as the lowland forests of central Africa expanded rapidly during the early Holocene, they became connected with the expanding highland forests along the Albertine Rift and enabled the descendants of this small group to widely disperse. The descendant populations significantly expanded their geographic range and population numbers relative to the gorillas of the Virunga Mountains and the Bwindi-Impenetrable Forest, ultimately resulting in the grauer gorilla subspecies recognized today. This founder-effect hypothesis offers some optimism for

  2. Messy biology and the origins of evolutionary innovations.

    Science.gov (United States)

    Tawfik, Dan S

    2010-10-01

    Biological messiness relates to infidelity, heterogeneity, stochastic noise and variation--both genetic and phenotypic--at all levels, from single proteins to organisms. Messiness comes from the complexity and evolutionary history of biological systems and from the high cost of accuracy. For better or for worse, messiness is inherent to biology. It also provides the raw material for physiological and evolutionary adaptations to new challenges.

  3. Deep evolutionary conservation of an intramolecular protein kinase activation mechanism.

    Directory of Open Access Journals (Sweden)

    Jingfen Han

    Full Text Available DYRK-family kinases employ an intramolecular mechanism to autophosphorylate a critical tyrosine residue in the activation loop. Once phosphorylated, DYRKs lose tyrosine kinase activity and function as serine/threonine kinases. DYRKs have been characterized in organisms from yeast to human; however, all entities belong to the Unikont supergroup, only one of five eukaryotic supergroups. To assess the evolutionary age and conservation of the DYRK intramolecular kinase-activation mechanism, we surveyed 21 genomes representing four of the five eukaryotic supergroups for the presence of DYRKs. We also analyzed the activation mechanism of the sole DYRK (class 2 DYRK present in Trypanosoma brucei (TbDYRK2, a member of the excavate supergroup and separated from Drosophila by ∼850 million years. Bioinformatics showed the DYRKs clustering into five known subfamilies, class 1, class 2, Yaks, HIPKs and Prp4s. Only class 2 DYRKs were present in all four supergroups. These diverse class 2 DYRKs also exhibited conservation of N-terminal NAPA regions located outside of the kinase domain, and were shown to have an essential role in activation loop autophosphorylation of Drosophila DmDYRK2. Class 2 TbDYRK2 required the activation loop tyrosine conserved in other DYRKs, the NAPA regions were critical for this autophosphorylation event, and the NAPA-regions of Trypanosoma and human DYRK2 complemented autophosphorylation by the kinase domain of DmDYRK2 in trans. Finally, sequential deletion analysis was used to further define the minimal region required for trans-complementation. Our analysis provides strong evidence that class 2 DYRKs were present in the primordial or root eukaryote, and suggest this subgroup may be the oldest, founding member of the DYRK family. The conservation of activation loop autophosphorylation demonstrates that kinase self-activation mechanisms are also primitive.

  4. Deep structure and origin of active volcanoes in China

    Institute of Scientific and Technical Information of China (English)

    Dapeng Zhao; Lucy Liu

    2010-01-01

    We synthesize significant recent results on the deep structure and origin of the active volcanoes in mainland China. Magmatism in the western Pacific arc and back-arc areas is caused by dehydration of the subducting slab and by corner flow in the mantle wedge, whereas the intraplate magmatism in China has different origins. The active volcanoes in Northeast China (such as the Changbai and Wudalianchi) are caused by hot upwelling in the big mantle wedge (BMW) above the stagnant slab in the mantle transition zone and deep slab dehydration as well. The Tengchong volcano in Southwest China is caused by a similar process in the BMW above the subducting Burma microplate (or Indian plate).The Hainan volcano in southernmost China is a hotspot fed by a lower-mantle plume which may be associated with the Pacific and Philippine Sea slabs' deep subduction in the east and the Indian slab's deep subduction in the west down to the lower mantle. The stagnant slab finally collapses down to the bottom of the mantle, which can trigger the upwelling of hot mantle materials from the lower mantle to the shallow mantle beneath the subducting slabs and may cause the slab-plume interactions.

  5. Deep structure and origin of active volcanoes in China

    Directory of Open Access Journals (Sweden)

    Dapeng Zhao

    2010-10-01

    Full Text Available We synthesize significant recent results on the deep structure and origin of the active volcanoes in mainland China. Magmatism in the western Pacific arc and back-arc areas is caused by dehydration of the subducting slab and by corner flow in the mantle wedge, whereas the intraplate magmatism in China has different origins. The active volcanoes in Northeast China (such as the Changbai and Wudalianchi are caused by hot upwelling in the big mantle wedge (BMW above the stagnant slab in the mantle transition zone and deep slab dehydration as well. The Tengchong volcano in Southwest China is caused by a similar process in the BMW above the subducting Burma microplate (or Indian plate. The Hainan volcano in southernmost China is a hotspot fed by a lower-mantle plume which may be associated with the Pacific and Philippine Sea slabs’ deep subduction in the east and the Indian slab’s deep subduction in the west down to the lower mantle. The stagnant slab finally collapses down to the bottom of the mantle, which can trigger the upwelling of hot mantle materials from the lower mantle to the shallow mantle beneath the subducting slabs and may cause the slab–plume interactions.

  6. The origins of pedagogy: developmental and evolutionary perspectives.

    Science.gov (United States)

    Skerry, Amy E; Lambert, Enoch; Powell, Lindsey J; McAuliffe, Katherine

    2013-07-18

    The question of whether and how information is actively transferred from knowledgeable to ignorant individuals has received much attention in psychology and evolutionary biology. Research in these fields has proceeded largely independently, with studies of nonhuman animals focusing on knowledgeable individuals and whether or not they meet a functional definition of teaching, while studies of children focus on the learner's assumptions and inferences. We argue that a comprehensive theory of teaching will benefit from integrating perspectives and empirical phenomena from evolutionary and developmental disciplines. In this review, we identify cases of seemingly purposeful information transfer (i.e. teaching) in human and nonhuman animals, discuss what is known about the cognitive processes that support teaching in different species, and highlight ways in which each discipline might be informed by extant theories and empirical tools from the other.

  7. Behavioral Genetic Toolkits: Toward the Evolutionary Origins of Complex Phenotypes.

    Science.gov (United States)

    Rittschof, C C; Robinson, G E

    2016-01-01

    The discovery of toolkit genes, which are highly conserved genes that consistently regulate the development of similar morphological phenotypes across diverse species, is one of the most well-known observations in the field of evolutionary developmental biology. Surprisingly, this phenomenon is also relevant for a wide array of behavioral phenotypes, despite the fact that these phenotypes are highly complex and regulated by many genes operating in diverse tissues. In this chapter, we review the use of the toolkit concept in the context of behavior, noting the challenges of comparing behaviors and genes across diverse species, but emphasizing the successes in identifying genetic toolkits for behavior; these successes are largely attributable to the creative research approaches fueled by advances in behavioral genomics. We have two general goals: (1) to acknowledge the groundbreaking progress in this field, which offers new approaches to the difficult but exciting challenge of understanding the evolutionary genetic basis of behaviors, some of the most complex phenotypes known, and (2) to provide a theoretical framework that encompasses the scope of behavioral genetic toolkit studies in order to clearly articulate the research questions relevant to the toolkit concept. We emphasize areas for growth and highlight the emerging approaches that are being used to drive the field forward. Behavioral genetic toolkit research has elevated the use of integrative and comparative approaches in the study of behavior, with potentially broad implications for evolutionary biologists and behavioral ecologists alike.

  8. The evolutionary origins and significance of drug addiction

    Directory of Open Access Journals (Sweden)

    Saah Tammy

    2005-06-01

    Full Text Available Abstract By looking at drug addiction from an evolutionary perspective, we may understand its underlying significance and evaluate its three-fold nature: biology, psychology, and social influences. In this investigation it is important to delve into the co-evolution of mammalian brains and ancient psychotropic plants. Gaining an understanding of the implications of ancient psychotropic substance use in altering mammalian brains will assist in assessing the causes and effects of addiction in a modern-day context. By exploring addiction in this manner, we may move towards more effective treatment early prevention, treating the root of the issue rather than the symptoms.

  9. Possible evolutionary origins of human female sexual fluidity.

    Science.gov (United States)

    Kanazawa, Satoshi

    2016-05-16

    I propose an evolutionary theory of human female sexual fluidity and argue that women may have been evolutionarily designed to be sexually fluid in order to allow them to have sex with their cowives in polygynous marriage and thus reduce conflict and tension inherent in such marriage. In addition to providing an extensive definition and operationalization of the concept of sexual fluidity and specifying its ultimate function for women, the proposed theory can potentially solve several theoretical and empirical puzzles in evolutionary psychology and sex research. Analyses of the National Longitudinal Study of Adolescent Health (Add Health) confirm the theory's predictions that: (i) women (but not men) who experience increased levels of sexual fluidity have a larger number of children (suggesting that female sexual fluidity, if heritable, may be evolutionarily selected); (ii) women (but not men) who experience marriage or parenthood early in adult life subsequently experience increased levels of sexual fluidity; and (iii) sexual fluidity is significantly positively correlated with known markers of unrestricted sexual orientation among women whereas it is significantly negatively correlated with such markers among men.

  10. Evolutionary origins of the blood vascular system and endothelium

    Science.gov (United States)

    Monahan-Earley, Rita; Dvorak, Ann M.; Aird, William C.

    2017-01-01

    Every biological trait requires both a proximate and evolutionary explanation. The field of vascular biology is focused primarily on proximate mechanisms in health and disease. Comparatively little attention has been given to the evolutionary basis of the cardiovascular system. Here, we employ a comparative approach to review the phylogenetic history of the blood vascular system and endothelium. In addition to drawing on the published literature, we provide primary ultrastructural data related to the lobster, earthworm, amphioxus and hagfish. Existing evidence suggests that the blood vascular system first appeared in an ancestor of the triploblasts over 600 million years ago, as a means to overcome the time-distance constraints of diffusion. The endothelium evolved in an ancestral vertebrate some 540–510 million years ago to optimize flow dynamics and barrier function, and/or to localize immune and coagulation functions. Finally, we emphasize that endothelial heterogeneity evolved as a core feature of the endothelium from the outset, reflecting its role in meeting the diverse needs of body tissues. PMID:23809110

  11. On the deep-mantle origin of the Deccan Traps

    Science.gov (United States)

    Glišović, Petar; Forte, Alessandro M.

    2017-02-01

    The Deccan Traps in west-central India constitute one of Earth’s largest continental flood basalt provinces, whose eruption played a role in the Cretaceous-Paleogene extinction event. The unknown mantle structure under the Indian Ocean at the start of the Cenozoic presents a challenge for connecting the event to a deep mantle origin. We used a back-and-forth iterative method for time-reversed convection modeling, which incorporates tomography-based, present-day mantle heterogeneity to reconstruct mantle structure at the start of the Cenozoic. We show a very low-density, deep-seated upwelling that ascends beneath the Réunion hot spot at the time of the Deccan eruptions. We found a second active upwelling below the Comores hot spot that likely contributed to the region of partial melt feeding the massive eruption.

  12. A conceptual framework for the evolutionary origins of multicellularity

    Science.gov (United States)

    Libby, Eric; Rainey, Paul B.

    2013-06-01

    The evolution of multicellular organisms from unicellular counterparts involved a transition in Darwinian individuality from single cells to groups. A particular challenge is to understand the nature of the earliest groups, the causes of their evolution, and the opportunities for emergence of Darwinian properties. Here we outline a conceptual framework based on a logical set of possible pathways for evolution of the simplest self-replicating groups. Central to these pathways is the recognition of a finite number of routes by which genetic information can be transmitted between individual cells and groups. We describe the form and organization of each primordial group state and consider factors affecting persistence and evolution of the nascent multicellular forms. Implications arising from our conceptual framework become apparent when attempting to partition fitness effects at individual and group levels. These are discussed with reference to the evolutionary emergence of individuality and its manifestation in extant multicellular life—including those of marginal Darwinian status.

  13. Evolutionary perspective on the origin of Haitian cholera outbreak strain.

    Science.gov (United States)

    Dasgupta, Anirban; Banerjee, Rachana; Das, Santasabuj; Basak, Surajit

    2012-01-01

    Cholera epidemic has not been reported in Haiti for at least 100 years, although cholera has been present in Latin America since 1991. Surprisingly, the recent cholera epidemic in Haiti (October 2010) recorded more than 250,000 cases and 4000 deaths in the first 6 months and became one of the most explosive and deadly cholera outbreak in recent history. In the present study, we conducted genomic analyses of pathogenicity islands of three Haitian Vibrio cholerae strains and compared them with nine different V. cholerae O1 El Tor genomes. Although CIRS101 is evolutionarily most similar to the Haitian strains, our study also provides some important differences in the genetic organization of pathogenicity islands of Haitian strains with CIRS101. Evolutionary analysis suggests that unusual functional constraints have been imposed on the Haitian strains and we hypothesize that amino acid substitution is more deleterious in Haitian strains than in nonHaitian strains.

  14. On the Origin and Evolutionary History of NANOG

    Science.gov (United States)

    Vivien, Céline; Kodjabachian, Laurent; Demeneix, Barbara; Coen, Laurent; Girardot, Fabrice

    2014-01-01

    Though pluripotency is well characterized in mammals, many questions remain to be resolved regarding its evolutionary history. A necessary prerequisite for addressing this issue is to determine the phylogenetic distributions and orthology relationships of the transcription factor families sustaining or modulating this property. In mammals, the NANOG homeodomain transcription factor is one of the core players in the pluripotency network. However, its evolutionary history has not been thoroughly studied, hindering the interpretation of comparative studies. To date, the NANOG family was thought to be monogenic, with numerous pseudogenes described in mammals, including a tandem duplicate in Hominidae. By examining a wide-array of craniate genomes, we provide evidence that the NANOG family arose at the latest in the most recent common ancestor of osteichthyans and that NANOG genes are frequently found as tandem duplicates in sarcopterygians and as a single gene in actinopterygians. Their phylogenetic distribution is thus reminiscent of that recently shown for Class V POU paralogues, another key family of pluripotency-controlling factors. However, while a single ancestral duplication has been reported for the Class V POU family, we suggest that multiple independent duplication events took place during evolution of the NANOG family. These multiple duplications could have contributed to create a layer of complexity in the control of cell competence and pluripotency, which could explain the discrepancies relative to the functional evolution of this important gene family. Further, our analysis does not support the hypothesis that loss of NANOG and emergence of the preformation mode of primordial germ cell specification are causally linked. Our study therefore argues for the need of further functional comparisons between NANOG paralogues, notably regarding the novel duplicates identified in sauropsids and non-eutherian mammals. PMID:24465486

  15. On the origin and evolutionary history of NANOG.

    Directory of Open Access Journals (Sweden)

    Pierluigi Scerbo

    Full Text Available Though pluripotency is well characterized in mammals, many questions remain to be resolved regarding its evolutionary history. A necessary prerequisite for addressing this issue is to determine the phylogenetic distributions and orthology relationships of the transcription factor families sustaining or modulating this property. In mammals, the NANOG homeodomain transcription factor is one of the core players in the pluripotency network. However, its evolutionary history has not been thoroughly studied, hindering the interpretation of comparative studies. To date, the NANOG family was thought to be monogenic, with numerous pseudogenes described in mammals, including a tandem duplicate in Hominidae. By examining a wide-array of craniate genomes, we provide evidence that the NANOG family arose at the latest in the most recent common ancestor of osteichthyans and that NANOG genes are frequently found as tandem duplicates in sarcopterygians and as a single gene in actinopterygians. Their phylogenetic distribution is thus reminiscent of that recently shown for Class V POU paralogues, another key family of pluripotency-controlling factors. However, while a single ancestral duplication has been reported for the Class V POU family, we suggest that multiple independent duplication events took place during evolution of the NANOG family. These multiple duplications could have contributed to create a layer of complexity in the control of cell competence and pluripotency, which could explain the discrepancies relative to the functional evolution of this important gene family. Further, our analysis does not support the hypothesis that loss of NANOG and emergence of the preformation mode of primordial germ cell specification are causally linked. Our study therefore argues for the need of further functional comparisons between NANOG paralogues, notably regarding the novel duplicates identified in sauropsids and non-eutherian mammals.

  16. Implications of the Deep Minimum for Slow Solar Wind Origin

    Science.gov (United States)

    Antiochos, S. K.; Mikic, Z.; Lionello, R.; Titov, V. S.; Linker, J. A.

    2009-12-01

    The origin of the slow solar wind has long been one of the most important problems in solar/heliospheric physics. Two observational constraints make this problem especially challenging. First, the slow wind has the composition of the closed-field corona, unlike the fast wind that originates on open field lines. Second, the slow wind has substantial angular extent, of order 30 degrees, which is much larger than the widths observed for streamer stalks or the widths expected theoretically for a dynamic heliospheric current sheet. We propose that the slow wind originates from an intricate network of narrow (possibly singular) open-field corridors that emanate from the polar coronal hole regions. Using topological arguments, we show that these corridors must be ubiquitous in the solar corona. The total solar eclipse in August 2008, near the lowest point of the Deep Minimum, affords an ideal opportunity to test this theory by using the ultra-high resolution Predictive Science's (PSI) eclipse model for the corona and wind. Analysis of the PSI eclipse model demonstrates that the extent and scales of the open-field corridors can account for both the angular width of the slow wind and its closed-field composition. We discuss the implications of our slow wind theory for the structure of the corona and heliosphere at the Deep Minimum and describe further observational and theoretical tests. This work has been supported by the NASA HTP, SR&T, and LWS programs.

  17. Food allergens of plant origin - their molecular and evolutionary relationships

    DEFF Research Database (Denmark)

    Mills, E. N. C.; Madsen, Charlotte Bernhard; Shewry, P. R.

    2003-01-01

    Along with other forms of allergic disease, food allergies appear to be on the increase, with childhood allergies to foods such as peanuts being of particular concern. Around 7-10 foods are responsible for the majority of allergies, including several of plant origin, notably peanut. Allergies are...

  18. Food allergens of plant origin : their molecular and evolutionary relationships

    NARCIS (Netherlands)

    Mills, E.N.C.; Madsen, C.; Shewry, P.R.; Wichers, H.J.

    2003-01-01

    Along with other forms of allergic disease, food allergies appear to be on the increase, with childhood allergies to foods such as peanuts being of particular concern. Around 7¿10 foods are responsible for the majority of allergies, including several of plant origin, notably peanut. Allergies are us

  19. On the evolutionary origins of differences in sexual preferences

    Directory of Open Access Journals (Sweden)

    Daniil eRyabko

    2015-05-01

    Full Text Available A novel general explanation of the evolutionary process leading to the appearance of differences insexual preferences is proposed. The explanation is fully general: it is not specific to any particular type of sexual preferences, nor to any species orpopulation. It shows how different sexual preferences can appear in any large group-living population in which sexual selection is sufficiently strong in each sex. The main idea is that the lack of interest towards a member of the opposite sex may be interpreted as a signal of popularity, and thus a sign of reproductive success. It is then boosted by the Fisher runaway process, resulting in a generalized trait~--- lack of interest towards the opposite sex. This trait develops far beyond the point when it gives a reproductive disadvantage, resulting in well-pronounced different sexual preferences. This hypothesis is placed into the context of other works on different sexual preferences in animals; supporting evidence from the literature is reviewed and additional research needed to confirm or refute the hypothesis in any given species is outlined.

  20. Metabolic integration during the evolutionary origin of mitochondria

    Institute of Scientific and Technical Information of China (English)

    DENNIS G SEARCY

    2003-01-01

    Although mitochondria provide eukaryotic cells with certain metabolic advantages, in other ways they may be disadvantageous. For example, mitochondria produce reactive oxygen species that damage both nucleocytoplasm and mitochondria, resulting in mutations, diseases, and aging. The relationship of mitochondria to the cytoplasm is best understood in the context of evolutionary history. Although it is clear that mitochondria evolved from symbiotic bacteria, the exact nature of the initial symbiosis is a matter of continuing debate. The exchange of nutrients between host and symbiont may have differed from that between the cytoplasm and mitochondria in modern cells. Speculations about the initial relationships include the following. (1) The pre-mitochondrion may have been an invasive, parasitic bacterium. The host did not benefit. (2) The relationship was a nutritional syntrophy based upon transfer of organic acids from host to symbiont. (3) The relationship was a syntrophy based upon H2 transfer from symbiont to host, where the host was a methanogen. (4) There was a syntrophy based upon reciprocal exchange of sulfur compounds.The last conjecture receives support from our detection in eukaryotic cells of substantial H2S-oxidizing activity in mitochondria, and sulfur-reducing activity in the cytoplasm.

  1. Evolutionary patterns from mass originations and mass extinctions.

    Science.gov (United States)

    Hewzulla, D; Boulter, M C; Benton, M J; Halley, J M

    1999-01-01

    The Fossil Record 2 database gives a stratigraphic range of most known animal and plant families. We have used it to plot the number of families extant through time and argue for an exponential fit, rather than a logistic one, on the basis of power spectra of the residuals from the exponential. The times of origins and extinctions, when plotted for all families of marine and terrestrial organisms over the last 600 Myr, reveal different origination and extinction peaks. This suggests that patterns of biological evolution are driven by its own internal dynamics as well as responding to upsets from external causes. Spectral analysis shows that the residuals from the exponential model of the marine system are more consistent with 1/f noise suggesting that self-organized criticality phenomena may be involved. PMID:10212492

  2. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Tyler, Brett M.; Tripathy, Sucheta; Zhang, Xuemin; Dehal, Paramvir; Jiang, Rays H. Y.; Aerts, Andrea; Arredondo, Felipe D.; Baxter, Laura; Bensasson, Douda; Beynon, JIm L.; Chapman, Jarrod; Damasceno, Cynthia M. B.; Dorrance, Anne E.; Dou, Daolong; Dickerman, Allan W.; Dubchak, Inna L.; Garbelotto, Matteo; Gijzen, Mark; Gordon, Stuart G.; Govers, Francine; Grunwald, NIklaus J.; Huang, Wayne; Ivors, Kelly L.; Jones, Richard W.; Kamoun, Sophien; Krampis, Konstantinos; Lamour, Kurt H.; Lee, Mi-Kyung; McDonald, W. Hayes; Medina, Monica; Meijer, Harold J. G.; Nordberg, Erik K.; Maclean, Donald J.; Ospina-Giraldo, Manuel D.; Morris, Paul F.; Phuntumart, Vipaporn; Putnam, Nicholas J.; Rash, Sam; Rose, Jocelyn K. C.; Sakihama, Yasuko; Salamov, Asaf A.; Savidor, Alon; Scheuring, Chantel F.; Smith, Brian M.; Sobral, Bruno W. S.; Terry, Astrid; Torto-Alalibo, Trudy A.; Win, Joe; Xu, Zhanyou; Zhang, Hongbin; Grigoriev, Igor V.; Rokhsar, Daniel S.; Boore, Jeffrey L.

    2006-04-17

    Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

  3. Wandering Tales: Evolutionary origins of mental time travel and language

    Directory of Open Access Journals (Sweden)

    Michael Charles Corballis

    2013-07-01

    Full Text Available A central component of mind wandering is mental time travel, the calling to mind of remembered past events and of imagined future ones. Mental time travel may also be critical to the evolution of language, which enables us to communicate about the nonpresent, sharing memories, plans, and ideas. Mental time travel is indexed in humans by hippocampal activity, and studies also suggest that the hippocampus in rats is active when the animals replay or pre play activity in a spatial environment, such as a maze. Mental time travel may have ancient origins, contrary to the view that it is unique to humans. Since mental time travel is also thought to underlie language, these findings suggest that language evolved gradually from pre-existing cognitive capacities, contrary to the view of Chomsky and others that language and symbolic thought emerged abruptly, in a single step, within the past 100,000 years.

  4. Wandering tales: evolutionary origins of mental time travel and language.

    Science.gov (United States)

    Corballis, Michael C

    2013-01-01

    A central component of mind wandering is mental time travel, the calling to mind of remembered past events and of imagined future ones. Mental time travel may also be critical to the evolution of language, which enables us to communicate about the non-present, sharing memories, plans, and ideas. Mental time travel is indexed in humans by hippocampal activity, and studies also suggest that the hippocampus in rats is active when the animals replay or pre play activity in a spatial environment, such as a maze. Mental time travel may have ancient origins, contrary to the view that it is unique to humans. Since mental time travel is also thought to underlie language, these findings suggest that language evolved gradually from pre-existing cognitive capacities, contrary to the view of Chomsky and others that language and symbolic thought emerged abruptly, in a single step, within the past 100,000 years.

  5. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL; Savidor, Alon [ORNL

    2006-01-01

    Genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, suggest a photosynthetic past and reveal recent massive expansion and diversification of potential pathogenicity gene families. Abstract: Draft genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, have been determined. O mycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms and the presence of many Phytophthora genes of probable phototroph origin support a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors and, in particular, a superfamily of 700 proteins with similarity to known o mycete avirulence genes.

  6. Food allergens of plant origin - their molecular and evolutionary relationships

    DEFF Research Database (Denmark)

    Mills, E. N. C.; Madsen, Charlotte Bernhard; Shewry, P. R.

    2003-01-01

    Along with other forms of allergic disease, food allergies appear to be on the increase, with childhood allergies to foods such as peanuts being of particular concern. Around 7-10 foods are responsible for the majority of allergies, including several of plant origin, notably peanut. Allergies...... are usually triggered by the protein components in a food, which are also known as allergens. However, not all the proteins in an allergenic food like peanut are allergens. Why should this be? This question has been addressed by an EU-funded inter-disciplinary network of clinicians, food chemists and plant...... biochemists called Protall. From the groups considerations it is clear that, whilst the abundance of a protein in a food is one factor involved in determining its allergenic potential, this is not sufficient on its own to predict its allergenicity. Through an analysis of common properties of plant food...

  7. Optimal Scheduling for Retrieval Jobs in Double-Deep AS/RS by Evolutionary Algorithms

    Directory of Open Access Journals (Sweden)

    Kuo-Yang Wu

    2013-01-01

    Full Text Available We investigate the optimal scheduling of retrieval jobs for double-deep type Automated Storage and Retrieval Systems (AS/RS in the Flexible Manufacturing System (FMS used in modern industrial production. Three types of evolutionary algorithms, the Genetic Algorithm (GA, the Immune Genetic Algorithm (IGA, and the Particle Swarm Optimization (PSO algorithm, are implemented to obtain the optimal assignments. The objective is to minimize the working distance, that is, the shortest retrieval time travelled by the Storage and Retrieval (S/R machine. Simulation results and comparisons show the advantages and feasibility of the proposed methods.

  8. Evolutionary origins of human herpes simplex viruses 1 and 2.

    Science.gov (United States)

    Wertheim, Joel O; Smith, Martin D; Smith, Davey M; Scheffler, Konrad; Kosakovsky Pond, Sergei L

    2014-09-01

    Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the only primate species known to be infected with two distinct herpes simplex viruses: HSV-1 and HSV-2. Human herpes simplex viruses are ubiquitous, with over two-thirds of the human population infected by at least one virus. Here, we investigated whether the additional human simplex virus is the result of ancient viral lineage duplication or cross-species transmission. We found that standard phylogenetic models of nucleotide substitution are inadequate for distinguishing among these competing hypotheses; the extent of synonymous substitutions causes a substantial underestimation of the lengths of some of the branches in the phylogeny, consistent with observations in other viruses (e.g., avian influenza, Ebola, and coronaviruses). To more accurately estimate ancient viral divergence times, we applied a branch-site random effects likelihood model of molecular evolution that allows the strength of natural selection to vary across both the viral phylogeny and the gene alignment. This selection-informed model favored a scenario in which HSV-1 is the result of ancient codivergence and HSV-2 arose from a cross-species transmission event from the ancestor of modern chimpanzees to an extinct Homo precursor of modern humans, around 1.6 Ma. These results provide a new framework for understanding human herpes simplex virus evolution and demonstrate the importance of using selection-informed models of sequence evolution when investigating viral origin hypotheses.

  9. Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis.

    Science.gov (United States)

    Chu, Xin-Yi; Jiang, Ling-Han; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

    2017-07-14

    The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information.

  10. Hypothesis: origin of life in deep-reaching tectonic faults.

    Science.gov (United States)

    Schreiber, Ulrich; Locker-Grütjen, Oliver; Mayer, Christian

    2012-02-01

    The worldwide discussion on the origin of life encounters difficulties when it comes to estimate the conditions of the early earth and to define plausible environments for the development of the first complex organic molecules. Until now, the role of the earth's crust has been more or less ignored. In our opinion, deep-reaching open, interconnected tectonic fault systems may provide possible reaction habitats ranging from nano- to centimetre and even larger dimensions for the formation of prebiotic molecules. In addition to the presence of all necessary raw materials including phosphate, as well as variable pressure and temperature conditions, we suggest that supercritical CO2 as a nonpolar solvent could have played an important role. A hypothetical model for the origin of life is proposed which will be used to design crucial experiments for the model's verification. Because all proposed processes could still occur in tectonic faults at the present time, it may be possible to detect and analyse the formation of prebiotic molecules in order to assess the validity of the proposed hypothesis.

  11. Evolutionary strategies of cells and viruses in deep-sea hydrothermal systems revealed through comparative metagenomics

    Science.gov (United States)

    Anderson, R.; Sogin, M. L.; Baross, J. A.

    2013-12-01

    The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems must also withstand these environmental extremes, and a high proportion of viruses in these systems are lysogenic. Comparative analysis of a cellular and viral metagenome from a diffuse flow hydrothermal vent has provided insights into the evolutionary strategies of both cells and viruses in hydrothermal systems. We detected numerous mobile elements in the viral and cellular gene pools as well as a large number of prophage in the cellular fraction. We show that the hydrothermal vent viral gene pool is relatively enriched in genes related to energy metabolism, a feature that is unique to the hydrothermal vent viral gene pool compared to viral gene pools from other environments, indicating a potential for integrated prophage to enhance host metabolic flexibility. We also detected stronger purifying selection in the viral versus cellular gene pool, indicating selection pressures that promote prolonged viral integration in the host. Our results support the hypothesis that viruses enhance host genomic plasticity and adaptability in this extreme and dynamic environment. Finally, we will discuss general implications of this work for understanding the viral impact on biogeochemical cycles and evolutionary trajectories of microbial populations in the deep subsurface biosphere.

  12. [Human origin and evolution. A review of advances in paleoanthropology, comparative genetics, and evolutionary psychology].

    Science.gov (United States)

    Markov, A V

    2009-01-01

    In his main work, "On the origin of species", Darwin has refrained from discusion of the origin of man; be only mentioned that his theory would "throw light" on this problem. This famous Darwin's phrase turned out to be one of the most succesful scientific predictions. In the present paper some of the most important recent adavnces in paleoanthroplogy, comparative genetics and evolutionary psychology are reviewed. These three disciplines currently contribute most to our knowledge of anthropogenesis. The review demonstrates that Darwin's ideas not only "threw light" on human origin and evolution; they provided a comprehensive framework for a great variety of studies concerning different aspects of anthropogenesis.

  13. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals

    Science.gov (United States)

    Foote, M.; Hunter, J. P.; Janis, C. M.; Sepkoski, J. J. Jr

    1999-01-01

    Some molecular clock estimates of divergence times of taxonomic groups undergoing evolutionary radiation are much older than the groups' first observed fossil record. Mathematical models of branching evolution are used to estimate the maximal rate of fossil preservation consistent with a postulated missing history, given the sum of species durations implied by early origins under a range of species origination and extinction rates. The plausibility of postulated divergence times depends on origination, extinction, and preservation rates estimated from the fossil record. For eutherian mammals, this approach suggests that it is unlikely that many modern orders arose much earlier than their oldest fossil records.

  14. Boule and the Evolutionary Origin of Metazoan Gametogenesis: A Grandpa's Tale

    Directory of Open Access Journals (Sweden)

    José M. Eirín-López

    2011-01-01

    Full Text Available The evolution of sex remains a hotly debated topic in evolutionary biology. In particular, studying the origins of the molecular mechanisms underlying sexual reproduction and gametogenesis (its fundamental component in multicellular eukaryotes has been difficult due to the rapid divergence of many reproductive proteins, pleiotropy, and by the fact that only a very small number of reproductive proteins specifically involved in reproduction are conserved across lineages. Consequently, during the last decade, many efforts have been put into answering the following question: did gametogenesis evolve independently in different animal lineages or does it share a common evolutionary origin in a single ancestral prototype? Among the various approaches carried out in order to solve this question, the characterization of the evolution of the DAZ gene family holds much promise because these genes encode reproductive proteins that are conserved across a wide range of animal phyla. Within this family, BOULE is of special interest because it represents the most ancestral member of this gene family (the “grandfather” of DAZ. Furthermore, BOULE has attracted most of the attention since it represents an ancient male gametogenic factor with an essential reproductive-exclusive requirement in urbilaterians, constituting a core component of the reproductive prototype. Within this context, the aim of the present work is to provide an up-to-date insight into the studies that lead to the characterization of the DAZ family members and the implications in helping decipher the evolutionary origin of gametogenesis in metazoan animals.

  15. Dredging Evolutionary Theory : the emergence of the deep sea as a transatlantic site for evolution, 1853-1876

    OpenAIRE

    Alaniz, Rodolfo John

    2014-01-01

    Marine invertebrate specimens from the ocean floor played a large role in the formation of evolutionary theory and they continued to help men of science adjudicate natural selection later into the nineteenth century. By 1880, the deep ocean floor had become "Darwin's laboratory," a place to test the "direct action of external conditions on organisms." According to dominant Victorian marine biology, the deep sea was an eternal, unchanging biogeographical space. There, and only there, could nat...

  16. Theories about evolutionary origins of human hepatitis B virus in primates and humans

    Directory of Open Access Journals (Sweden)

    Breno Frederico de Carvalho Dominguez Souza

    2014-09-01

    Full Text Available Introduction: The human hepatitis B virus causes acute and chronic hepatitis and is considered one of the most serious human health issues by the World Health Organization, causing thousands of deaths per year. There are similar viruses belonging to the Hepadnaviridae family that infect non-human primates and other mammals as well as some birds. The majority of non-human primate virus isolates were phylogenetically close to the human hepatitis B virus, but like the human genotypes, the origins of these viruses remain controversial. However, there is a possibility that human hepatitis B virus originated in primates. Knowing whether these viruses might be common to humans and primates is crucial in order to reduce the risk to humans. Objective: To review the existing knowledge about the evolutionary origins of viruses of the Hepadnaviridae family in primates. Methods: This review was done by reading several articles that provide information about the Hepadnaviridae virus family in non-human primates and humans and the possible origins and evolution of these viruses. Results: The evolutionary origin of viruses of the Hepadnaviridae family in primates has been dated back to several thousand years; however, recent analyses of genomic fossils of avihepadnaviruses integrated into the genomes of several avian species have suggested a much older origin of this genus. Conclusion: Some hypotheses about the evolutionary origins of human hepatitis B virus have been debated since the '90s. One theory suggested a New World origin because of the phylogenetic co-segregation between some New World human hepatitis B virus genotypes F and H and woolly B virus in basal sister-relationship to the Old monkey human hepatitis World non-human primates and human hepatitis B virus variants. Another theory suggests an Old World origin of human hepatitis B virus, and that it would have been spread following prehistoric human migrations over 100,000 years ago. A third theory

  17. Evolutionary origin and phylogeography of the diploid obligate parthenogen Artemia parthenogenetica (Branchiopoda: Anostraca.

    Directory of Open Access Journals (Sweden)

    Joaquín Muñoz

    Full Text Available BACKGROUND: Understanding the evolutionary origin and the phylogeographic patterns of asexual taxa can shed light on the origin and maintenance of sexual reproduction. We assessed the geographic origin, genetic diversity, and phylogeographic history of obligate parthenogen diploid Artemia parthenogenetica populations, a widespread halophilic crustacean. METHODOLOGY/PRINCIPAL FINDINGS: We analysed a partial sequence of the Cytochrome c Oxidase Subunit I mitochondrial gene from an extensive set of localities (including Eurasia, Africa, and Australia, and examined their phylogeographic patterns and the phylogenetic relationships of diploid A. parthenogenetica and its closest sexual relatives. Populations displayed an extremely low level of mitochondrial genetic diversity, with one widespread haplotype shared by over 79% of individuals analysed. Phylogenetic and phylogeographic analyses indicated a multiple and recent evolutionary origin of diploid A. parthenogenetica, and strongly suggested that the geographic origin of parthenogenesis in Artemia was in Central Asia. Our results indicate that the maternal sexual ancestors of diploid A. parthenogenetica were an undescribed species from Kazakhstan and A. urmiana. CONCLUSIONS/SIGNIFICANCE: We found evidence for multiple origin of parthenogenesis in Central Asia. Our results indicated that, shortly after its origin, diploid A. parthenogenetica populations underwent a rapid range expansion from Central Asia towards the Mediterranean region, and probably to the rest of its current geographic distribution. This contrasts with the restricted geographic distribution, strong genetic structure, and regional endemism of sexual Artemia lineages and other passively dispersed sexual continental aquatic invertebrates. We hypothesize that diploid parthenogens might have reached their current distribution in historical times, with a range expansion possibly facilitated by an increased availability of suitable

  18. [Genetic mechanism and evolutionary significance of the origin of parthenogenetic insects].

    Science.gov (United States)

    Wang, Cheng-Ye

    2011-12-01

    There is a high proportion of parthenogenesis in insecta, and the parthenogenetic potential of insects is an important but often ignored threaten factor for the agricultural and forestry production. The maintenance of parthenogenetic species is a puzzling issue in evolutionary biology. In recent years, although the cellular mechanisms during parthenogenesis in some species have been well studied, the underlying genetic mechanisms that cause the switch from sexual reproduction to parthenogenesis have not been defined. While, understanding the genetic mechanism and evolutionary significance of the origin of parthenogenetic insects is crucial for preventing the pests in agricultural and forestry production. Here we summarized recent studies aimed at identifying the underlying genetic mechanism of parthenogenesis in insects, and briefly discussed its potential application in this filed.

  19. Bacterial Vesicle Secretion and the Evolutionary Origin of the Eukaryotic Endomembrane System.

    Science.gov (United States)

    Gould, Sven B; Garg, Sriram G; Martin, William F

    2016-07-01

    Eukaryotes possess an elaborate endomembrane system with endoplasmic reticulum, nucleus, Golgi, lysosomes, peroxisomes, autophagosomes, and dynamic vesicle traffic. Theories addressing the evolutionary origin of eukaryotic endomembranes have overlooked the outer membrane vesicles (OMVs) that bacteria, archaea, and mitochondria secrete into their surroundings. We propose that the eukaryotic endomembrane system originated from bacterial OMVs released by the mitochondrial ancestor within the cytosol of its archaeal host at eukaryote origin. Confined within the host's cytosol, OMVs accumulated naturally, fusing either with each other or with the host's plasma membrane. This matched the host's archaeal secretory pathway for cotranslational protein insertion with outward bound mitochondrial-derived vesicles consisting of bacterial lipids, forging a primordial, secretory endoplasmic reticulum as the cornerstone of the eukaryotic endomembrane system. VIDEO ABSTRACT.

  20. Evolutionary origin of the Scombridae (tunas and mackerels: members of a paleogene adaptive radiation with 14 other pelagic fish families.

    Directory of Open Access Journals (Sweden)

    Masaki Miya

    Full Text Available Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences and (ii subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.

  1. Origination, expansion, evolutionary trajectory, and expression bias of AP2/ERF superfamily in Brassica napus

    Directory of Open Access Journals (Sweden)

    Xiaoming Song

    2016-08-01

    Full Text Available The AP2/ERF superfamily, one of the most important transcription factor families, plays crucial roles in response to biotic and abiotic stresses. So far, a comprehensive evolutionary inference of its origination and expansion has not been available. Here, we identified 515 AP2/ERF genes in B. napus, a neo-tetraploid forming ~7500 years ago, and found that 82.14% of them were duplicated in the tetraploidization. A prominent subgenome bias was revealed in gene expression, tissue-specific, and gene conversion. Moreover, a large-scale analysis across plants and alga suggested that this superfamily could have been originated from AP2 family, expanding to form other families (ERF, and RAV. This process was accompanied by duplicating and/or alternative deleting AP2 domain, intragenic domain sequence conversion, and/or by acquiring other domains, resulting in copy number variations, alternatively contributing to functional innovation. We found that significant positive selection occurred at certain critical nodes during the evolution of land plants, possibly responding to changing environment. In conclusion, the present research revealed origination, functional innovation, and evolutionary trajectory of the AP2/ERF superfamily, contributing to understanding their roles in plant stress tolerance.

  2. Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus

    Science.gov (United States)

    Song, Xiaoming; Wang, Jinpeng; Ma, Xiao; Li, Yuxian; Lei, Tianyu; Wang, Li; Ge, Weina; Guo, Di; Wang, Zhenyi; Li, Chunjin; Zhao, Jianjun; Wang, Xiyin

    2016-01-01

    The AP2/ERF superfamily, one of the most important transcription factor families, plays crucial roles in response to biotic and abiotic stresses. So far, a comprehensive evolutionary inference of its origination and expansion has not been available. Here, we identified 515 AP2/ERF genes in B. napus, a neo-tetraploid forming ~7500 years ago, and found that 82.14% of them were duplicated in the tetraploidization. A prominent subgenome bias was revealed in gene expression, tissue-specific, and gene conversion. Moreover, a large-scale analysis across plants and alga suggested that this superfamily could have been originated from AP2 family, expanding to form other families (ERF, and RAV). This process was accompanied by duplicating and/or alternative deleting AP2 domain, intragenic domain sequence conversion, and/or by acquiring other domains, resulting in copy number variations, alternatively contributing to functional innovation. We found that significant positive selection occurred at certain critical nodes during the evolution of land plants, possibly responding to changing environment. In conclusion, the present research revealed origination, functional innovation, and evolutionary trajectory of the AP2/ERF superfamily, contributing to understanding their roles in plant stress tolerance. PMID:27570529

  3. The multiple evolutionary histories of dioxygen reductases: Implications for the origin and evolution of aerobic respiration.

    Science.gov (United States)

    Brochier-Armanet, Celine; Talla, Emmanuel; Gribaldo, Simonetta

    2009-02-01

    Understanding the origin and evolution of cellular processes is fundamental to understand how biological activity has shaped the history of our planet. Among these, aerobic respiration is probably one of the most debated. We have applied a phylogenomics approach to investigate the origin and evolution of dioxygen reductases (O(2)Red), the key enzymes of aerobic respiratory chains. The distribution and phylogenetic analysis of the four types of O(2)Red (Cyt-bd and the A, B, and C families of heme-copper O(2)Red) from 673 complete bacterial and archaeal genomes show that these enzymes have very different evolutionary histories: Cyt-bd are of bacterial origin and were transferred to a few archaea; C-O(2)Red are of proteobacterial origin and were transferred to a few other bacteria; B-O(2)Red are of archaeal origin and were transferred to a few bacteria; and A-O(2)Red are the most ancient O(2)Red and were already present prior to the divergence of major present-day bacterial and archaeal phyla, thus before the emergence of Cyanobacteria and oxygenic photosynthesis. Implications for the origin and the evolution of aerobic respiration are discussed.

  4. A lunar rock of deep crustal origin - Sample 76535

    Science.gov (United States)

    Gooley, R.; Brett, R.; Warner, J.; Smyth, J. R.

    1974-01-01

    Review of the mineral chemistry, crystallography, mosaic assemblages, and oriented inclusions of lunar rock sample 76535, and discussion of its depth of formation. Its texture, chemistry, and phase relationships are shown to indicate that it formed deep within the lunar crust. It is the first crystalline lunar rock found to date to contain evidence of a high pressure mineral assemblage formed under static conditions.

  5. Bats, Primates, and the Evolutionary Origins and Diversification of Mammalian Gammaherpesviruses

    Directory of Open Access Journals (Sweden)

    Marina Escalera-Zamudio

    2016-11-01

    Full Text Available Gammaherpesviruses (γHVs are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis of two viral genes using the largest sample of mammalian γHVs to date, integrating for the first time bat γHV sequences available from public repositories and newly generated viral sequences from two vampire bat species (Desmodus rotundus and Diphylla ecaudata. Bat and primate viruses frequently represented deep branches within the supported phylogenies and clustered among viruses from distantly related mammalian taxa. Following evolutionary scenario testing, we determined the number of host-switching and cospeciation events. Cross-species transmissions have occurred much more frequently than previously estimated, and most of the transmissions were attributable to bats and primates. We conclude that the evolution of the Gammaherpesvirinae subfamily has been driven by both cross-species transmissions and subsequent cospeciation within specific viral lineages and that the bat and primate orders may have potentially acted as superspreaders to other mammalian taxa throughout evolutionary history.

  6. Function and Evolutionary Origin of Unicellular Camera-Type Eye Structure

    KAUST Repository

    Hayakawa, Shiho

    2015-03-03

    The ocelloid is an extraordinary eyespot organelle found only in the dinoflagellate family Warnowiaceae. It contains retina- and lens-like structures called the retinal body and the hyalosome. The ocelloid has been an evolutionary enigma because of its remarkable resemblance to the multicellular camera-type eye. To determine if the ocelloid is functionally photoreceptive, we investigated the warnowiid dinoflagellate Erythropsidinium. Here, we show that the morphology of the retinal body changed depending on different illumination conditions and the hyalosome manifests the refractile nature. Identifying a rhodopsin gene fragment in Erythropsidinium ESTs that is expressed in the retinal body by in situ hybridization, we also show that ocelloids are actually light sensitive photoreceptors. The rhodopsin gene identified is most closely related to bacterial rhodopsins. Taken together, we suggest that the ocelloid is an intracellular camera-type eye, which might be originated from endosymbiotic origin. © 2015 Hayakawa et al.

  7. The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications.

    Directory of Open Access Journals (Sweden)

    J Alistair Crame

    Full Text Available The extensive Late Cretaceous - Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves, representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous - Paleogene (K/Pg boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF (56% of neogastropod genera and Early - Middle Eocene La Meseta Formation (LMF (47%, with the Conoidea (25% being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early - Middle Eocene. Evolutionary source - sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds.

  8. From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors.

    Directory of Open Access Journals (Sweden)

    Alberto Lindner

    Full Text Available Shallow-water tropical reefs and the deep sea represent the two most diverse marine environments. Understanding the origin and diversification of this biodiversity is a major quest in ecology and evolution. The most prominent and well-supported explanation, articulated since the first explorations of the deep sea, holds that benthic marine fauna originated in shallow, onshore environments, and diversified into deeper waters. In contrast, evidence that groups of marine organisms originated in the deep sea is limited, and the possibility that deep-water taxa have contributed to the formation of shallow-water communities remains untested with phylogenetic methods. Here we show that stylasterid corals (Cnidaria: Hydrozoa: Stylasteridae--the second most diverse group of hard corals--originated and diversified extensively in the deep sea, and subsequently invaded shallow waters. Our phylogenetic results show that deep-water stylasterid corals have invaded the shallow-water tropics three times, with one additional invasion of the shallow-water temperate zone. Our results also show that anti-predatory innovations arose in the deep sea, but were not involved in the shallow-water invasions. These findings are the first robust evidence that an important group of tropical shallow-water marine animals evolved from deep-water ancestors.

  9. Prevalence and evolutionary origins of autoimmune susceptibility alleles in natural mouse populations.

    Science.gov (United States)

    Limaye, N; Belobrajdic, K A; Wandstrat, A E; Bonhomme, F; Edwards, S V; Wakeland, E K

    2008-01-01

    The evolutionary origin of genetic diversity in the SLAM/CD2 gene cluster, implicated in autoimmune lupus susceptibility in mice, was investigated by sequence analysis of exons from six members of the cluster in 48 wild mouse samples derived from the global mouse population. A total of 80 coding region SNPs were identified among the six genes analyzed, indicating that this gene cluster is highly polymorphic in natural mouse populations. Phylogenetic analyses of these allelic sequences revealed clustering of alleles derived from multiple Mus species and subspecies, indicating alleles at several SLAM/CD2 loci were present in ancestral Mus populations prior to speciation and have persisted as polymorphisms for more than 1 million years. Analyses of nonsynonymous/synonymous ratios using likelihood codon substitution models identified several segments in Cd229, Cd48 and Cd84 that were impacted by positive diversifying selective pressures. These findings support the interpretation that selection favoring the generation and retention of functional polymorphisms has played a role in the evolutionary origin of genetic polymorphisms that are predisposing to autoimmunity.

  10. Parallel evolutionary trajectories underlie the origin of giant suspension-feeding whales and bony fishes.

    Science.gov (United States)

    Friedman, Matt

    2012-03-07

    Giant suspension feeders such as mysticete whales, basking and whale sharks, and the extinct (indicated by '†') †pachycormiform teleosts are conspicuous members of modern and fossil marine vertebrate faunas. Whether convergent anatomical features common to these clades arose along similar evolutionary pathways has remained unclear because of a lack of information surrounding the origins of all groups of large-bodied suspension feeders apart from baleen whales. New investigation reveals that the enigmatic ray-finned fish †Ohmdenia, from the Lower Jurassic (Toarcian, 183.0-175.6 Ma) Posidonia Shale Lagerstätte, represents the immediate sister group of edentulous †pachycormiforms, the longest lived radiation of large vertebrate suspension feeders. †Ohmdenia bisects the long morphological branch leading to suspension-feeding †pachycormiforms, providing information on the sequence of anatomical transformations preceding this major ecological shift that can be compared to changes associated with the origin of modern mysticetes. Similarities include initial modifications to jaw geometry associated with the reduction of dentition, followed by the loss of teeth. The evolution of largest body sizes within both radiations occurs only after the apparent onset of microphagy. Comparing the fit of contrasting evolutionary models to functionally relevant morphological measurements for whales and †pachycormiform fishes reveals strong support for a common adaptive peak shared by suspension-feeding members of both clades.

  11. Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today.

    Science.gov (United States)

    Kutschera, Ulrich

    2009-11-01

    The book On the Origin of Species, published in November 1859, is an "abstract" without references, compiled by Charles Darwin from a much longer manuscript entitled "Natural Selection." Here, I summarize the five theories that can be extracted from Darwin's monograph, explain the true meaning of the phrase "struggle for life" (i.e., competition and cooperation), and outline Darwin's original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that "selection only eliminates but is not creative" is still alive today. However, I document that August Weismann (Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen (Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this "Weismann-Schmalhausen principle" with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky (Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by prokaryotic microbes. Eubacteria

  12. The evolutionary origins and ecological context of tool use in New Caledonian crows.

    Science.gov (United States)

    Rutz, Christian; St Clair, James J H

    2012-02-01

    New Caledonian (NC) crows Corvus moneduloides are the most prolific avian tool users. In the wild, they use at least three distinct tool types to extract invertebrate prey from deadwood and vegetation, with some of their tools requiring complex manufacture, modification and/or deployment. Experiments with captive-bred, hand-raised NC crows have demonstrated that the species has a strong genetic predisposition for basic tool use and manufacture, suggesting that this behaviour is an evolved adaptation. This view is supported by recent stable-isotope analyses of the diets of wild crows, which revealed that tool use provides access to highly profitable hidden prey, with preliminary data indicating that parents preferentially feed their offspring with tool-derived food. Building on this work, our review examines the possible evolutionary origins of these birds' remarkable tool-use behaviour. Whilst robust comparative analyses are impossible, given the phylogenetic rarity of animal tool use, our examination of a wide range of circumstantial evidence enables a first attempt at reconstructing a plausible evolutionary scenario. We suggest that a common ancestor of NC crows, originating from a (probably) non-tool-using South-East Asian or Australasian crow population, colonised New Caledonia after its last emersion several million years ago. The presence of profitable but out-of-reach food, in combination with a lack of direct competition for these resources, resulted in a vacant woodpecker-like niche. Crows may have possessed certain behavioural and/or morphological features upon their arrival that predisposed them to express tool-use rather than specialised prey-excavation behaviour, although it is possible that woodpecker-like foraging preceded tool use. Low levels of predation risk may have further facilitated tool-use behaviour, by allowing greater expenditure of time and energy on object interaction and exploration, as well as the evolution of a 'slow' life-history, in

  13. Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys.

    Science.gov (United States)

    Walter, Stephanie; Rasche, Andrea; Moreira-Soto, Andrés; Pfaender, Stephanie; Bletsa, Magda; Corman, Victor Max; Aguilar-Setien, Alvaro; García-Lacy, Fernando; Hans, Aymeric; Todt, Daniel; Schuler, Gerhard; Shnaiderman-Torban, Anat; Steinman, Amir; Roncoroni, Cristina; Veneziano, Vincenzo; Rusenova, Nikolina; Sandev, Nikolay; Rusenov, Anton; Zapryanova, Dimitrinka; García-Bocanegra, Ignacio; Jores, Joerg; Carluccio, Augusto; Veronesi, Maria Cristina; Cavalleri, Jessika M V; Drosten, Christian; Lemey, Philippe; Steinmann, Eike; Drexler, Jan Felix

    2017-01-01

    The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in 278 animals (31.5%), and viral RNA was found in 3 animals (0.3%), all of which were simultaneously seropositive. A low RNA prevalence in spite of high seroprevalence suggests a predominance of acute infection, a possible difference from the mostly chronic hepacivirus infection pattern seen in horses and humans. Limitation of transmission due to short courses of infection may explain the existence of entirely seronegative groups of animals. Donkey and horse EqHV strains were paraphyletic and 97.5 to 98.2% identical in their translated polyprotein sequences, making virus/host cospeciation unlikely. Evolutionary reconstructions supported host switches of EqHV between horses and donkeys without the involvement of adaptive evolution. Global admixture of donkey and horse hepaciviruses was compatible with anthropogenic alterations of EqHV ecology. In summary, our findings do not support EqHV as the origin of the significantly more diversified HCV. Identification of a host system with predominantly acute hepacivirus infection may enable new insights into the chronic infection pattern associated with HCV. The evolutionary origins of the human hepatitis C virus (HCV) are unclear. The closest animal-associated relative of HCV occurs in horses (equine hepacivirus [EqHV]). The low EqHV genetic diversity implies a relatively recent acquisition of EqHV by horses, limiting the time span for

  14. Genetic enablers underlying the clustered evolutionary origins of C4 photosynthesis in angiosperms.

    Science.gov (United States)

    Christin, Pascal-Antoine; Arakaki, Mónica; Osborne, Colin P; Edwards, Erika J

    2015-04-01

    The evolutionary accessibility of novel adaptations varies among lineages, depending in part on the genetic elements present in each group. However, the factors determining the evolutionary potential of closely related genes remain largely unknown. In plants, CO2-concentrating mechanisms such as C4 and crassulacean acid metabolism (CAM) photosynthesis have evolved numerous times in distantly related groups of species, and constitute excellent systems to study constraints and enablers of evolution. It has been previously shown for multiple proteins that grasses preferentially co-opted the same gene lineage for C4 photosynthesis, when multiple copies were present. In this work, we use comparative transcriptomics to show that this bias also exists within Caryophyllales, a distantly related group with multiple C4 origins. However, the bias is not the same as in grasses and, when all angiosperms are considered jointly, the number of distinct gene lineages co-opted is not smaller than that expected by chance. These results show that most gene lineages present in the common ancestor of monocots and eudicots produced gene descendants that were recruited into C4 photosynthesis, but that C4-suitability changed during the diversification of angiosperms. When selective pressures drove C4 evolution, some copies were preferentially co-opted, probably because they already possessed C4-like expression patterns. However, the identity of these C4-suitable genes varies among clades of angiosperms, and C4 phenotypes in distant angiosperm groups thus represent genuinely independent realizations, based on different genetic precursors.

  15. The origins of C4 grasslands: integrating evolutionary and ecosystem science.

    Science.gov (United States)

    Edwards, Erika J; Osborne, Colin P; Strömberg, Caroline A E; Smith, Stephen A; Bond, William J; Christin, Pascal-Antoine; Cousins, Asaph B; Duvall, Melvin R; Fox, David L; Freckleton, Robert P; Ghannoum, Oula; Hartwell, James; Huang, Yongsong; Janis, Christine M; Keeley, Jon E; Kellogg, Elizabeth A; Knapp, Alan K; Leakey, Andrew D B; Nelson, David M; Saarela, Jeffery M; Sage, Rowan F; Sala, Osvaldo E; Salamin, Nicolas; Still, Christopher J; Tipple, Brett

    2010-04-30

    The evolution of grasses using C4 photosynthesis and their sudden rise to ecological dominance 3 to 8 million years ago is among the most dramatic examples of biome assembly in the geological record. A growing body of work suggests that the patterns and drivers of C4 grassland expansion were considerably more complex than originally assumed. Previous research has benefited substantially from dialog between geologists and ecologists, but current research must now integrate fully with phylogenetics. A synthesis of grass evolutionary biology with grassland ecosystem science will further our knowledge of the evolution of traits that promote dominance in grassland systems and will provide a new context in which to evaluate the relative importance of C4 photosynthesis in transforming ecosystems across large regions of Earth.

  16. Evolutionary Asiacentrism, Peking man, and the origins of sinocentric ethno-nationalism.

    Science.gov (United States)

    Yen, Hsiao-Pei

    2014-01-01

    This paper discusses how the theory of evolutionary Asiacentrism and the Peking Man findings at the Zhoukoudian site stimulated Chinese intellectuals to construct Sinocentric ethno-nationalism during the period from the late 1920s to the early 1940s. It shows that the theory was first popularized by foreign scientists in Beijing, and the Peking man discoveries further provided strong evidence for the idea that Central Asia, or to be more specific, Tibet, Xinjiang, and Mongolia, was the original cradle of humans. Chinese scholars in the late 1930s and 1940s appropriated the findings to construct the monogenesis theory of the Chinese, which designated that all the diverse ethnic groups within the territory of China shared a common ancestor back to antiquity.

  17. On the origin and evolutionary consequences of gene body DNA methylation.

    Science.gov (United States)

    Bewick, Adam J; Ji, Lexiang; Niederhuth, Chad E; Willing, Eva-Maria; Hofmeister, Brigitte T; Shi, Xiuling; Wang, Li; Lu, Zefu; Rohr, Nicholas A; Hartwig, Benjamin; Kiefer, Christiane; Deal, Roger B; Schmutz, Jeremy; Grimwood, Jane; Stroud, Hume; Jacobsen, Steven E; Schneeberger, Korbinian; Zhang, Xiaoyu; Schmitz, Robert J

    2016-08-01

    In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.

  18. Dimensions of integration in interdisciplinary explanations of the origin of evolutionary novelty.

    Science.gov (United States)

    Love, Alan C; Lugar, Gary L

    2013-12-01

    Many philosophers of biology have embraced a version of pluralism in response to the failure of theory reduction but overlook how concepts, methods, and explanatory resources are in fact coordinated, such as in interdisciplinary research where the aim is to integrate different strands into an articulated whole. This is observable for the origin of evolutionary novelty-a complex problem that requires a synthesis of intellectual resources from different fields to arrive at robust answers to multiple allied questions. It is an apt locus for exploring new dimensions of explanatory integration because it necessitates coordination among historical and experimental disciplines (e.g., geology and molecular biology). These coordination issues are widespread for the origin of novel morphologies observed in the Cambrian Explosion. Despite an explicit commitment to an integrated, interdisciplinary explanation, some potential disciplinary contributors are excluded. Notable among these exclusions is the physics of ontogeny. We argue that two different dimensions of integration-data and standards-have been insufficiently distinguished. This distinction accounts for why physics-based explanatory contributions to the origin of novelty have been resisted: they do not integrate certain types of data and differ in how they conceptualize the standard of uniformitarianism in historical, causal explanations. Our analysis of these different dimensions of integration contributes to the development of more adequate and integrated explanatory frameworks.

  19. The environmental and evolutionary history of Lake Ohrid (FYROM/Albania): interim results from the SCOPSCO deep drilling project

    Science.gov (United States)

    Wagner, Bernd; Wilke, Thomas; Francke, Alexander; Albrecht, Christian; Baumgarten, Henrike; Bertini, Adele; Combourieu-Nebout, Nathalie; Cvetkoska, Aleksandra; D'Addabbo, Michele; Donders, Timme H.; Föller, Kirstin; Giaccio, Biagio; Grazhdani, Andon; Hauffe, Torsten; Holtvoeth, Jens; Joannin, Sebastien; Jovanovska, Elena; Just, Janna; Kouli, Katerina; Koutsodendris, Andreas; Krastel, Sebastian; Lacey, Jack H.; Leicher, Niklas; Leng, Melanie J.; Levkov, Zlatko; Lindhorst, Katja; Masi, Alessia; Mercuri, Anna M.; Nomade, Sebastien; Nowaczyk, Norbert; Panagiotopoulos, Konstantinos; Peyron, Odile; Reed, Jane M.; Regattieri, Eleonora; Sadori, Laura; Sagnotti, Leonardo; Stelbrink, Björn; Sulpizio, Roberto; Tofilovska, Slavica; Torri, Paola; Vogel, Hendrik; Wagner, Thomas; Wagner-Cremer, Friederike; Wolff, George A.; Wonik, Thomas; Zanchetta, Giovanni; Zhang, Xiaosen S.

    2017-04-01

    This study reviews and synthesises existing information generated within the SCOPSCO (Scientific Collaboration on Past Speciation Conditions in Lake Ohrid) deep drilling project. The four main aims of the project are to infer (i) the age and origin of Lake Ohrid (Former Yugoslav Republic of Macedonia/Republic of Albania), (ii) its regional seismotectonic history, (iii) volcanic activity and climate change in the central northern Mediterranean region, and (iv) the influence of major geological events on the evolution of its endemic species. The Ohrid basin formed by transtension during the Miocene, opened during the Pliocene and Pleistocene, and the lake established de novo in the still relatively narrow valley between 1.9 and 1.3 Ma. The lake history is recorded in a 584 m long sediment sequence, which was recovered within the framework of the International Continental Scientific Drilling Program (ICDP) from the central part (DEEP site) of the lake in spring 2013. To date, 54 tephra and cryptotephra horizons have been found in the upper 460 m of this sequence. Tephrochronology and tuning biogeochemical proxy data to orbital parameters revealed that the upper 247.8 m represent the last 637 kyr. The multi-proxy data set covering these 637 kyr indicates long-term variability. Some proxies show a change from generally cooler and wetter to drier and warmer glacial and interglacial periods around 300 ka. Short-term environmental change caused, for example, by tephra deposition or the climatic impact of millennial-scale Dansgaard-Oeschger and Heinrich events are superimposed on the long-term trends. Evolutionary studies on the extant fauna indicate that Lake Ohrid was not a refugial area for regional freshwater animals. This differs from the surrounding catchment, where the mountainous setting with relatively high water availability provided a refuge for temperate and montane trees during the relatively cold and dry glacial periods. Although Lake Ohrid experienced

  20. Origin and evolutionary plasticity of the gastric caecum in sea urchins (Echinodermata: Echinoidea

    Directory of Open Access Journals (Sweden)

    Rolet Gauthier

    2010-10-01

    Full Text Available Abstract Background The digestive tract of many metazoan invertebrates is characterized by the presence of caeca or diverticula that serve secretory and/or absorptive functions. With the development of various feeding habits, distinctive digestive organs may be present in certain taxa. This also holds true for sea urchins (Echinodermata: Echinoidea, in which a highly specialized gastric caecum can be found in members of a derived subgroup, the Irregularia (cake urchins, sea biscuits, sand dollars, heart urchins, and related forms. As such a specialized caecum has not been reported from "regular" sea urchin taxa, the aim of this study was to elucidate its evolutionary origin. Results Using morphological data derived from dissection, magnetic resonance imaging, and extensive literature studies, we compare the digestive tract of 168 echinoid species belonging to 51 extant families. Based on a number of characters such as topography, general morphology, mesenterial suspension, and integration into the haemal system, we homologize the gastric caecum with the more or less pronounced dilation of the anterior stomach that is observed in most "regular" sea urchin taxa. In the Irregularia, a gastric caecum can be found in all taxa except in the Laganina and Scutellina. It is also undeveloped in certain spatangoid species. Conclusions According to our findings, the sea urchin gastric caecum most likely constitutes a synapomorphy of the Euechinoidea. Its occurrence in "regular" euechinoids is linked to the presence of an additional festoon of the anterior stomach in ambulacrum III. Both structures, the additional festoon and the gastric caecum, are absent in the sister taxon to the Euechinoidea, the Cidaroida. Since the degree of specialization of the gastric caecum is most pronounced in the predominantly sediment-burrowing irregular taxa, we hypothesize that its evolution is closely linked to the development of more elaborate infaunal lifestyles. We

  1. The Origin and Evolutionary History of HIV-1 Subtype C in Senegal

    Science.gov (United States)

    Jung, Matthieu; Leye, Nafissatou; Vidal, Nicole; Fargette, Denis; Diop, Halimatou; Toure Kane, Coumba; Gascuel, Olivier; Peeters, Martine

    2012-01-01

    Background The classification of HIV-1 strains in subtypes and Circulating Recombinant Forms (CRFs) has helped in tracking the course of the HIV pandemic. In Senegal, which is located at the tip of West Africa, CRF02_AG predominates in the general population and Female Sex Workers (FSWs). In contrast, 40% of Men having Sex with Men (MSM) in Senegal are infected with subtype C. In this study we analyzed the geographical origins and introduction dates of HIV-1 C in Senegal in order to better understand the evolutionary history of this subtype, which predominates today in the MSM population Methodology/Principal Findings We used a combination of phylogenetic analyses and a Bayesian coalescent-based approach, to study the phylogenetic relationships in pol of 56 subtype C isolates from Senegal with 3,025 subtype C strains that were sampled worldwide. Our analysis shows a significantly well supported cluster which contains all subtype C strains that circulate among MSM in Senegal. The MSM cluster and other strains from Senegal are widely dispersed among the different subclusters of African HIV-1 C strains, suggesting multiple introductions of subtype C in Senegal from many different southern and east African countries. More detailed analyses show that HIV-1 C strains from MSM are more closely related to those from southern Africa. The estimated date of the MRCA of subtype C in the MSM population in Senegal is estimated to be in the early 80's. Conclusions/Significance Our evolutionary reconstructions suggest that multiple subtype C viruses with a common ancestor originating in the early 1970s entered Senegal. There was only one efficient spread in the MSM population, which most likely resulted from a single introduction, underlining the importance of high-risk behavior in spread of viruses. PMID:22470456

  2. Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis.

    Science.gov (United States)

    Markov, Alexander V; Kaznacheev, Ilya S

    2016-06-08

    The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis) may have already existed in the basal eukaryotes. The mating system of the halophilic archaeon Haloferax volcanii probably represents an intermediate stage between typical prokaryotic and eukaryotic sex. H. volcanii is highly polyploid, as well as many other Archaea. Here, we use computer simulation to explore genetic and evolutionary outcomes of polyploidy in amitotic prokaryotes and its possible role in the origin of mitosis, meiosis and eukaryotic sex. Modeling suggests that polyploidy can confer strong short-term evolutionary advantage to amitotic prokaryotes. However, it also promotes the accumulation of recessive deleterious mutations and the risk of extinction in the long term, especially in highly mutagenic environment. There are several possible strategies that amitotic polyploids can use in order to reduce the genetic costs of polyploidy while retaining its benefits. Interestingly, most of these strategies resemble different components or aspects of eukaryotic sex. They include asexual ploidy cycles, equalization of genome copies by gene conversion, high-frequency lateral gene transfer between relatives, chromosome exchange coupled with homologous recombination, and the evolution of more accurate chromosome distribution during cell division (mitosis). Acquisition of mitosis by an amitotic polyploid results in chromosome diversification and specialization. Ultimately, it transforms a polyploid cell into a functionally monoploid one with multiple unique, highly redundant chromosomes. Specialization of chromosomes makes the previously evolved modes of promiscuous chromosome shuffling deleterious. This can result in selective pressure to develop accurate mechanisms of homolog pairing, and, ultimately, meiosis. Emergence of mitosis and the first

  3. Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology

    Science.gov (United States)

    Badyaev, Alexander V.

    2011-01-01

    In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework—natural selection and inheritance—the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification. PMID:21490021

  4. Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology.

    Science.gov (United States)

    Badyaev, Alexander V

    2011-07-07

    In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework-natural selection and inheritance-the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification.

  5. Unusual bilateral origins of the deep artery of thigh and associated variations

    Directory of Open Access Journals (Sweden)

    Shankar N

    2009-08-01

    Full Text Available During routine dissection of a middle aged male cadaver, an unusual origin of the deep artery of thigh was observed bilaterally. It arose from the femoral artery less than 1 cm distal to the inguinal ligament. On both sides, its diameter was greater than that of the femoral artery. An unusually distal origin of the lateral circumflex femoral artery was observed bilaterally. An unnamed branch from the deep artery of thigh on the left side was seen coursing superolaterally towards the anterior superior iliac spine. The deep external pudendal artery arose from the medial circumflex femoral artery on either side. On the right side, the femoral nerve emerged in the femoral triangle by piercing the iliacus muscle. As the deep artery of thigh is often used in vascular reconstructive procedures and is frequently visualized by various radiological imaging techniques, anatomical variations of itself as well as its branches have significant clinical implications.

  6. Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system.

    Science.gov (United States)

    Dirks-Mulder, Anita; Butôt, Roland; van Schaik, Peter; Wijnands, Jan Willem P M; van den Berg, Roel; Krol, Louie; Doebar, Sadhana; van Kooperen, Kelly; de Boer, Hugo; Kramer, Elena M; Smets, Erik F; Vos, Rutger A; Vrijdaghs, Alexander; Gravendeel, Barbara

    2017-03-23

    Thousands of flowering plant species attract pollinators without offering rewards, but the evolution of this deceit is poorly understood. Rewardless flowers of the orchid Erycina pusilla have an enlarged median sepal and incised median petal ('lip') to attract oil-collecting bees. These bees also forage on similar looking but rewarding Malpighiaceae flowers that have five unequally sized petals and gland-carrying sepals. The lip of E. pusilla has a 'callus' that, together with winged 'stelidia', mimics these glands. Different hypotheses exist about the evolutionary origin of the median sepal, callus and stelidia of orchid flowers. The evolutionary origin of these organs was investigated using a combination of morphological, molecular and phylogenetic techniques to a developmental series of floral buds of E. pusilla. The vascular bundle of the median sepal indicates it is a first whorl organ but its convex epidermal cells reflect convergence of petaloid features. Expression of AGL6 EpMADS4 and APETALA3 EpMADS14 is low in the median sepal, possibly correlating with its petaloid appearance. A vascular bundle indicating second whorl derivation leads to the lip. AGL6 EpMADS5 and APETALA3 EpMADS13 are most highly expressed in lip and callus, consistent with current models for lip identity. Six vascular bundles, indicating a stamen-derived origin, lead to the callus, stelidia and stamen. AGAMOUS is not expressed in the callus, consistent with its sterilization. Out of three copies of AGAMOUS and four copies of SEPALLATA, EpMADS22 and EpMADS6 are most highly expressed in the stamen. Another copy of AGAMOUS, EpMADS20, and the single copy of SEEDSTICK, EpMADS23, are most highly expressed in the stelidia, suggesting EpMADS22 may be required for fertile stamens. The median sepal, callus and stelidia of E. pusilla appear to be derived from a sepal, a stamen that gained petal identity, and stamens, respectively. Duplications, diversifying selection and changes in spatial

  7. Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today

    Science.gov (United States)

    Kutschera, Ulrich

    2009-11-01

    The book On the Origin of Species, published in November 1859, is an “abstract” without references, compiled by Charles Darwin from a much longer manuscript entitled “Natural Selection.” Here, I summarize the five theories that can be extracted from Darwin’s monograph, explain the true meaning of the phrase “struggle for life” (i.e., competition and cooperation), and outline Darwin’s original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that “selection only eliminates but is not creative” is still alive today. However, I document that August Weismann ( Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen ( Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this “Weismann-Schmalhausen principle” with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky ( Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by

  8. Ancient evolutionary origin of vertebrate enteric neurons from trunk-derived neural crest.

    Science.gov (United States)

    Green, Stephen A; Uy, Benjamin R; Bronner, Marianne E

    2017-04-06

    The enteric nervous system of jawed vertebrates arises primarily from vagal neural crest cells that migrate to the foregut and subsequently colonize and innervate the entire gastrointestinal tract. Here we examine development of the enteric nervous system in the basal jawless vertebrate the sea lamprey (Petromyzon marinus) to gain insight into its evolutionary origin. Surprisingly, we find no evidence for the existence of a vagally derived enteric neural crest population in the lamprey. Rather, labelling with the lipophilic dye DiI shows that late-migrating cells, originating from the trunk neural tube and associated with nerve fibres, differentiate into neurons within the gut wall and typhlosole. We propose that these trunk-derived neural crest cells may be homologous to Schwann cell precursors, recently shown in mammalian embryos to populate post-embryonic parasympathetic ganglia, including enteric ganglia. Our results suggest that neural-crest-derived Schwann cell precursors made an important contribution to the ancient enteric nervous system of early jawless vertebrates, a role that was largely subsumed by vagal neural crest cells in early gnathostomes.

  9. Tracing Behçet's disease origins along the Silk Road: an anthropological evolutionary genetics perspective.

    Science.gov (United States)

    Sazzini, Marco; Garagnani, Paolo; Sarno, Stefania; De Fanti, Sara; Lazzano, Teresa; Yang Yao, Daniele; Boattini, Alessio; Pazzola, Giulia; Maramotti, Sally; Boiardi, Luigi; Franceschi, Claudio; Salvarani, Carlo; Luiselli, Donata

    2015-01-01

    Behçet's disease is a multifactorial vasculitis that shows its highest prevalence in geographical areas historically involved in the Silk Road, suggesting that it might have originated somewhere along these ancient trade routes. This study aims to provide a first clue towards genetic evidence for this hypothesis by testing it via an anthropological evolutionary genetics approach. Behçet's disease variation at ancestry informative mitochondrial DNA control region and haplogroup diagnostic sites was characterised in 185 disease subjects of Italian descent and set into the Eurasian mitochondrial landscape by comparison with nearly 9,000 sequences representative of diversity observable in Italy and along the main Silk Road routes. Dissection of the actual genetic ancestry of disease individuals by means of population structure, spatial autocorrelation and haplogroup analyses revealed their closer relationships with some Middle Eastern and Central Asian groups settled along the Silk Road than with healthy Italians. These findings support the hypothesis that the Behçet's disease genetic risk has migrated to western Eurasia in parallel with ancestry components typical of Silk Road-related groups. This provided new insights that are useful to improve the understanding of disease origins and diffusion, as well as to inform future association studies aimed at properly accounting for the actual genetic ancestry of the examined Behçet's disease samples in order to minimise the detection of spurious associations and to improve the identification of genetic variants with actual clinical relevance.

  10. Evolutionary origin of the insect wing via integration of two developmental modules.

    Science.gov (United States)

    Niwa, Nao; Akimoto-Kato, Ai; Niimi, Teruyuki; Tojo, Koji; Machida, Ryuichiro; Hayashi, Shigeo

    2010-01-01

    Insect wing is a key evolutionary innovation for insect radiation, but its origins and intermediate forms are absent from the fossil record. To understand the ancestral state of the wing, expression of three key regulatory genes in insect wing development, wingless (wg), vestigial (vg), and apterous (ap) was studied in two basal insects, mayfly and bristletail. These basal insects develop dorsal limb branches, tracheal gill and stylus, respectively, that have been considered candidates for wing origin. Here we show that wg and vg are expressed in primordia for tracheal gill and stylus. Those primordia are all located in the lateral body region marked by down-regulation of early segmental wg stripes, but differ in their dorsal-ventral position, indicating their positions drifted within the lateral body region. On the other hand, ap expression was detected in terga of mayfly and bristletail. Notably, the extensive outgrowth of the paranotal lobe of apterygote bristletail developed from the border of ap-expressing tergal margin, and also expressed wg and vg. The data suggest that two regulatory modules involving wg-vg are present in apterygote insects: one associated with lateral body region and induces stick-like dorsal limb branches, the other associated with the boundary of dorsal and lateral body regions and the flat outgrowth of their interface. A combinatorial model is proposed in which dorsal limb branch was incorporated into dorsal-lateral boundary and acquired flat limb morphology through integration of the two wg-vg modules, allowing rapid evolution of the wing.

  11. Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics.

    Science.gov (United States)

    Pascal, Robert; Pross, Addy; Sutherland, John D

    2013-11-06

    A sudden transition in a system from an inanimate state to the living state-defined on the basis of present day living organisms-would constitute a highly unlikely event hardly predictable from physical laws. From this uncontroversial idea, a self-consistent representation of the origin of life process is built up, which is based on the possibility of a series of intermediate stages. This approach requires a particular kind of stability for these stages-dynamic kinetic stability (DKS)-which is not usually observed in regular chemistry, and which is reflected in the persistence of entities capable of self-reproduction. The necessary connection of this kinetic behaviour with far-from-equilibrium thermodynamic conditions is emphasized and this leads to an evolutionary view for the origin of life in which multiplying entities must be associated with the dissipation of free energy. Any kind of entity involved in this process has to pay the energetic cost of irreversibility, but, by doing so, the contingent emergence of new functions is made feasible. The consequences of these views on the studies of processes by which life can emerge are inferred.

  12. Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence.

    Science.gov (United States)

    De Baets, Kenneth; Dentzien-Dias, Paula; Upeniece, Ieva; Verneau, Olivier; Donoghue, Philip C J

    2015-01-01

    Novel fossil discoveries have contributed to our understanding of the evolutionary appearance of parasitism in flatworms. Furthermore, genetic analyses with greater coverage have shifted our views on the coevolution of parasitic flatworms and their hosts. The putative record of parasitic flatworms is consistent with extant host associations and so can be used to put constraints on the evolutionary origin of the parasites themselves. The future lies in new molecular clock analyses combined with additional discoveries of exceptionally preserved flatworms associated with hosts and coprolites. Besides direct evidence, the host fossil record and biogeography have the potential to constrain their evolutionary history, albeit with caution needed to avoid circularity, and a need for calibrations to be implemented in the most conservative way. This might result in imprecise, but accurate divergence estimates for the evolution of parasitic flatworms.

  13. Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility

    Directory of Open Access Journals (Sweden)

    Hoeppner Marc P

    2012-09-01

    Full Text Available Abstract Background Small nucleolar (snoRNAs are required for posttranscriptional processing and modification of ribosomal, spliceosomal and messenger RNAs. Their presence in both eukaryotes and archaea indicates that snoRNAs are evolutionarily ancient. The location of some snoRNAs within the introns of ribosomal protein genes has been suggested to belie an RNA world origin, with the exons of the earliest protein-coding genes having evolved around snoRNAs after the advent of templated protein synthesis. Alternatively, this intronic location may reflect more recent selection for coexpression of snoRNAs and ribosomal components, ensuring rRNA modification by snoRNAs during ribosome synthesis. To gain insight into the evolutionary origins of this genetic organization, we examined the antiquity of snoRNA families and the stability of their genomic location across 44 eukaryote genomes. Results We report that dozens of snoRNA families are traceable to the Last Eukaryotic Common Ancestor (LECA, but find only weak similarities between the oldest eukaryotic snoRNAs and archaeal snoRNA-like genes. Moreover, many of these LECA snoRNAs are located within the introns of host genes independently traceable to the LECA. Comparative genomic analyses reveal the intronic location of LECA snoRNAs is not ancestral however, suggesting the pattern we observe is the result of ongoing intragenomic mobility. Analysis of human transcriptome data indicates that the primary requirement for hosting intronic snoRNAs is a broad expression profile. Consistent with ongoing mobility across broadly-expressed genes, we report a case of recent migration of a non-LECA snoRNA from the intron of a ubiquitously expressed non-LECA host gene into the introns of two LECA genes during the evolution of primates. Conclusions Our analyses show that snoRNAs were a well-established family of RNAs at the time when eukaryotes began to diversify. While many are intronic, this association is not

  14. Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps.

    Science.gov (United States)

    Tennessen, Jacob A; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron

    2014-12-04

    Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes.

  15. Processos evolutivos e a origem das plantas cultivadas Evolutionary processes and the origin of crop plants

    Directory of Open Access Journals (Sweden)

    Elizabeth Ann Veasey

    2011-07-01

    Full Text Available A evolução das plantas cultivadas, que teve início há cerca de 13.000 anos, está sujeita aos mesmos processos evolutivos naturais, aliada à ação do homem de forma consciente ou inconsciente, levando à domesticação. Nesta revisão, são apresentados os principais fatores evolutivos, tais como mutação, hibridação, migração, seleção e deriva genética, que, de alguma maneira, estão envolvidos com a origem, evolução e domesticação de plantas cultivadas. São apresentados também exemplos de como esses processos influenciaram na diversidade intra e interespecífica de plantas cultivadas, com o aparecimento de novas variedades ou mesmo de novas espécies. De modo geral, tais processos atuaram na ampliação, na manutenção, bem como na redução da variabilidade genética das plantas cultivadas.The evolution of crop plants, which began at about 13,000 years ago, is subject to the same natural evolutionary processes, coupled with the action of man, consciously or unconsciously, leading to domestication. This review presents the main evolutionary factors such as mutation, hybridization, migration, selection and genetic drift, which somehow are involved in the origin, evolution and domestication of crop plants. Examples of how these processes influenced in the intra and interespecific diversity of crop plants, with the uprise of new varieties or even of new species, are also presented. In general, these processes have worked well in the increase, maintenance, as well as in the reduction of genetic diversity of crop plants.

  16. Evolutionary scenarios for the origin of an Antarctic tardigrade species based on molecular clock analyses and biogeographic data

    NARCIS (Netherlands)

    Guidetti, R.; McInnes, S.J.; Cesari, M.; Rebecchi, L.; Rota-Stabelli, O.

    2017-01-01

    The origin of the Antarctic continental extant fauna is a highly debated topic, complicated by the paucity of organisms for which we have clear biogeographic distributions and understanding of their evolutionary timescale. To shed new light on this topic, we coupled molecular clock analyses with

  17. Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28.

    Science.gov (United States)

    Delbridge, Margaret L; Patel, Hardip R; Waters, Paul D; McMillan, Daniel A; Marshall Graves, Jennifer A

    2009-08-01

    Comparative gene mapping of human X-borne genes in marsupials defined an ancient conserved region and a recently added region of the eutherian X, and the separate evolutionary origins of these regions was confirmed by their locations on chicken chromosomes 4p and 1q, respectively. However, two groups of genes, from the pericentric region of the short arm of the human X (at Xp11) and a large group of genes from human Xq28, were thought to be part of a third evolutionary block, being located in a single region in fish, but mapping to chicken chromosomes other than 4p and 1q. We tested this hypothesis by comparative mapping of genes in these regions. Our gene mapping results show that human Xp11 genes are located on the marsupial X chromosome and platypus chromosome 6, indicating that the Xp11 region was part of original therian X chromosome. We investigated the evolutionary origin of genes from human Xp11 and Xq28, finding that chicken paralogs of human Xp11 and Xq28 genes had been misidentified as orthologs, and their true orthologs are represented in the chicken EST database, but not in the current chicken genome assembly. This completely undermines the evidence supporting a separate evolutionary origin for this region of the human X chromosome, and we conclude, instead, that it was part of the ancient autosome, which became the conserved region of the therian X chromosome 166 million years ago.

  18. The origin, source, and cycling of methane in deep crystalline rock biosphere

    Science.gov (United States)

    Kietäväinen, Riikka; Purkamo, Lotta

    2015-01-01

    The emerging interest in using stable bedrock formations for industrial purposes, e.g., nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. Considering the origin and evolution of life on Earth, these environments may also serve as windows to the past. Various geological, chemical, and biological processes can influence the deep carbon cycle. Conditions of CH4 formation, available substrates and time scales can be drastically different from surface environments. This paper reviews the origin, source, and cycling of methane in deep terrestrial crystalline bedrock with an emphasis on microbiology. In addition to potential formation pathways of CH4, microbial consumption of CH4 is also discussed. Recent studies on the origin of CH4 in continental bedrock environments have shown that the traditional separation of biotic and abiotic CH4 by the isotopic composition can be misleading in substrate-limited environments, such as the deep crystalline bedrock. Despite of similarities between Precambrian continental sites in Fennoscandia, South Africa and North America, where deep methane cycling has been studied, common physicochemical properties which could explain the variation in the amount of CH4 and presence or absence of CH4 cycling microbes were not found. However, based on their preferred carbon metabolism, methanogenic microbes appeared to have similar spatial distribution among the different sites. PMID:26236303

  19. The origin, source, and cycling of methane in deep crystalline rock biosphere.

    Science.gov (United States)

    Kietäväinen, Riikka; Purkamo, Lotta

    2015-01-01

    The emerging interest in using stable bedrock formations for industrial purposes, e.g., nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. Considering the origin and evolution of life on Earth, these environments may also serve as windows to the past. Various geological, chemical, and biological processes can influence the deep carbon cycle. Conditions of CH4 formation, available substrates and time scales can be drastically different from surface environments. This paper reviews the origin, source, and cycling of methane in deep terrestrial crystalline bedrock with an emphasis on microbiology. In addition to potential formation pathways of CH4, microbial consumption of CH4 is also discussed. Recent studies on the origin of CH4 in continental bedrock environments have shown that the traditional separation of biotic and abiotic CH4 by the isotopic composition can be misleading in substrate-limited environments, such as the deep crystalline bedrock. Despite of similarities between Precambrian continental sites in Fennoscandia, South Africa and North America, where deep methane cycling has been studied, common physicochemical properties which could explain the variation in the amount of CH4 and presence or absence of CH4 cycling microbes were not found. However, based on their preferred carbon metabolism, methanogenic microbes appeared to have similar spatial distribution among the different sites.

  20. The origin, source and cycling of methane in deep crystalline rock biosphere

    Directory of Open Access Journals (Sweden)

    Riikka eKietäväinen

    2015-07-01

    Full Text Available The emerging interest in using stable bedrock formations for industrial purposes, e.g. nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. Considering the origin and evolution of life on Earth, these environments may also serve as windows to the past. Various geological, chemical and biological processes can influence the deep carbon cycle. Conditions of CH4 formation, available substrates and time scales can be drastically different from surface environments. This paper reviews the origin, source and cycling of methane in deep terrestrial crystalline bedrock with an emphasis on microbiology. In addition to potential formation pathways of CH4, microbial consumption of CH4 is also discussed. Recent studies on the origin of CH4 in continental bedrock environments have shown that the traditional separation of biotic and abiotic CH4 by the isotopic composition can be misleading in substrate-limited environments, such as the deep crystalline bedrock. Despite of similarities between Precambrian continental sites in Fennoscandia, South Africa and North America, where deep methane cycling has been studied, common physicochemical properties which could explain the variation in the amount of CH4 and presence or absence of CH4 cycling microbes were not found. However, based on their preferred carbon metabolism, methanogenic microbes appeared to have similar spatial distribution among the different sites.

  1. The evolutionary history of testicular externalization and the origin of the scrotum

    Indian Academy of Sciences (India)

    Karel Kleisner; Richard Ivell; Jaroslav Flegr

    2010-03-01

    This paper re-examines the evolution of the scrotum and testicular descent in the context of the recent phylogeny of mammals. The adaptive significance of testicular descent and scrotality is briefly discussed. We mapped four character states reflecting the position of testes and presence of scrotum onto recent mammalian phylogeny. Our results are interpreted as follows: as to the presence of testicondy in Monotremata and most of Atlantogenata, which represent the basal group of all eutherians, we argue that primary testicondy represents a plesiomorphic condition for Eutheria as well as for all mammals. This is in opposition to the previous hypothesis of Werdelin and Nilsonne that the scrotum may have evolved before the origin of mammals and then repeatedly disappeared in many groups including monotremes. We suggest that the scrotum evolved at least twice during the evolutionary history of mammals, within Marsupialia and Boreoeutheria, and has subsequently been lost by many groups; this trend is especially strong in Laurasiatheria. We suggest that the recent diversity in testicular position within mammals is the result of multiple selection pressures stemming from the need to provide conditions suitable for sperm development and storage, or to protect the male gonads from excessive physical and physiological disturbance.

  2. Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos.

    Science.gov (United States)

    Delsuc, Frédéric; Superina, Mariella; Tilak, Marie-Ka; Douzery, Emmanuel J P; Hassanin, Alexandre

    2012-02-01

    Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]). Phylogenetic analyses provided a reference phylogeny and timescale for living xenarthran genera. Our results reveal monophyletic pichiciegos as members of a major armadillo subfamily (Chlamyphorinae). Their strictly fossorial lifestyle probably evolved as a response to the Oligocene aridification that occurred in South America after their divergence from Tolypeutinae around 32 million years ago (Mya). The ancient divergence date (∼17Mya) for separation between the two species supports their taxonomic classification into distinct genera. The synchronicity with Middle Miocene marine incursions along the Paraná river basin suggests a vicariant origin for pichiciegos by the disruption of their ancestral range. Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority.

  3. Auditory hallucinations as primary disorders of syntax: an evolutionary theory of the origins of language.

    Science.gov (United States)

    Crow, Timothy J

    2004-01-01

    A theory of the evolutionary origins of language is built around: (1) the notion that language is a sapiens-specific capacity that arose in the speciation event that separated modern Homo sapiens from a prior hominid species, and (2) Broca's concept of asymmetry (subsequently recognised as a "torque" from right frontal to left occipital cortices) as the defining characteristic of the human brain. The four chambers of human association cortex thus created allow the separation of "thought" from the speech output and "meaning" from the speech input, these abstractions representing the associations in the nondominant hemisphere of the motor and sensory phonological representations in the dominant hemisphere. The nuclear symptoms of schizophrenia are conceived as manifestations of the breakdown of the boundaries between these four compartments, and as indicating the necessity of the separation of motor and sensory speech engrams as the basis for the speaker-hearer distinction. They further illustrate a requirement for a "deictic core" to the cerebral organisation of language as Mueller and Buehler proposed. In this sense the nuclear symptoms are disorders of the syntax of universal grammar.

  4. Genomic insights into the evolutionary origin of Xanthomonas axonopodis pv. citri and its ecological relatives.

    Science.gov (United States)

    Midha, Samriti; Patil, Prabhu B

    2014-10-01

    Xanthomonas axonopodis pv. citri (Xac) is the causal agent of citrus bacterial canker (CBC) and is a serious problem worldwide. Like CBC, several important diseases in other fruits, such as mango, pomegranate, and grape, are also caused by Xanthomonas pathovars that display remarkable specificity toward their hosts. While citrus and mango diseases were documented more than 100 years ago, the pomegranate and grape diseases have been known only since the 1950s and 1970s, respectively. Interestingly, diseases caused by all these pathovars were noted first in India. Our genome-based phylogenetic studies suggest that these diverse pathogens belong to a single species and these pathovars may be just a group of rapidly evolving strains. Furthermore, the recently reported pathovars, such as those infecting grape and pomegranate, form independent clonal lineages, while the citrus and mango pathovars that have been known for a long time form one clonal lineage. Such an understanding of their phylogenomic relationship has further allowed us to understand major and unique variations in the lineages that give rise to these pathovars. Whole-genome sequencing studies including ecological relatives from their putative country of origin has allowed us to understand the evolutionary history of Xac and other pathovars that infect fruits.

  5. The scolopidial accessory organs and Nebenorgans in orthopteroid insects: Comparative neuroanatomy, mechanosensory function, and evolutionary origin.

    Science.gov (United States)

    Strauß, Johannes

    2017-09-18

    Scolopidial sensilla in insects often form large sensory organs involved in proprioception or exteroception. Here the knowledge on Nebenorgans and accessory organs, two organs consisting of scolopidial sensory cells, is summarised. These organs are present in some insects which are model organisms for the physiology of mechanosensory systems (cockroaches and tettigoniids). Recent comparative studies documented the accessory organ in several taxa of Orthoptera (including tettigoniids, cave crickets, Jerusalem crickets) and the Nebenorgan in related insects (Mantophasmatodea). The accessory organ or Nebenorgan is usually a small organ of 8-15 sensilla located in the posterior leg tibia of all leg pairs. The physiological properties of the accessory organs and Nebenorgans are so far largely unknown. Taking together neuroanatomical and electrophysiological data from disparate taxa, there is considerable evidence that the accessory organ and Nebenorgan are vibrosensitive. They thus complement the larger vibrosensitive subgenual organ in the tibia. This review summarises the comparative studies of these sensory organs, in particular the arguments and criteria for the homology of the accessory organ and Nebenorgan among orthopteroid insects. Different scenarios of repeated evolutionary origins or losses of these sensory organs are discussed. Neuroanatomy allows to distinguish individual sensory organs for analysis of sensory physiology, and to infer scenarios of sensory evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Evolutionary origin and status of two insect acetylcholinesterases and their structural conservation and differentiation.

    Science.gov (United States)

    Cha, Deok Jea; Lee, Si Hyeock

    2015-01-01

    Acetylcholinesterase (AChE) plays a pivotal role in synaptic transmission in the cholinergic nervous system of most animals, including insects. Insects possess duplicated AChE gene loci (ace1 vs. ace2) encoding two distinct AChEs (AChE1 and AChE2). A phylogenetic analysis suggested that the last common ancestor of two aces shared its origin with Platyhelminthes. In addition, the ace duplication event likely occurred after the divergence of Protostomian but before the split of Ecdysozoa. The ace1 lineage exhibited a significantly lower evolutionary rate (d and dN/dS ratio) than the ace2 lineage, suggesting that the ace1 lineage has retained the essential function of synaptic transmission following its duplication. Therefore, the putative functional transition from ace1 to ace2 observed in some Hymenopteran insects appears to be a local and relatively recent event. The amino acid sequence comparison and three-dimensional modeling of insect AChEs identified a few consistent differences in the amino acid residues in functionally crucial domains between two AChEs, which are likely responsible for the functional differentiation between two AChEs. A unique amino acid substitution causing a dramatic reduction in the catalytic activity of AChE1 in some Hymenopteran insects was suggested to be responsible for the aforementioned functional transition of ace. © 2014 Wiley Periodicals, Inc.

  7. Diverse adaptations of an ancestral gill: a common evolutionary origin for wings, breathing organs, and spinnerets.

    Science.gov (United States)

    Damen, Wim G M; Saridaki, Theodora; Averof, Michalis

    2002-10-01

    Changing conditions of life impose new requirements on the morphology and physiology of an organism. One of these changes is the evolutionary transition from aquatic to terrestrial life, leading to adaptations in locomotion, breathing, reproduction, and mechanisms for food capture. We have shown previously that insects' wings most likely originated from one of the gills of ancestral aquatic arthropods during their transition to life on land. Here we investigate the fate of these ancestral gills during the evolution of another major arthropod group, the chelicerates. We examine the expression of two developmental genes, pdm/nubbin and apterous, that participate in the specification of insects' wings and are expressed in particular crustacean epipods/gills. In the horseshoe crab, a primitively aquatic chelicerate, pdm/nubbin is specifically expressed in opisthosomal appendages that give rise to respiratory organs called book gills. In spiders (terrestrial chelicerates), pdm/nubbin and apterous are expressed in successive segmental primordia that give rise to book lungs, lateral tubular tracheae, and spinnerets, novel structures that are used by spiders to breathe on land and to spin their webs. Combined with morphological and palaeontological evidence, these observations suggest that fundamentally different new organs (wings, air-breathing organs, and spinnerets) evolved from the same ancestral structure (gills) in parallel instances of terrestrialization.

  8. Evolutionary Origin of Higher-Order Repeat Structure in Alpha-Satellite DNA of Primate Centromeres

    Science.gov (United States)

    Koga, Akihiko; Hirai, Yuriko; Terada, Shoko; Jahan, Israt; Baicharoen, Sudarath; Arsaithamkul, Visit; Hirai, Hirohisa

    2014-01-01

    Alpha-satellite DNA (AS) is a main DNA component of primate centromeres, consisting of tandemly repeated units of ∼170 bp. The AS of humans contains sequences organized into higher-order repeat (HOR) structures, in which a block of multiple repeat units forms a larger repeat unit and the larger units are repeated tandemly. The presence of HOR in AS is widely thought to be unique to hominids (family Hominidae; humans and great apes). Recently, we have identified an HOR-containing AS in the siamang, which is a small ape species belonging to the genus Symphalangus in the family Hylobatidae. This result supports the view that HOR in AS is an attribute of hominoids (superfamily Hominoidea) rather than hominids. A single example is, however, not sufficient for discussion of the evolutionary origin of HOR-containing AS. In the present study, we developed an efficient method for detecting signs of large-scale HOR and demonstrated HOR of AS in all the three other genera. Thus, AS organized into HOR occurs widely in hominoids. Our results indicate that (i) HOR-containing AS was present in the last common ancestor of hominoids or (ii) HOR-containing AS emerged independently in most or all basal branches of hominoids. We have also confirmed HOR occurrence in centromeric AS in the Hylobatidae family, which remained unclear in our previous study because of the existence of AS in subtelomeric regions, in addition to centromeres, of siamang chromosomes. PMID:24585002

  9. The evolutionary origin of the need to sleep: An inevitable consequence of synaptic neurotransmission?

    Directory of Open Access Journals (Sweden)

    Robert S. Cantor

    2015-09-01

    Full Text Available It is proposed that the evolutionary origin of the need to sleep is the removal of neurotransmitters (NTs that escape reuptake and accumulate in brain interstitial fluid. Recent work suggests that the activity of ionotropic postsynaptic receptors, rapidly initiated by binding of NTs to extracellular sites, is modulated over longer times by adsorption of these NTs to the lipid bilayers in which the receptors are embedded. This bilayer-mediated mechanism is far less molecularly specific than binding, so bilayer adsorption of NTs that have diffused into synapses for other receptors would modulate their activity as well. Although NTs are recycled by membrane protein reuptake, the process is less than 100% efficient; a fraction escapes the region in which these specific reuptake proteins are localized and eventually diffuses throughout the interstitial fluid. It is estimated that even if only 0.1% of NTs escape reuptake, they would accumulate and adsorb to bilayers in synapses of other receptors sufficiently to affect receptor activity, the harmful consequences of which are avoided by sleep: a period of efficient convective clearance of solutes together with greatly reduced synaptic activity.

  10. The evolutionary and genetic origins of consciousness in the Cambrian Period over 500 million years ago

    Science.gov (United States)

    Feinberg, Todd E.; Mallatt, Jon

    2013-01-01

    Vertebrates evolved in the Cambrian Period before 520 million years ago, but we do not know when or how consciousness arose in the history of the vertebrate brain. Here we propose multiple levels of isomorphic or somatotopic neural representations as an objective marker for sensory consciousness. All extant vertebrates have these, so we deduce that consciousness extends back to the group's origin. The first conscious sense may have been vision. Then vision, coupled with additional sensory systems derived from ectodermal placodes and neural crest, transformed primitive reflexive systems into image forming brains that map and perceive the external world and the body's interior. We posit that the minimum requirement for sensory consciousness and qualia is a brain including a forebrain (but not necessarily a developed cerebral cortex/pallium), midbrain, and hindbrain. This brain must also have (1) hierarchical systems of intercommunicating, isomorphically organized, processing nuclei that extensively integrate the different senses into representations that emerge in upper levels of the neural hierarchy; and (2) a widespread reticular formation that integrates the sensory inputs and contributes to attention, awareness, and neural synchronization. We propose a two-step evolutionary history, in which the optic tectum was the original center of multi-sensory conscious perception (as in fish and amphibians: step 1), followed by a gradual shift of this center to the dorsal pallium or its cerebral cortex (in mammals, reptiles, birds: step 2). We address objections to the hypothesis and call for more studies of fish and amphibians. In our view, the lamprey has all the neural requisites and is likely the simplest extant vertebrate with sensory consciousness and qualia. Genes that pattern the proposed elements of consciousness (isomorphism, neural crest, placodes) have been identified in all vertebrates. Thus, consciousness is in the genes, some of which are already known. PMID

  11. Evolutionary origin of GnIH and NPFF in chordates: insights from novel amphioxus RFamide peptides.

    Directory of Open Access Journals (Sweden)

    Tomohiro Osugi

    Full Text Available Gonadotropin-inhibitory hormone (GnIH is a newly identified hypothalamic neuropeptide that inhibits pituitary hormone secretion in vertebrates. GnIH has an LPXRFamide (X = L or Q motif at the C-terminal in representative species of gnathostomes. On the other hand, neuropeptide FF (NPFF, a neuropeptide characterized as a pain-modulatory neuropeptide, in vertebrates has a PQRFamide motif similar to the C-terminal of GnIH, suggesting that GnIH and NPFF have diverged from a common ancestor. Because GnIH and NPFF belong to the RFamide peptide family in vertebrates, protochordate RFamide peptides may provide important insights into the evolutionary origin of GnIH and NPFF. In this study, we identified a novel gene encoding RFamide peptides and two genes of their putative receptors in the amphioxus Branchiostoma japonicum. Molecular phylogenetic analysis and synteny analysis indicated that these genes are closely related to the genes of GnIH and NPFF and their receptors of vertebrates. We further identified mature RFamide peptides and their receptors in protochordates. The identified amphioxus RFamide peptides inhibited forskolin induced cAMP signaling in the COS-7 cells with one of the identified amphioxus RFamide peptide receptors expressed. These results indicate that the identified protochordate RFamide peptide gene is a common ancestral form of GnIH and NPFF genes, suggesting that the origin of GnIH and NPFF may date back to the time of the emergence of early chordates. GnIH gene and NPFF gene may have diverged by whole-genome duplication in the course of vertebrate evolution.

  12. The evolutionary and genetic origins of consciousness in the Cambrian Period over 500 million years ago

    Directory of Open Access Journals (Sweden)

    Todd E Feinberg

    2013-10-01

    Full Text Available Vertebrates evolved in the Cambrian Period before 520 million years ago, but we do not know when or how consciousness arose in the history of the vertebrate brain. Here we propose multiple levels of isomorphic or somatotopic neural representations as an objective marker for sensory consciousness. All extant vertebrates have these, so we deduce that consciousness extends back to the group’s origin. The first conscious sense may have been vision. Then vision, coupled with additional sensory systems derived from ectodermal placodes and neural crest, transformed primitive reflexive systems into image forming brains that map and perceive the external world and the body’s interior. We posit that the minimum requirement for sensory consciousness and qualia is a brain including a forebrain (but not necessarily a developed cerebral cortex/pallium, midbrain and hindbrain. This brain must also have 1 hierarchical systems of intercommunicating, isomorphically organized, processing nuclei that extensively integrate the different senses into representations that emerge in upper levels of the neural hierarchy; and 2 a widespread reticular formation that integrates the sensory inputs and contributes to attention, awareness, and neural synchronization. We propose a two-step evolutionary history, in which the optic tectum was the original center of multi-sensory conscious perception (as in fish and amphibians: step 1, followed by a gradual shift of this center to the dorsal pallium or its cerebral cortex (in mammals, reptiles, birds: step 2. We address objections to the hypothesis and call for more studies of fish and amphibians. In our view, the lamprey has all the neural requisites and is likely the simplest extant vertebrate with sensory consciousness and qualia. Genes that pattern the proposed elements of consciousness (isomorphism, neural crest, placodes have been identified in all vertebrates. Thus, consciousness is in the genes, some of which are

  13. Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms.

    Directory of Open Access Journals (Sweden)

    Sacha Coesel

    Full Text Available Carotenoids are produced by all photosynthetic organisms, where they play essential roles in light harvesting and photoprotection. The carotenoid biosynthetic pathway of diatoms is largely unstudied, but is of particular interest because these organisms have a very different evolutionary history with respect to the Plantae and are thought to be derived from an ancient secondary endosymbiosis between heterotrophic and autotrophic eukaryotes. Furthermore, diatoms have an additional xanthophyll-based cycle for dissipating excess light energy with respect to green algae and higher plants. To explore the origins and functions of the carotenoid pathway in diatoms we searched for genes encoding pathway components in the recently completed genome sequences of two marine diatoms. Consistent with the supplemental xanthophyll cycle in diatoms, we found more copies of the genes encoding violaxanthin de-epoxidase (VDE and zeaxanthin epoxidase (ZEP enzymes compared with other photosynthetic eukaryotes. However, the similarity of these enzymes with those of higher plants indicates that they had very probably diversified before the secondary endosymbiosis had occurred, implying that VDE and ZEP represent early eukaryotic innovations in the Plantae. Consequently, the diatom chromist lineage likely obtained all paralogues of ZEP and VDE genes during the process of secondary endosymbiosis by gene transfer from the nucleus of the algal endosymbiont to the host nucleus. Furthermore, the presence of a ZEP gene in Tetrahymena thermophila provides the first evidence for a secondary plastid gene encoded in a heterotrophic ciliate, providing support for the chromalveolate hypothesis. Protein domain structures and expression analyses in the pennate diatom Phaeodactylum tricornutum indicate diverse roles for the different ZEP and VDE isoforms and demonstrate that they are differentially regulated by light. These studies therefore reveal the ancient origins of several

  14. Evolutionary origin of peptidoglycan recognition proteins in vertebrate innate immune system

    Directory of Open Access Journals (Sweden)

    Tsujino Fumi

    2011-03-01

    Full Text Available Abstract Background Innate immunity is the ancient defense system of multicellular organisms against microbial infection. The basis of this first line of defense resides in the recognition of unique motifs conserved in microorganisms, and absent in the host. Peptidoglycans, structural components of bacterial cell walls, are recognized by Peptidoglycan Recognition Proteins (PGRPs. PGRPs are present in both vertebrates and invertebrates. Although some evidence for similarities and differences in function and structure between them has been found, their evolutionary history and phylogenetic relationship have remained unclear. Such studies have been severely hampered by the great extent of sequence divergence among vertebrate and invertebrate PGRPs. Here we investigate the birth and death processes of PGRPs to elucidate their origin and diversity. Results We found that (i four rounds of gene duplication and a single domain duplication have generated the major variety of present vertebrate PGRPs, while in invertebrates more than ten times the number of duplications are required to explain the repertoire of present PGRPs, and (ii the death of genes in vertebrates appears to be almost null whereas in invertebrates it is frequent. Conclusion These results suggest that the emergence of new PGRP genes may have an impact on the availability of the repertoire and its function against pathogens. These striking differences in PGRP evolution of vertebrates and invertebrates should reflect the differences in the role of their innate immunity. Insights on the origin of PGRP genes will pave the way to understand the evolution of the interaction between host and pathogens and to lead to the development of new treatments for immune diseases that involve proteins related to the recognition of self and non-self.

  15. Origin and evolutionary dynamics of Hepatitis B virus (HBV) genotype E in Madagascar.

    Science.gov (United States)

    Lo Presti, Alessandra; Andriamandimby, Soa Fy; Lai, Alessia; Angeletti, Silvia; Cella, Eleonora; Mottini, Giovanni; Guarino, Michele Pier Luca; Balotta, Claudia; Galli, Massimo; Heraud, Jean-Michel; Zehender, Gianguglielmo; Ciccozzi, Massimo

    2017-02-01

    Africa is one of the endemic regions of HBV infection. In particular, genotype E is highly endemic in most of sub-Saharan Africa such as West African countries where it represents more than 90% of total infections. Madagascar, which is classified as a high endemic area for HBV and where the most prevalent genotype is E, might play a relevant role in the dispersion of this genotype due to its crucial position in the Indian Ocean. The aim of this study was to investigate the origin, population dynamics, and circulation of HBV-E genotype in Madagascar through high-resolution phylogenetic and phylodynamic approaches. The phylogenetic tree indicated that Malagasy isolates were intermixed and closely related with sequences mostly from West African countries. The Bayesian tree highlighted three statistically supported clusters of Malagasy strains which dated back to the years 1981 (95% HPD: 1971-1992), 1986 (95% HPD: 1974-1996), and 1989 (95% HPD: 1974-2001). Population dynamics analysis showed an exponential increase in the number of HBV-E infections approximately from the year 1975 until 2000s. The migration analysis was also performed and a dynamic pattern of gene flow was identified. In conclusion, this study confirms previous observation of HBV-E circulation in Africa and expands these findings at Madagascar demonstrating its recent introduction, and highlighting the role of the African countries in the spread of HBV-E genotype. Further studies on molecular epidemiology of HBV genotype E are needed to clarify the evolutionary history of this genotype.

  16. Tyrannobdella rex n. gen. n. sp. and the evolutionary origins of mucosal leech infestations.

    Directory of Open Access Journals (Sweden)

    Anna J Phillips

    Full Text Available BACKGROUND: Leeches have gained a fearsome reputation by feeding externally on blood, often from human hosts. Orificial hirudiniasis is a condition in which a leech enters a body orifice, most often the nasopharyngeal region, but there are many cases of leeches infesting the eyes, urethra, vagina, or rectum. Several leech species particularly in Africa and Asia are well-known for their propensity to afflict humans. Because there has not previously been any data suggesting a close relationship for such geographically disparate species, this unnerving tendency to be invasive has been regarded only as a loathsome oddity and not a unifying character for a group of related organisms. PRINCIPAL FINDINGS: A new genus and species of leech from Perú was found feeding from the nasopharynx of humans. Unlike any other leech previously described, this new taxon has but a single jaw with very large teeth. Phylogenetic analyses of nuclear and mitochondrial genes using parsimony and Bayesian inference demonstrate that the new species belongs among a larger, global clade of leeches, all of which feed from the mucosal surfaces of mammals. CONCLUSIONS: This new species, found feeding from the upper respiratory tract of humans in Perú, clarifies an expansion of the family Praobdellidae to include the new species Tyrannobdella rex n. gen. n. sp., along with others in the genera Dinobdella, Myxobdella, Praobdella and Pintobdella. Moreover, the results clarify a single evolutionary origin of a group of leeches that specializes on mucous membranes, thus, posing a distinct threat to human health.

  17. Evolutionary origins of C-terminal (GPPn 3-hydroxyproline formation in vertebrate tendon collagen.

    Directory of Open Access Journals (Sweden)

    David M Hudson

    Full Text Available Approximately half the proline residues in fibrillar collagen are hydroxylated. The predominant form is 4-hydroxyproline, which helps fold and stabilize the triple helix. A minor form, 3-hydroxyproline, still has no clear function. Using peptide mass spectrometry, we recently revealed several previously unknown molecular sites of 3-hydroxyproline in fibrillar collagen chains. In fibril-forming A-clade collagen chains, four new partially occupied 3-hydroxyproline sites were found (A2, A3, A4 and (GPPn in addition to the fully occupied A1 site at Pro986. The C-terminal (GPPn motif has five consecutive GPP triplets in α1(I, four in α2(I and three in α1(II, all subject to 3-hydroxylation. The evolutionary origins of this substrate sequence were investigated by surveying the pattern of its 3-hydroxyproline occupancy from early chordates through amphibians, birds and mammals. Different tissue sources of type I collagen (tendon, bone and skin and type II collagen (cartilage and notochord were examined by mass spectrometry. The (GPPn domain was found to be a major substrate for 3-hydroxylation only in vertebrate fibrillar collagens. In higher vertebrates (mouse, bovine and human, up to five 3-hydroxyproline residues per (GPPn motif were found in α1(I and four in α2(I, with an average of two residues per chain. In vertebrate type I collagen the modification exhibited clear tissue specificity, with 3-hydroxyproline prominent only in tendon. The occupancy also showed developmental changes in Achilles tendon, with increasing 3-hydroxyproline levels with age. The biological significance is unclear but the level of 3-hydroxylation at the (GPPn site appears to have increased as tendons evolved and shows both tendon type and developmental variations within a species.

  18. Erasmus Darwin, Herbert Spencer, and the origins of the evolutionary worldview in British provincial scientific culture, 1770-1850.

    Science.gov (United States)

    Elliott, Paul

    2003-03-01

    The significance of Herbert Spencer's evolutionary philosophy has been generally recognized for over a century, as the familiarity of his phrase "survival of the fittest" indicates, yet accounts of the origins of his system still tend to follow too closely his own description, written many decades later. This essay argues that Spencer's own interpretation of his intellectual development gives an inadequate impression of the debt he owed to provincial scientific culture and its institutions. Most important, it shows that his evolutionism was originally stimulated by his association with the Derby philosophical community, for it was through this group--of which his father, who also appears to have espoused a deistic evolutionary theory, was a member--that he was first exposed to progressive Englightenment social and educational philosophies and to the evolutionary worldview of Erasmus Darwin, the first president of the Derby Philosophical Society. Darwin's scheme was the first to incorporate biological evolution, associationist psychology, evolutionary geology, and cosmological developmentalism. Spencer's own implicit denials of the link with Darwin are shown to be implausible in the face of Darwin's continuing influence on the Derby savants, the product of insecurity in his later years when he feared for his reputation as Lamarckism became increasingly untenable.

  19. Hot, deep origin of petroleum: shelf and shallow basin evidence and application

    Science.gov (United States)

    Price, Leigh C.

    1978-01-01

    Oil and gas pools in shallow basins or on the shallow, stable shelves of deeper sedimentary basins may not be exceptions to the model of a hot deep origin of petroleum. The oil in shallow basins is directly associated with faulting extending out of the deepest parts of the basin. Evidence exists that some of these shallow basins have been much hotter in the past either from igneous activity or from a higher geothermal gradient. Uplift and erosion may also have removed substantial thicknesses of sediments in some of these basins. Oil on the stable shallow shelves of deep basins may have originated in the deeper part of the basin and undergone long lateral migration to the traps where it is now found. Conduits for such migration have been sandstones in delta-distributary systems (eastern Oklahoma and Kansas), reef trends (Alberta, Canada), or regional porosity and permeability in sheet carbonates (Anadarko basin, western Oklahoma and Kansas).

  20. Deep neck space abscesses of dental origin: the impact of Streptococcus group Milleri.

    Science.gov (United States)

    Terzic, Andrej; Scolozzi, Paolo

    2014-10-01

    In recent years, there has been rising interest in Streptococcus group Milleri (SM) because high mortality rates have been related to it. In case of deep neck infections (DNI), whatever the origin, mortality rates as high as 26% were reported. But there are no data available for DNI with SM of purely dental origin. The aim of our article was to describe and analyse DNI of purely dental origin involving on one hand SM and on the other hand infections without presence of SM. We compared these two groups and statistically investigated if there were differences in clinical presentation (age, mouth opening, length of hospital stay, laboratory parameters) or clinical behaviour (re-operation, re-hospitalisation, secondary osteomyelitis, stay at intensive care, length of antibiotic treatment, presence of resistances against antibiotics, incapacity to work). For this, we retrospectively searched medical records of our institution for all purulent DNI treated from 2004 till 2012. We found 81 patients meeting all inclusion criteria. Thirty-four patients had involvement of SM, 47 did not. The only statistically significant difference between the SM group and the non-SM group was the length of incapacity to work. All other parameters were non-significant. Furthermore, there were no fatalities. In conclusion, the clinical importance of this article is that patients with deep neck abscesses of purely dental origin involving SM do not need more or different care when compared to all other DNI of dental origin.

  1. Evolutionary history of two divergent Dmrt1 genes reveals two rounds of polyploidy origins in gibel carp.

    Science.gov (United States)

    Li, Xi-Yin; Zhang, Xiao-Juan; Li, Zhi; Hong, Wei; Liu, Wei; Zhang, Jun; Gui, Jian-Fang

    2014-09-01

    Polyploidy lineages, despite very rare in vertebrates, have been proposed to play significant role in speciation and evolutionary success, but the occurrence history and consequences are still largely unknown. In this study, we used the conserved Dmrt1 to analyze polyploidy occurrence and evolutionary process in polyploid gibel carp. We identified two divergent Dmrt1 genes and respectively localized the two genes on three homologous chromosomes. Subsequently, the corresponding full-length cDNAs and genomic sequences of Dmrt1 genes were also characterized from the closely related species including Carassius auratus auratus and Cyprinus carpio, and their two Dmrt1 genes were respectively localized on two homologous chromosomes. Significantly, the evolutionary relationship analyses among cDNA and genomic DNA sequences of these Dmrt1 genes revealed two rounds of polyploidy origins in the gibel carp: an early polyploidy might result in an common tetraploid ancestor of Carassius auratus gibelio, Carassius auratus auratus and Cyprinus carpio before 18.49 million years ago (Mya), and an late polyploidy might occur from evolutionary branch of Carassius auratus at around 0.51 Mya, which lead to the occurrence of the hexaploid gibel carp. Therefore, this study provides clear genetic evidence for understanding occurrence time and historical process of polyploidy in polyploid vertebrates.

  2. The origins of the evolutionary signal used to predict protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Swapna Lakshmipuram S

    2012-12-01

    Full Text Available Abstract Background The correlation of genetic distances between pairs of protein sequence alignments has been used to infer protein-protein interactions. It has been suggested that these correlations are based on the signal of co-evolution between interacting proteins. However, although mutations in different proteins associated with maintaining an interaction clearly occur (particularly in binding interfaces and neighbourhoods, many other factors contribute to correlated rates of sequence evolution. Proteins in the same genome are usually linked by shared evolutionary history and so it would be expected that there would be topological similarities in their phylogenetic trees, whether they are interacting or not. For this reason the underlying species tree is often corrected for. Moreover processes such as expression level, are known to effect evolutionary rates. However, it has been argued that the correlated rates of evolution used to predict protein interaction explicitly includes shared evolutionary history; here we test this hypothesis. Results In order to identify the evolutionary mechanisms giving rise to the correlations between interaction proteins, we use phylogenetic methods to distinguish similarities in tree topologies from similarities in genetic distances. We use a range of datasets of interacting and non-interacting proteins from Saccharomyces cerevisiae. We find that the signal of correlated evolution between interacting proteins is predominantly a result of shared evolutionary rates, rather than similarities in tree topology, independent of evolutionary divergence. Conclusions Since interacting proteins do not have tree topologies that are more similar than the control group of non-interacting proteins, it is likely that coevolution does not contribute much to, if any, of the observed correlations.

  3. On the origin and evolutionary state of RZ Cas, KO Aql and S Equ

    CERN Document Server

    Mennekens, N; Van Rensbergen, W; Yungelson, L R

    2008-01-01

    Aims. Determination of the present evolutionary state and the restrictions on the initial mass ratios of RZ Cas, KO Aql and S Equ. Methods. Comparison of mass gaining stars with evolutionary models of single stars with the same mass and subsequent comparison with accretion tracks from simultaneous conservative binary evolution. Results. The gainers are in an early main sequence stage (Xc greater than 0.5), with KO Aql being almost unevolved. The initial donor/gainer mass ratios Mdi/Mgi must be larger than three to obtain the present mass and luminosity of the gainers.

  4. A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time

    Science.gov (United States)

    Harmon, Luke J.; Blank, Carrine E.

    2016-01-01

    Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record—phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth’s history have shaped—and been shaped by—evolution in Cyanobacteria. We identify a robust core cyanobacterial phylogeny and a smaller set of taxa that exhibit long-branch attraction artifacts. We estimated the age of nodes and reconstruct the ancestral character states of 43 phenotypic characters. We find high levels of phylogenetic signal for nearly all traits, indicating the phylogeny carries substantial predictive power. The earliest cyanobacterial lineages likely lived in freshwater habitats, had small cell diameters, were benthic or sessile, and possibly epilithic/endolithic with a sheath. We jointly analyzed a subset of 25 binary traits to determine whether rates of trait evolution have shifted over time in conjunction with major geologic events. Phylogenetic comparative analysis reveal an overriding signal of decreasing rates of trait evolution through time. Furthermore, the data suggest two major rate shifts in trait evolution associated with bursts of evolutionary innovation. The first rate shift occurs in the aftermath of the Great Oxidation Event and “Snowball Earth” glaciations and is associated with decrease in the evolutionary rates around 1.8–1.6 Ga. This rate shift seems to indicate the end of a major diversification of cyanobacterial phenotypes–particularly related to traits associated with filamentous morphology, heterocysts and motility in freshwater ecosystems. Another burst appears around the time of the Neoproterozoic

  5. Getting emotional with evolutionary simulations: the origin of affective processing in artificial neural networks

    NARCIS (Netherlands)

    B.T. Heerebout

    2011-01-01

    The main purpose of the present thesis was to investigate the evolutionary roots of basic affective processes and their underlying neural mechanisms. To this end, simulations were performed with agents that evolved artificial neural networks. Our general working hypothesis was that positive and nega

  6. Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing.

    Science.gov (United States)

    Senkevich, Tatiana G; Bruno, Daniel; Martens, Craig; Porcella, Stephen F; Wolf, Yuri I; Moss, Bernard

    2015-09-01

    Poxviruses reproduce in the host cytoplasm and encode most or all of the enzymes and factors needed for expression and synthesis of their double-stranded DNA genomes. Nevertheless, the mode of poxvirus DNA replication and the nature and location of the replication origins remain unknown. A current but unsubstantiated model posits only leading strand synthesis starting at a nick near one covalently closed end of the genome and continuing around the other end to generate a concatemer that is subsequently resolved into unit genomes. The existence of specific origins has been questioned because any plasmid can replicate in cells infected by vaccinia virus (VACV), the prototype poxvirus. We applied directional deep sequencing of short single-stranded DNA fragments enriched for RNA-primed nascent strands isolated from the cytoplasm of VACV-infected cells to pinpoint replication origins. The origins were identified as the switching points of the fragment directions, which correspond to the transition from continuous to discontinuous DNA synthesis. Origins containing a prominent initiation point mapped to a sequence within the hairpin loop at one end of the VACV genome and to the same sequence within the concatemeric junction of replication intermediates. These findings support a model for poxvirus genome replication that involves leading and lagging strand synthesis and is consistent with the requirements for primase and ligase activities as well as earlier electron microscopic and biochemical studies implicating a replication origin at the end of the VACV genome.

  7. Analysis of Origin of Multi-Ring Basins by Theory of Deep Water Waves

    Institute of Scientific and Technical Information of China (English)

    SHI Jian-Chun; MA Yue-Hua; CHEN Dao-Han; BAO Gang

    2008-01-01

    The tsunami model of the origin of multi-ring basins is analysed with the theory of deep water waves generated by an initial surface deformation,which is set as a parabolic crater.We obtain an approximate formula for calculating the ring radius.The formula applied to some multi-ring basins on the Moon,Mercury and Mars gives almost equidistant spacing of the rings within the main ring (the IV ring); this agrees with the previous conclusion that the IV ring marks the end of the fluidized region.Besides this,the theory of deep water waves does not require similar crustal structure at each basin-impact site on all three planets which is required in the theory of shallow water waves.

  8. Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change†

    Science.gov (United States)

    Xie, Gary; Keyhani, Nemat O.; Bonner; Jensen, Roy A.

    2003-01-01

    The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting

  9. Fragaria: A genus with deep historical roots and ripe for evolutionary and ecological insights

    Science.gov (United States)

    Aaron Liston; Richard Cronn; Tia-Lynn Ashman

    2014-01-01

    The cultivated strawberry, Fragaria × ananassa , is one of the youngest domesticated plants. Its 18th century origin via hybridization in Europe between the North American F. virginiana and the South American F. chiloensis was documented by the botanist Antoine Nicolas Duchesne. His 1766 “Natural History of Strawberries” is an extraordinary work that integrates...

  10. Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences

    Directory of Open Access Journals (Sweden)

    Keiko Tanaka

    2013-01-01

    Full Text Available Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi, Chlamydoselachus anguineus (frilled shark is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved as Chlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus, H. nakamurai. Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.

  11. Deep global evolutionary radiation in birds: diversification and trait evolution in the cosmopolitan bird family Rallidae.

    Science.gov (United States)

    Garcia-R, Juan C; Gibb, Gillian C; Trewick, Steve A

    2014-12-01

    Sufficient breadth of taxon sampling in major organisms groups is important to identify more realistic biological diversification processes that reveal the degree of historical biogeographic signal and net diversification retained in the current lineage distribution. We examine the mechanisms driving diversity in one of the major avian clades with an exceptional large-scale radiation, the family Rallidae, using the most complete species-level (∼70%) time calibrated hypothesis of evolutionary relationships produced to date. We find that Rallidae exhibit a pattern of diversification involving episodes of range expansion and regional speciation that results in most clades represented in all habitable continents. Our results suggest that several features may have played an important role on the diversification rates in Rallidae. Lineage accumulation is nearly constant and morphology (frontal shield and body size), innovate (flightlessness), habitat (forest) and distribution (insular) traits are possibly associated with increasing diversification rates along with spatial and ecological processes during the Miocene and Pliocene. Diversification and the global retention of lineage diversity have occurred in multiple lineages in Rallidae due to their dispersal ability and exploitation of ecological opportunities.

  12. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    Science.gov (United States)

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.

  13. Deep Water Compositions From the Los Angeles Basin and the Origin of Formation Water Salinity

    Science.gov (United States)

    Boles, J.; Giles, G.; Lockman, D.

    2005-12-01

    Deep basin formation waters represent original depositional waters that have been modified by diagenetic processes at elevated temperatures and pressures. In addition, they may be diluted by meteoric incursion from elevated structural blocks along basin flanks. It has long been thought that deep basin formation waters have salinities greater than sea water due to various processes like clay membrane filtration or other types of water-rock interaction. However, our work and similar studies in the San Joaquin basin show that formation waters in deep basins are more likely to become diluted rather than concentrated in the absence of soluble evaporite deposits that might underlie the basin. The idea of increased salinity with depth arose from studies in which the underpinning of the basin consisted of soluble evaporate deposits such as the Texas Gulf Coast, Illinois, Michigan, and some North Sea areas. There are very few deep formation water analyses from the Los Angeles Basin. Furthermore, very few of the current produced waters from any depth can be considered pristine because of the widespread formation water injection programs and commingling of fluids from different levels. Here, we describe the first analyses from a deep, previously untouched part of the basin that is currently being developed in the Inglewood Oil Field. We have analyzed a suite of formation waters from the mid-Miocene marine Sentous sandstone from sub-sea level depths of 2250 m to 2625 m at temperatures of about 110 to 126°C and pressures of about 27 MPa. The original depositional waters in the Sentous Formation were sea water whereas the sampled waters are diluted by about 20% from sea water and some show as much as 50% dilution. Based on comparison of oxygen and deuterium isotopes between the meteoric water trend and these waters, we conclude that the smectite to illite dehydration reaction is the major cause of dilution to the original formation water. Other notable differences include

  14. Two new deep-reef basslets (Teleostei, Grammatidae, Lipogramma, with comments on the eco-evolutionary relationships of the genus

    Directory of Open Access Journals (Sweden)

    Carole C. Baldwin

    2016-12-01

    Full Text Available The banded basslet, Lipogramma evides Robins & Colin, 1979, is shown to comprise two species: L. evides, which inhabits depths of 133–302 m, and a new species described here as Lipogramma levinsoni, which inhabits depths of 108–154 m and previously was considered to represent the juvenile of L. evides. A second new species of banded basslet, described here as Lipogramma haberi, inhabits depths of 152–233 m and was previously not reported in the literature. Morphologically, the three species differ in color patterns and modal numbers of gill rakers, whereas various other morphological features distinguish L. levinsoni from L. evides and L. haberi. DNA barcode data and multilocus, coalescent-based, species-delimitation analysis support the recognition of the three species. Phylogenetic analysis of mitochondrial and nuclear genetic data supports a sister-group relationship between the two deepest-living of the three species, L. evides and L. haberi, and suggests that the shallower L. levinsoni is more closely related to L. anabantoides Böhlke, 1960, which inhabits depths < 120 m. Evolutionary relationships within Lipogramma thus appear to be correlated with species depth ranges, an eco-evolutionary pattern that has been observed in other Caribbean marine teleosts and that warrants further investigation. The new species represent the eleventh and twelfth new fish species described in recent years from exploratory submersible diving in the Caribbean in the globally poorly studied depth zone of 50–300 m. This study suggests that there are at least two additional cryptic species of Lipogramma, which are being analyzed in ongoing investigations of Caribbean deep-reef ecosystems.

  15. At the crossroads of evolutionary computation and music: self-programming synthesizers, swarm orchestras and the origins of melody.

    Science.gov (United States)

    Miranda, Eduardo Reck

    2004-01-01

    This paper introduces three approaches to using Evolutionary Computation (EC) in Music (namely, engineering, creative and musicological approaches) and discusses examples of representative systems that have been developed within the last decade, with emphasis on more recent and innovative works. We begin by reviewing engineering applications of EC in Music Technology such as Genetic Algorithms and Cellular Automata sound synthesis, followed by an introduction to applications where EC has been used to generate musical compositions. Next, we introduce ongoing research into EC models to study the origins of music and detail our own research work on modelling the evolution of melody.

  16. Dental peculiarities in the silvery mole-rat: an original model for studying the evolutionary and biological origins of continuous dental generation in mammals

    Directory of Open Access Journals (Sweden)

    Helder Gomes Rodrigues

    2015-09-01

    Full Text Available Unravelling the evolutionary and developmental mechanisms that have impacted the mammalian dentition, since more than 200 Ma, is an intricate issue. Interestingly, a few mammal species, including the silvery mole-rat Heliophobius argenteocinereus, are able to replace their dentition by the addition of supernumerary molars at the back of jaw migrating then toward the front. The aim here was to demonstrate the potential interest of further studying this rodent in order to better understand the origins of continuous dental replacement in mammals, which could also provide interesting data concerning the evolution of limited dental generation occurring in first mammals. In the present study, we described the main stages of the dental eruptive sequence in the silvery mole-rat and the associated characteristics of horizontal replacement using X-ray microtomography. This was coupled to the investigation of other African mole-rats which have no dental replacement. This method permitted to establish evidence that the initial development of the dentition in Heliophobius is comparable to what it is observed in most of African mole-rats. This rodent first has premolars, but then identical additional molars, a mechanism convergent to manatees and the pygmy rock-wallaby. Evidence of continuous replacement and strong dental dynamics were also illustrated in Heliophobius, and stressed the need to deeply investigate these aspects for evolutionary, functional and developmental purposes. We also noticed that two groups of extinct non-mammalian synapsids convergently acquired this dental mechanism, but in a way differing from extant mammals. The discussion on the diverse evolutionary origins of horizontal dental replacement put emphasis on the necessity of focusing on biological parameters potentially involved in both continuous and limited developments of teeth in mammals. In that context, the silvery mole-rat could appear as the most appropriate candidate to do so.

  17. Lead isotopes and the origin of granulite and eclogite inclusions in deep-seated pipes

    Science.gov (United States)

    Lovering, J.F.; Tatsumoto, M.

    1968-01-01

    The isotopic composition of lead and the concentrations of lead, uranium, and thorium in Delegate basic pipes from Australia and in South African kimberlite pipes have been determined. The observed 238U/204Pb and observed 232Th/238U of eclogite inclusions in the pipes range from 2.9 to 18.7 and from 3.5 to 5.9, respectively. This result as well as the isotopic composition of lead suggests that the upper mantle is chemically heterogeneous with regard to the trace elements. Pyrochemically extracted leads from eclogite inclusions in the Delegate basic pipes and in a South African kimberlite pipe appear to be different in isotopic compositions from leads extracted from the host rock (matrix). These data are consistent with the hypothesis that the eclogitic inclusions in deep-seated pipes are of "accidental" origin and represent upper mantle materials caught up in the host materials during their intrusion. Lead extracted from a two-pyroxene granulite inclusion in one of the Delegate pipes has an isotopic composition indistinguishable from lead in the host rock. This observation is consistent either with a "cognate" origin for the granulite inclusion or with a modified "accidental" origin in which the isotopic composition of the original lead in the inclusion has been contaminated by lead from the host magma. Other evidence would indicate that an "accidental" origin be preferred. ?? 1968.

  18. Ecological and evolutionary consequences of benthic community stasis in the very deep sea (>1500 m)

    Science.gov (United States)

    Buzas, Martin A.; Hayek, Lee-Ann C.; Culver, Stephen J.; Hayward, Bruce W.; Osterman, Lisa E.

    2014-01-01

    An enigma of deep-sea biodiversity research is that the abyss with its low productivity and densities appears to have a biodiversity similar to that of shallower depths. This conceptualization of similarity is based mainly on per-sample estimates (point diversity, within-habitat, or α-diversity). Here, we use a measure of between-sample within-community diversity (β1H) to examine benthic foraminiferal diversity between 333 stations within 49 communties from New Zealand, the South Atlantic, the Gulf of Mexico, the Norwegian Sea, and the Arctic. The communities are grouped into two depth categories: 200–1500 m and >1500 m. β1H diversity exhibits no evidence of regional differences. Instead, higher values at shallower depths are observed worldwide. At depths of >1500 m the average β1H is zero, indicating stasis or no biodiversity gradient. The difference in β1H-diversity explains why, despite species richness often being greater per sample at deeper depths, the total number of species is greater at shallower depths. The greater number of communities and higher rate of evolution resulting in shorter species durations at shallower depths is also consistent with higher β1H values.

  19. Evolutionary origin of the immune system: a dialogue with Rod Langman.

    Science.gov (United States)

    Nagy, Z A

    2008-04-01

    The need of a specific defence mechanism against intracellular pathogens is proposed to have arisen very early in evolution, perhaps already in protozoa, e.g. amoebae. The phagocytic machinery of amoebae lends itself as a possible starting point for the evolution of such a mechanism. The hypothetical evolutionary pathway described here has been constructed to demonstrate the feasibility of developing a defence system against pathogens in the amoeba, which bears resemblances to contemporary cell-mediated immunity, and can thus be considered as its ancestor.

  20. The evolutionary origin of the vertebrate body plan: the problem of head segmentation.

    Science.gov (United States)

    Onai, Takayuki; Irie, Naoki; Kuratani, Shigeru

    2014-01-01

    The basic body plan of vertebrates, as typified by the complex head structure, evolved from the last common ancestor approximately 530 Mya. In this review, we present a brief overview of historical discussions to disentangle the various concepts and arguments regarding the evolutionary development of the vertebrate body plan. We then explain the historical transition of the arguments about the vertebrate body plan from merely epistemological comparative morphology to comparative embryology as a scientific treatment on this topic. Finally, we review the current progress of molecular evidence regarding the basic vertebrate body plan, focusing on the link between the basic vertebrate body plan and the evolutionarily conserved developmental stages (phylotypic stages).

  1. A Historical Taxonomy of Origin of Species Problems and Its Relevance to the Historiography of Evolutionary Thought.

    Science.gov (United States)

    Tanghe, Koen B

    2016-11-07

    Historians tend to speak of the problem of the origin of species or the species question, as if it were a monolithic problem. In reality, the phrase (or similar variants) refers to a, historically, surprisingly fluid and pluriform scientific issue. It has, in the course of the past five centuries, been used in no less than ten different ways or contexts. A clear taxonomy of these separate problems is useful or relevant in two ways. It certainly helps to disentangle confusions that have inevitably emerged in the literature in its absence. It may, secondly, also help us to gain a more thorough understanding, or sharper view, of the (pre)history of evolutionary thought. A consequent problem-centric look at that (pre)history through the lens of various origin of species problems certainly yields intriguing results, including and particularly for our understanding of the genesis of the Wallace-Darwin theory of evolution through natural selection.

  2. Interchromosomal duplications on the Bactrocera oleae Y chromosome imply a distinct evolutionary origin of the sex chromosomes compared to Drosophila.

    Science.gov (United States)

    Gabrieli, Paolo; Gomulski, Ludvik M; Bonomi, Angelica; Siciliano, Paolo; Scolari, Francesca; Franz, Gerald; Jessup, Andrew; Malacrida, Anna R; Gasperi, Giuliano

    2011-03-07

    Diptera have an extraordinary variety of sex determination mechanisms, and Drosophila melanogaster is the paradigm for this group. However, the Drosophila sex determination pathway is only partially conserved and the family Tephritidae affords an interesting example. The tephritid Y chromosome is postulated to be necessary to determine male development. Characterization of Y sequences, apart from elucidating the nature of the male determining factor, is also important to understand the evolutionary history of sex chromosomes within the Tephritidae. We studied the Y sequences from the olive fly, Bactrocera oleae. Its Y chromosome is minute and highly heterochromatic, and displays high heteromorphism with the X chromosome. A combined Representational Difference Analysis (RDA) and fluorescence in-situ hybridization (FISH) approach was used to investigate the Y chromosome to derive information on its sequence content. The Y chromosome is strewn with repetitive DNA sequences, the majority of which are also interdispersed in the pericentromeric regions of the autosomes. The Y chromosome appears to have accumulated small and large repetitive interchromosomal duplications. The large interchromosomal duplications harbour an importin-4-like gene fragment. Apart from these importin-4-like sequences, the other Y repetitive sequences are not shared with the X chromosome, suggesting molecular differentiation of these two chromosomes. Moreover, as the identified Y sequences were not detected on the Y chromosomes of closely related tephritids, we can infer divergence in the repetitive nature of their sequence contents. The identification of Y-linked sequences may tell us much about the repetitive nature, the origin and the evolution of Y chromosomes. We hypothesize how these repetitive sequences accumulated and were maintained on the Y chromosome during its evolutionary history. Our data reinforce the idea that the sex chromosomes of the Tephritidae may have distinct evolutionary

  3. Interchromosomal duplications on the Bactrocera oleae Y chromosome imply a distinct evolutionary origin of the sex chromosomes compared to Drosophila.

    Directory of Open Access Journals (Sweden)

    Paolo Gabrieli

    Full Text Available BACKGROUND: Diptera have an extraordinary variety of sex determination mechanisms, and Drosophila melanogaster is the paradigm for this group. However, the Drosophila sex determination pathway is only partially conserved and the family Tephritidae affords an interesting example. The tephritid Y chromosome is postulated to be necessary to determine male development. Characterization of Y sequences, apart from elucidating the nature of the male determining factor, is also important to understand the evolutionary history of sex chromosomes within the Tephritidae. We studied the Y sequences from the olive fly, Bactrocera oleae. Its Y chromosome is minute and highly heterochromatic, and displays high heteromorphism with the X chromosome. METHODOLOGY/PRINCIPAL FINDINGS: A combined Representational Difference Analysis (RDA and fluorescence in-situ hybridization (FISH approach was used to investigate the Y chromosome to derive information on its sequence content. The Y chromosome is strewn with repetitive DNA sequences, the majority of which are also interdispersed in the pericentromeric regions of the autosomes. The Y chromosome appears to have accumulated small and large repetitive interchromosomal duplications. The large interchromosomal duplications harbour an importin-4-like gene fragment. Apart from these importin-4-like sequences, the other Y repetitive sequences are not shared with the X chromosome, suggesting molecular differentiation of these two chromosomes. Moreover, as the identified Y sequences were not detected on the Y chromosomes of closely related tephritids, we can infer divergence in the repetitive nature of their sequence contents. CONCLUSIONS/SIGNIFICANCE: The identification of Y-linked sequences may tell us much about the repetitive nature, the origin and the evolution of Y chromosomes. We hypothesize how these repetitive sequences accumulated and were maintained on the Y chromosome during its evolutionary history. Our data

  4. Different Evolutionary Origins for the Reach and the Grasp: An Explanation for Dual Visuomotor Channels in Primate Parietofrontal Cortex

    Directory of Open Access Journals (Sweden)

    Jenni M Karl

    2013-12-01

    Full Text Available The Dual Visuomotor Channel Theory proposes that manual prehension consists of two temporally integrated movements, each subserved by distinct visuomotor pathways in occipitoparietofrontal cortex. The Reach is mediated by a dorsomedial pathway and transports the hand in relation to the target’s extrinsic properties (i.e., location and orientation. The Grasp is mediated by a dorsolateral pathway and opens, preshapes, and closes the hand in relation to the target’s intrinsic properties (i.e., size and shape. Here, neuropsychological, developmental, and comparative evidence is reviewed to show that the Reach and the Grasp have different evolutionary origins. First, the removal or degradation of vision causes prehension to decompose into its constituent Reach and Grasp components, which are then executed in sequence or isolation. Similar decomposition occurs in optic ataxic patients following cortical injury to the Reach and Grasp pathways and after corticospinal tract lesions in non-human primates. Second, early nonvisual PreReach and PreGrasp movements develop into mature Reach and Grasp movements but are only integrated under visual control after a prolonged developmental period. Third, comparative studies reveal many similarities between stepping movements and the Reach and between food handling movements and the Grasp, suggesting that the Reach and Grasp are derived from different evolutionary antecedents. The evidence is discussed in relation to the ideas that dual visuomotor channels in primate parietofrontal cortex emerged as a result of distinct evolutionary origins for the Reach and Grasp; that foveated vision in primates serves to integrate the Reach and Grasp into a single prehensile act; and, that flexible recombination of discrete Reach and Grasp movements under various forms of sensory and cognitive control can produce adaptive behavior.

  5. Paedomorphosis as an Evolutionary Driving Force: Insights from Deep-Sea Brittle Stars

    Science.gov (United States)

    Stöhr, Sabine; Martynov, Alexander

    2016-01-01

    Heterochronic development has been proposed to have played an important role in the evolution of echinoderms. In the class Ophiuroidea, paedomorphosis (retention of juvenile characters into adulthood) has been documented in the families Ophiuridae and Ophiolepididae but not been investigated on a broader taxonomic scale. Historical errors, confusing juvenile stages with paedomorphic species, show the difficulties in correctly identifying the effects of heterochrony on development and evolution. This study presents a detailed analysis of 40 species with morphologies showing various degrees of juvenile appearance in late ontogeny. They are compared to a range of early ontogenetic stages from paedomorphic and non-paedomorphic species. Both quantitative and qualitative measurements are taken and analysed. The results suggest that strongly paedomorphic species are usually larger than other species at comparable developmental stage. The findings support recent notions of polyphyletic origin of the families Ophiuridae and Ophiolepididae. The importance of paedomorphosis and its correct recognition for the practice of taxonomy and phylogeny are emphasized. PMID:27806039

  6. In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India

    Directory of Open Access Journals (Sweden)

    Vanniarajan Ayyasamy

    2006-06-01

    Full Text Available Abstract Background Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups. Results Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31. Conclusion Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2. Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.

  7. The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms

    Directory of Open Access Journals (Sweden)

    Postberg Jan

    2010-08-01

    Full Text Available Abstract Background The phenotype of an organism is an outcome of both its genotype, encoding the primary sequence of proteins, and the developmental orchestration of gene expression. The substrate of gene expression in eukaryotes is the chromatin, whose fundamental units are nucleosomes composed of DNA wrapped around each two of the core histone types H2A, H2B, H3 and H4. Key regulatory steps involved in the determination of chromatin conformations are posttranslational modifications (PTM at histone tails as well as the assembly of histone variants into nucleosomal arrays. Although the mechanistic background is fragmentary understood, it appears that the chromatin signature of metazoan cell types is inheritable over generations. Even less understood is the conservation of epigenetic mechanisms among eukaryotes and their origins. Results In the light of recent progress in understanding the tree of eukaryotic life we discovered the origin of histone H3 by phylogenetic analyses of variants from all supergroups, which allowed the reconstruction of ancestral states. We found that H3 variants evolved frequently but independently within related species of almost all eukaryotic supergroups. Interestingly, we found all core histone types encoded in the genome of a basal dinoflagellate and H3 variants in two other species, although is was reported that dinoflagellate chromatin is not organized into nucleosomes. Most probably one or more animal/nuclearid H3.3-like variants gave rise to H3 variants of all opisthokonts (animals, choanozoa, fungi, nuclearids, Amoebozoa. H3.2 and H3.1 as well as H3.1t are derivatives of H3.3, whereas H3.2 evolved already in early branching animals, such as Trichoplax. H3.1 and H3.1t are probably restricted to mammals. We deduced a model for protoH3 of the last eukaryotic common ancestor (LECA confirming a remarkable degree of sequence conservation in comparison to canonical human H3.1. We found evidence that multiple PTMs are

  8. Os-He Isotope Systematics of Iceland Picrites: Evidence for a Deep Origin of the Iceland Plume

    Science.gov (United States)

    Brandon, Alan D.; Graham, David W.; Waight, Tod; Gautason, Bjarni

    2007-01-01

    Recent work on the origin of the Iceland hotspot suggests that it may result from upwelling upper mantle material rather than a deep plume. To constrain the depths of origins of Iceland mantle sources, Os and He isotope systematics were obtained on a suite picrites that span the compositional range observed within the neovolcanic zones.

  9. In silico Evolutionary Developmental Neurobiology and the Origin of Natural Language

    Science.gov (United States)

    Szathmáry, Eörs; Szathmáry, Zoltán; Ittzés, Péter; Orbaán, Geroő; Zachár, István; Huszár, Ferenc; Fedor, Anna; Varga, Máté; Számadó, Szabolcs

    It is justified to assume that part of our genetic endowment contributes to our language skills, yet it is impossible to tell at this moment exactly how genes affect the language faculty. We complement experimental biological studies by an in silico approach in that we simulate the evolution of neuronal networks under selection for language-related skills. At the heart of this project is the Evolutionary Neurogenetic Algorithm (ENGA) that is deliberately biomimetic. The design of the system was inspired by important biological phenomena such as brain ontogenesis, neuron morphologies, and indirect genetic encoding. Neuronal networks were selected and were allowed to reproduce as a function of their performance in the given task. The selected neuronal networks in all scenarios were able to solve the communication problem they had to face. The most striking feature of the model is that it works with highly indirect genetic encoding--just as brains do.

  10. Origin, development and evolutionary model of shelf desertization environment in late stage of Upper Pleistocene

    Institute of Scientific and Technical Information of China (English)

    赵松龄; 于洪军; 刘敬圃

    1997-01-01

    Based on the study of palaeo-environmental evolution in the shelves of the Eastern China Seas, the concept of "shelf desertization" in the late stage of Upper Pleistocene is defined; the environmental background and evolutionary process of shelf desertization are analysed. Study on the records of subbottom profiling and the data of core samples from shelf areas revealed that during low sea-level stages, the sedimentary environment in the exposed shelf plains was dominated by aeolian depositional process under cold and dry climatic conditions, i.e. under the action of strong winter-monsoon winds. Parts of the exposed marine strata were disintegrated, and aeolian sand dunes were formed on the disintegrated marine deposits, from which the finer sediment grains were blown away by wind and deposited in the downwind areas to form the derivative loess deposits. Thus a desertization environmental system was formed in the exposed shelf plains of the Eastern China Seas.

  11. Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family

    Science.gov (United States)

    Wheeler, Lucas C.; Donor, Micah T.; Prell, James S.

    2016-01-01

    The S100 proteins are a large family of signaling proteins that play critical roles in biology and disease. Many S100 proteins bind Zn2+, Cu2+, and/or Mn2+ as part of their biological functions; however, the evolutionary origins of binding remain obscure. One key question is whether divalent transition metal binding is ancestral, or instead arose independently on multiple lineages. To tackle this question, we combined phylogenetics with biophysical characterization of modern S100 proteins. We demonstrate an earlier origin for established S100 subfamilies than previously believed, and reveal that transition metal binding is widely distributed across the tree. Using isothermal titration calorimetry, we found that Cu2+ and Zn2+ binding are common features of the family: the full breadth of human S100 paralogs—as well as two early-branching S100 proteins found in the tunicate Oikopleura dioica—bind these metals with μM affinity and stoichiometries ranging from 1:1 to 3:1 (metal:protein). While binding is consistent across the tree, structural responses to binding are quite variable. Further, mutational analysis and structural modeling revealed that transition metal binding occurs at different sites in different S100 proteins. This is consistent with multiple origins of transition metal binding over the evolution of this protein family. Our work reveals an evolutionary pattern in which the overall phenotype of binding is a constant feature of S100 proteins, even while the site and mechanism of binding is evolutionarily labile. PMID:27764152

  12. Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster

    Directory of Open Access Journals (Sweden)

    Meiering Elizabeth M

    2008-11-01

    Full Text Available Abstract Background Clostridial neurotoxins (CNTs are the most deadly toxins known and causal agents of botulism and tetanus neuroparalytic diseases. Despite considerable progress in understanding CNT structure and function, the evolutionary origins of CNTs remain a mystery as they are unique to Clostridium and possess a sequence and structural architecture distinct from other protein families. Uncovering the origins of CNTs would be a significant contribution to our understanding of how pathogens evolve and generate novel toxin families. Results The C. botulinum strain A genome was examined for potential homologues of CNTs. A key link was identified between the neurotoxin and the flagellin gene (CBO0798 located immediately upstream of the BoNT/A neurotoxin gene cluster. This flagellin sequence displayed the strongest sequence similarity to the neurotoxin and NTNH homologue out of all proteins encoded within C. botulinum strain A. The CBO0798 gene contains a unique hypervariable region, which in closely related flagellins encodes a collagenase-like domain. Remarkably, these collagenase-containing flagellins were found to possess the characteristic HEXXH zinc-protease motif responsible for the neurotoxin's endopeptidase activity. Additional links to collagenase-related sequences and functions were detected by further analysis of CNTs and surrounding genes, including sequence similarities to collagen-adhesion domains and collagenases. Furthermore, the neurotoxin's HCRn domain was found to exhibit both structural and sequence similarity to eukaryotic collagen jelly-roll domains. Conclusion Multiple lines of evidence suggest that the neurotoxin and adjacent genes evolved from an ancestral collagenase-like gene cluster, linking CNTs to another major family of clostridial proteolytic toxins. Duplication, reshuffling and assembly of neighboring genes within the BoNT/A neurotoxin gene cluster may have lead to the neurotoxin's unique architecture. This

  13. The proepicardium keeps a potential for glomerular marker expression which supports its evolutionary origin from the pronephros.

    Science.gov (United States)

    Cano, Elena; Carmona, Rita; Velecela, Víctor; Martínez-Estrada, Ofelia; Muñoz-Chápuli, Ramón

    2015-01-01

    The proepicardium is the embryonic primordium of the epicardium. This transient structure is essential for cardiac development giving rise to the epicardium and supplying the heart with vascular and cardiac connective tissue progenitors. However, their nature and evolutionary origin are poorly-known. We have suggested elsewhere (Pombal et al. Evol. Dev. 10: 210-216, 2008; Cano et al., J. Dev. Biol. 1: 3-19, 2013) that the proepicardium is an evolutionary derivative of the primordium of an ancient external pronephric glomerulus, devoid of its original excretory function. In this study, we describe for the first time expression of two podocyte markers in the chick proepicardium (glepp1 and synaptopodin) and we have shown how these podocyte markers as well as the intermediate mesoderm marker Pax2 are strongly upregulated when the proepicardium is cultured with nephrogenic inducers. Retinoic acid treatment also induced in the proepicardium expression of Hoxb4, a gene which confers to intermediate mesoderm competence to respond to nephrogenic signals. Thus, a latent nephrogenic potential persists in the proepicardium and also that its original glomerular fate can be partially rescued. The transcription factor Wt1, essential for kidney and epicardial development, plays opposite roles in both tissues, inducing epithelial-mesenchymal transition in the proepicardium and promoting epithelialization in the kidneys (Essafi et al., Dev. Cell 21: 559-574, 2011). Consistently with this antithetical function of Wt1, we have observed an upregulation of podocalyxin in the epicardium of mouse embryos with conditional deletion of the Wt1 gene, while this protein is transcriptionally activated by Wt1 in podocytes.

  14. Evolutionary dynamics of RNA-like replicators : A bioinformatic approach to the origin of life

    NARCIS (Netherlands)

    Takeuchi, N.

    2010-01-01

    The origin of life has always attracted scientific inquiries. The RNA world hypothesis suggests that, before the evolution of DNAs and proteins, primordial life was based on RNAs both for information storage and chemical catalysis. In its simplest form, an RNA world consists of RNA molecules that ca

  15. Art in the making. The evolutionary origins of visual art as a communication signal

    NARCIS (Netherlands)

    Mendoza Straffon, Larissa

    2014-01-01

    The corpus of art from the Pleistocene has grown substantially in recent decades, and with it, the earliest evidence of visual art has become much older than previously anticipated, going back over 100,000 years. This new information has rendered some traditional ideas about the recent origins of

  16. Art in the making. The evolutionary origins of visual art as a communication signal

    NARCIS (Netherlands)

    Mendoza Straffon, Larissa

    2014-01-01

    The corpus of art from the Pleistocene has grown substantially in recent decades, and with it, the earliest evidence of visual art has become much older than previously anticipated, going back over 100,000 years. This new information has rendered some traditional ideas about the recent origins of vi

  17. The intersubjective and cooperative origins of consciousness: an evolutionary-developmental approach.

    Science.gov (United States)

    Cortina, Mauricio; Liotti, Giovanni

    2010-01-01

    We discuss consciousness from evolutionary and developmental perspectives. The expansion of communicative abilities was a necessary step for the emergence of a new type of cooperation based on equality that probably appeared for the first time among nomadic hunter gatherers during the upper Paleolithic era. In turn, this new level of cooperation gave raise to an expanded form of consciousness. From a developmental perspective an expansion of intersubjective abilities and consciousness go together. Three basic levels of intersubjectivity are present in humans. A primary form of intersubjective communication is accompanied by a primary form of consciousness that is not easily accessible for conscious scrutiny. During the second year of human life secondary forms of intersubjectivity expand consciousness from the immediacy of one-to-one interactions, to include a shared understanding of intentions and goals with caregivers. Secondary forms of intersubjectivity give raise to the type of consciousness characterized by preverbal symbols and images--a primordial form of conceptual knowledge. A further step in intersubjective communication uses the meanings and concepts that have emerged earlier in development and transforms them into words. The leap into language allows our species to conceive past, present, and future simultaneously. The cultural transmission of knowledge and social mores depends on these abilities. This further expands the scope of consciousness and creates conditions for self reflection, a type of consciousness that is uniquely human.

  18. Multiple evolutionary origins of Australian soil-burrowing cockroaches driven by climate change in the Neogene.

    Science.gov (United States)

    Lo, Nathan; Tong, K Jun; Rose, Harley A; Ho, Simon Y W; Beninati, Tiziana; Low, David L T; Matsumoto, Tadao; Maekawa, Kiyoto

    2016-02-24

    Parallel evolution is the independent appearance of similar derived phenotypes from similar ancestral forms. It is of key importance in the debate over whether evolution is stochastic and unpredictable, or subject to constraints that limit available phenotypic options. Nevertheless, its occurrence has rarely been demonstrated above the species level. Climate change on the Australian landmass over the last approximately 20 Myr has provided conditions conducive to parallel evolution, as taxa at the edges of shrinking mesic habitats adapted to drier biomes. Here, we investigate the phylogeny and evolution of Australian soil-burrowing and wood-feeding blaberid cockroaches. Soil burrowers (subfamily Geoscapheinae) are found in relatively dry sclerophyllous and scrubland habits, whereas wood feeders (subfamily Panesthiinae) are found in rainforest and wet sclerophyll. We sequenced and analysed mitochondrial and nuclear markers from 142 specimens, and estimated the evolutionary time scale of the two subfamilies. We found evidence for the parallel evolution of soil-burrowing taxa from wood-feeding ancestors on up to nine occasions. These transitions appear to have been driven by periods of aridification during the Miocene and Pliocene across eastern Australia. Our results provide an illuminating example of climate-driven parallel evolution among species. © 2016 The Author(s).

  19. A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses.

    Science.gov (United States)

    Clayton, Adam L; Oakeson, Kelly F; Gutin, Maria; Pontes, Arthur; Dunn, Diane M; von Niederhausern, Andrew C; Weiss, Robert B; Fisher, Mark; Dale, Colin

    2012-01-01

    Despite extensive study, little is known about the origins of the mutualistic bacterial endosymbionts that inhabit approximately 10% of the world's insects. In this study, we characterized a novel opportunistic human pathogen, designated "strain HS," and found that it is a close relative of the insect endosymbiont Sodalis glossinidius. Our results indicate that ancestral relatives of strain HS have served as progenitors for the independent descent of Sodalis-allied endosymbionts found in several insect hosts. Comparative analyses indicate that the gene inventories of the insect endosymbionts were independently derived from a common ancestral template through a combination of irreversible degenerative changes. Our results provide compelling support for the notion that mutualists evolve from pathogenic progenitors. They also elucidate the role of degenerative evolutionary processes in shaping the gene inventories of symbiotic bacteria at a very early stage in these mutualistic associations.

  20. A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses.

    Directory of Open Access Journals (Sweden)

    Adam L Clayton

    Full Text Available Despite extensive study, little is known about the origins of the mutualistic bacterial endosymbionts that inhabit approximately 10% of the world's insects. In this study, we characterized a novel opportunistic human pathogen, designated "strain HS," and found that it is a close relative of the insect endosymbiont Sodalis glossinidius. Our results indicate that ancestral relatives of strain HS have served as progenitors for the independent descent of Sodalis-allied endosymbionts found in several insect hosts. Comparative analyses indicate that the gene inventories of the insect endosymbionts were independently derived from a common ancestral template through a combination of irreversible degenerative changes. Our results provide compelling support for the notion that mutualists evolve from pathogenic progenitors. They also elucidate the role of degenerative evolutionary processes in shaping the gene inventories of symbiotic bacteria at a very early stage in these mutualistic associations.

  1. Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life.

    Science.gov (United States)

    Takeuchi, Nobuto; Hogeweg, Paulien

    2012-09-01

    We review computational studies on prebiotic evolution, focusing on informatic processes in RNA-like replicator systems. In particular, we consider the following processes: the maintenance of information by replicators with and without interactions, the acquisition of information by replicators having a complex genotype-phenotype map, the generation of information by replicators having a complex genotype-phenotype-interaction map, and the storage of information by replicators serving as dedicated templates. Focusing on these informatic aspects, we review studies on quasi-species, error threshold, RNA-folding genotype-phenotype map, hypercycle, multilevel selection (including spatial self-organization, classical group selection, and compartmentalization), and the origin of DNA-like replicators. In conclusion, we pose a future question for theoretical studies on the origin of life.

  2. Diversification of the kinetic properties of yeast NADP-glutamate-dehydrogenase isozymes proceeds independently of their evolutionary origin.

    Science.gov (United States)

    Campero-Basaldua, Carlos; Quezada, Héctor; Riego-Ruíz, Lina; Márquez, Dariel; Rojas, Erendira; González, James; El-Hafidi, Mohammed; González, Alicia

    2016-11-19

    In the yeast Saccharomyces cerevisiae, the ScGDH1 and ScGDH3 encoded glutamate dehydrogenases (NADP-GDHs) catalyze the synthesis of glutamate from ammonium and α-ketoglutarate (α-KG). Previous kinetic characterization showed that these enzymes displayed different allosteric properties and respectively high or low rate of α-KG utilization. Accordingly, the coordinated action of ScGdh1 and ScGdh3, regulated balanced α-KG utilization for glutamate biosynthesis under either fermentative or respiratory conditions, safeguarding energy provision. Here, we have addressed the question of whether there is a correlation between the regulation and kinetic properties of the NADP-GDH isozymes present in S. cerevisiae (ScGdh1 and ScGdh3), Kluyveromyces lactis (KlGdh1), and Lachancea kluyveri (LkGdh1) and their evolutionary history. Our results show that the kinetic properties of K. lactis and L. kluyveri single NADP-GDHs are respectively similar to either ScGDH3 or ScGDH1, which arose from the whole genome duplication event of the S. cerevisiae lineage, although, KlGDH1 and LkGDH1 originated from a GDH clade, through an ancient interspecies hybridization event that preceded the divergence between the Saccharomyces clade and the one containing the genera Kluyveromyces, Lachancea, and Eremothecium. Thus, the kinetic properties which determine the NADP-GDHs capacity to utilize α-KG and synthesize glutamate do not correlate with their evolutionary origin.

  3. Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction

    Directory of Open Access Journals (Sweden)

    Elnaz Mehdizadeh Aghdam

    2014-05-01

    Full Text Available Purpose: Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA, raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. Methods: Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting “A site” of 16S rRNA to riboswitches via docking method. Results: There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8 hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with “16S rRNA A site”. Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA “A site” suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. Conclusion: These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.

  4. Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas.

    Directory of Open Access Journals (Sweden)

    Diane I Schroeder

    2015-08-01

    Full Text Available Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs and highly methylated domains (HMDs with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.

  5. Vertebrate brains and evolutionary connectomics: on the origins of the mammalian 'neocortex'.

    Science.gov (United States)

    Karten, Harvey J

    2015-12-19

    The organization of the non-mammalian forebrain had long puzzled neurobiologists. Unlike typical mammalian brains, the telencephalon is not organized in a laminated 'cortical' manner, with distinct cortical areas dedicated to individual sensory modalities or motor functions. The two major regions of the telencephalon, the basal ventricular ridge (BVR) and the dorsal ventricular ridge (DVR), were loosely referred to as being akin to the mammalian basal ganglia. The telencephalon of non-mammalian vertebrates appears to consist of multiple 'subcortical' groups of cells. Analysis of the nuclear organization of the avian brain, its connections, molecular properties and physiology, and organization of its pattern of circuitry and function relative to that of mammals, collectively referred to as 'evolutionary connectomics', revealed that only a restricted portion of the BVR is homologous to the basal ganglia of mammals. The remaining dorsal regions of the DVR, wulst and arcopallium of the avian brain contain telencephalic inputs and outputs remarkably similar to those of the individual layers of the mammalian 'neocortex', hippocampus and amygdala, with instances of internuclear connections strikingly similar to those found between cortical layers and within radial 'columns' in the mammalian sensory and motor cortices. The molecular properties of these 'nuclei' in birds and reptiles are similar to those of the corresponding layers of the mammalian neocortex. The fundamental pathways and cell groups of the auditory, visual and somatosensory systems of the thalamus and telencephalon are homologous at the cellular, circuit, network and gene levels, and are of great antiquity. A proposed altered migration of these homologous neurons and circuits during development is offered as a mechanism that may account for the altered configuration of mammalian telencephalae.

  6. Independent evolutionary origin of fem paralogous genes and complementary sex determination in hymenopteran insects.

    Science.gov (United States)

    Koch, Vasco; Nissen, Inga; Schmitt, Björn D; Beye, Martin

    2014-01-01

    The primary signal of sex determination in the honeybee, the complementary sex determiner (csd) gene, evolved from a gene duplication event from an ancestral copy of the fem gene. Recently, other paralogs of the fem gene have been identified in several ant and bumblebee genomes. This discovery and the close phylogenetic relationship of the paralogous gene sequences led to the hypothesis of a single ancestry of the csd genetic system of complementary sex determination in the Hymenopteran insects, in which the fem and csd gene copies evolved as a unit in concert with the mutual transfers of sequences (concerted evolution). Here, we show that the paralogous gene copies evolved repeatedly through independent gene duplication events in the honeybee, bumblebee, and ant lineage. We detected no sequence tracts that would indicate a DNA transfer between the fem and the fem1/csd genes between different ant and bee species. Instead, we found tracts of duplication events in other genomic locations, suggesting that gene duplication was a frequent event in the evolution of these genes. These and other evidences suggest that the fem1/csd gene originated repeatedly through gene duplications in the bumblebee, honeybee, and ant lineages in the last 100 million years. Signatures of concerted evolution were not detectable, implicating that the gene tree based on neutral synonymous sites represents the phylogenetic relationships and origins of the fem and fem1/csd genes. Our results further imply that the fem1 and csd gene in bumblebees, honeybees, and ants are not orthologs, because they originated independently from the fem gene. Hence, the widely shared and conserved complementary sex determination mechanism in Hymenopteran insects is controlled by different genes and molecular processes. These findings highlight the limits of comparative genomics and emphasize the requirement to study gene functions in different species and major hymenopteran lineages.

  7. Carboxylesterase gene amplifications associated with insecticide resistance in Aedes albopictus: Geographical distribution and evolutionary origin.

    Directory of Open Access Journals (Sweden)

    Linda Grigoraki

    2017-04-01

    Full Text Available Aedes albopictus is one of the most invasive human disease vectors. Its control has been largely based on insecticides, such as the larvicide temephos. Temephos resistance has been associated with the up-regulation, through gene amplification, of two carboxylesterase (CCE genes closely linked on the genome, capable of sequestering and metabolizing temephos oxon, the activated form of temephos.Here, we investigated the occurrence, geographical distribution and origin of the CCE amplicon in Ae. albopictus populations from several geographical regions worldwide. The haplotypic diversity at the CCEae3a locus revealed high polymorphism, while phylogenetic analysis showed an absence of correlation between haplotype similarity and geographic origin. Two types of esterase amplifications were found, in two locations only (Athens and Florida: one, previously described, results in the amplification of both CCEae3a and CCEae6a; the second is being described for the first time and results in the amplification of CCEae3a only. The two amplification events are independent, as confirmed by sequence analysis. All individuals from Athens and Florida carrying the CCEae3a-CCEae6a co-amplicon share a common haplotype, indicating a single amplification event, which spread between the two countries.The importance of passive transportation of disease vectors, including individuals carrying resistance mechanisms, is discussed in the light of efficient and sustainable vector control strategies.

  8. Evolutionary history of true crabs (Crustacea: Decapoda: Brachyura) and the origin of freshwater crabs.

    Science.gov (United States)

    Tsang, Ling Ming; Schubart, Christoph D; Ahyong, Shane T; Lai, Joelle C Y; Au, Eugene Y C; Chan, Tin-Yam; Ng, Peter K L; Chu, Ka Hou

    2014-05-01

    Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of the group. Here, we reconstruct the most comprehensive phylogeny of Brachyura to date using sequence data of six nuclear protein-coding genes and two mitochondrial rRNA genes from more than 140 species belonging to 58 families. The gene tree confirms that the "Podotremata," are paraphyletic. Within the monophyletic Eubrachyura, the reciprocal monophyly of the two subsections, Heterotremata and Thoracotremata, is supported. Monophyly of many superfamilies, however, is not recovered, indicating the prevalence of morphological convergence and the need for further taxonomic studies. Freshwater crabs were derived early in the evolution of Eubrachyura and are shown to have at least two independent origins. Bayesian relaxed molecular methods estimate that freshwater crabs separated from their closest marine sister taxa ~135 Ma, that is, after the break up of Pangaea (∼200 Ma) and that a Gondwanan origin of these freshwater representatives is untenable. Most extant families and superfamilies arose during the late Cretaceous and early Tertiary.

  9. Deep divergences of human gene trees and models of human origins.

    Science.gov (United States)

    Blum, Michael G B; Jakobsson, Mattias

    2011-02-01

    Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000-200,000 years ago and spread throughout the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow between archaic and emerging modern humans. In the last two decades, the young time estimates--between 100,000 and 200,000 years--of the most recent common ancestors for the mitochondrion and the Y chromosome provided evidence in favor of a recent African origin of modern humans. However, the presence of very old lineages for autosomal and X-linked genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked genes are indeed very old, living, on average, respectively, 1,500,000 and 1,000,000 years ago. However, contrary to previous conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings from the mitochondrion on the one hand, with the autosomes and the X chromosome on the other hand.

  10. Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms.

    Science.gov (United States)

    Ueoka, Reiko; Uria, Agustinus R; Reiter, Silke; Mori, Tetsushi; Karbaum, Petra; Peters, Eike E; Helfrich, Eric J N; Morinaka, Brandon I; Gugger, Muriel; Takeyama, Haruko; Matsunaga, Shigeki; Piel, Jörn

    2015-09-01

    Actin-targeting macrolides comprise a large, structurally diverse group of cytotoxins isolated from remarkably dissimilar micro- and macroorganisms. In spite of their disparate origins and structures, many of these compounds bind actin at the same site and exhibit structural relationships reminiscent of modular, combinatorial drug libraries. Here we investigate biosynthesis and evolution of three compound groups: misakinolides, scytophycin-type compounds and luminaolides. For misakinolides from the sponge Theonella swinhoei WA, our data suggest production by an uncultivated 'Entotheonella' symbiont, further supporting the relevance of these bacteria as sources of bioactive polyketides and peptides in sponges. Insights into misakinolide biosynthesis permitted targeted genome mining for other members, providing a cyanobacterial luminaolide producer as the first cultivated source for this dimeric compound family. The data indicate that this polyketide family is bacteria-derived and that the unusual macrolide diversity is the result of combinatorial pathway modularity for some compounds and of convergent evolution for others.

  11. The evolutionary origin of auditory receptors in Tettigonioidea: the complex tibial organ of Schizodactylidae.

    Science.gov (United States)

    Strauss, Johannes; Lakes-Harlan, Reinhard

    2009-01-01

    Audition in insects is of polyphyletic origin. Tympanal ears derived from proprioceptive or vibratory receptor organs, but many questions of the evolution of insect auditory systems are still open. Despite the rather typical bauplan of the insect body, e.g., with a fixed number of segments, tympanal ears evolved at very different places, but only ensiferans have ears at the foreleg tibia, located in the tibial organ. The homology and monophyly of ensiferan ears is controversial, and no precursor organ was unambiguously identified for auditory receptors. The latter can only be identified by comparative study of recent atympanate taxa. These atympanate taxa are poorly investigated. In this paper, we report the neuroanatomy of the tibial organ of Comicus calcaris (Irish 1986), an atympanate Schizodactylid (splay-footed cricket). This representative of a Gondwana relict group has a tripartite sensory organ, homologous to tettigoniid ears. A comparison with morphology-based cladistic phylogeny indicates that the tripartite neuronal organization present in the majority of Tettigonioidea presumably preceded evolution of a hearing sense in the Tettigonioidea. Furthermore, the absence of a tripartite organ in Grylloidea argues against a monophyletic origin and homology of the cricket and katydid ears. The tracheal attachment of sensory neurons typical for ears of Tettigonioidea is present in C. calcaris and may have facilitated cooption for auditory function. The functional auditory organ was presumably formed in evolution by successive non-neural modifications of trachea and tympana. This first investigation of the neuroanatomy of Schizodactylidae suggests a non-auditory chordotonal organ as the precursor for auditory receptors of related tympanate taxa and adds evidence for the phylogenetic position of the group.

  12. Delphinium L. Subgen. Delphinium: origin and evolutionary trends

    Directory of Open Access Journals (Sweden)

    Blanché, Cèsar

    1990-12-01

    Full Text Available The advanced features of Delphinium lo subgen. Delphinium(annual taxa are compared with those of subgen. Delphinastrum (DC. Wang and subgen. Oligophyllon Dimitrova (perennial taxa. F1ower morphology shows a functional interchange between lateral petals and upper petals. and inflorescence structure favours geitonogamy-autogamy rates. Karyotype evolution is based on a decrease in the total length of chromosomes and on an increase in the degree of asymmetry: the chromosome number remains constant (2n = 16 in the subgen. Delphinium.The dispersal efficiency of the annual species is higher than that of perennials due to seed set increase and improved floatability. both in water and in air. Other advanced adaptive features are the acquisition or new chemical weapons and the emergence of a new embryonogenic type. The ecological niches or subgen. Delphinium correspond to open and disturbed habitats in contrast to the stable and relatively closed ones or subgenera Delphinastum and Oligophyllon. A final hypothesis is made concerning the evolutionary trends observed in annuals vs. perennials in connexion with biogeographical considerations, and a final taxonomic summary is given.

    [ca] Les característiques avançades de Delphinium L. subgèn. Delphinium (tàxons anuals són comparades amb les del subgèn. Delphinastrum (DC. Wang i del subgèn. Oligophyllon Dimitrova (tàxons perennes. La morfologia norai mostra un intercanvi de funcions entre els pètals laterals i els pètals superiors i l'estructura de la inflorescència de molts tàxons anuals afavoreix un augment de les taxes de geitonogàmia-autogàmia. L'evolució dels cariotips és basada en una disminució de la longitud total dels cromosomes i en un increment del grau d'asimetria; el nombre cromosòmic roman constant per a totes les espècies anuals (2n = 16. l'eficàcia de la dispersió de les esp

  13. Manipulation of Fgf and Bmp signaling in teleost fishes suggests potential pathways for the evolutionary origin of multicuspid teeth.

    Science.gov (United States)

    Jackman, William R; Davies, Shelby H; Lyons, David B; Stauder, Caitlin K; Denton-Schneider, Benjamin R; Jowdry, Andrea; Aigler, Sharon R; Vogel, Scott A; Stock, David W

    2013-01-01

    Teeth with two or more cusps have arisen independently from an ancestral unicuspid condition in a variety of vertebrate lineages, including sharks, teleost fishes, amphibians, lizards, and mammals. One potential explanation for the repeated origins of multicuspid teeth is the existence of multiple adaptive pathways leading to them, as suggested by their different uses in these lineages. Another is that the addition of cusps required only minor changes in genetic pathways regulating tooth development. Here we provide support for the latter hypothesis by demonstrating that manipulation of the levels of Fibroblast growth factor (Fgf) or Bone morphogenetic protein (Bmp) signaling produces bicuspid teeth in the zebrafish (Danio rerio), a species lacking multicuspid teeth in its ancestry. The generality of these results for teleosts is suggested by the conversion of unicuspid pharyngeal teeth into bicuspid teeth by similar manipulations of the Mexican Tetra (Astyanax mexicanus). That these manipulations also produced supernumerary teeth in both species supports previous suggestions of similarities in the molecular control of tooth and cusp number. We conclude that despite their apparent complexity, the evolutionary origin of multicuspid teeth is positively constrained, likely requiring only slight modifications of a pre-existing mechanism for patterning the number and spacing of individual teeth.

  14. Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.

    Science.gov (United States)

    Caetano-Anollés, Gustavo; Wang, Minglei; Caetano-Anollés, Derek

    2013-01-01

    The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the 'operational' RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.

  15. Evolutionary origin and demographic history of an ancient conifer (Juniperus microsperma) in the Qinghai-Tibetan Plateau.

    Science.gov (United States)

    Shang, Hui-Ying; Li, Zhong-Hu; Dong, Miao; Adams, Robert P; Miehe, Georg; Opgenoorth, Lars; Mao, Kang-Shan

    2015-05-15

    All Qinghai-Tibetan Plateau (QTP) endemic species are assumed to have originated recently, although very rare species most likely diverged early. These ancient species provide an excellent model to examine the origin and evolution of QTP endemic plants in response to the QTP uplifts and the climate changes that followed in this high altitude region. In this study, we examined these hypotheses by employing sequence variation from multiple nuclear and chloroplast DNA of 239 individuals of Juniperus microsperma and its five congeners. Both phylogenetic and population genetic analyses revealed that J. microsperma diverged from its sister clade comprising two species with long isolation around the Early Miocene, which corresponds to early QTP uplift. Demographic modeling and coalescent tests suggest that J. microsperma experienced an obvious bottleneck event during the Quaternary when the global climate greatly oscillated. The results presented here support the hypotheses that the QTP uplifts and Quaternary climate changes played important roles in shaping the evolutionary history of this rare juniper.

  16. Genetic-evolutionary studies on cultivated cannas : VI. Origin and evolution of ornamental taxa.

    Science.gov (United States)

    Khoshoo, T N; Mukherjee, I

    1970-01-01

    Hybridization has played a dominant and decisive role in the origin of ornamental cannas. This has been made possible by the ecospecific differentiation of the parental species, which implies lack of barriers and a good deal of recombination associated with reasonably high fertility.Colour differences between species are controlled by a number of genes and their intensifiers, inhibitors, lethals, etc. From recombination in interspecific hybrids of such a wide range of genes, segregating simultaneously and involving complex segregation, arises a wide array of heterozygous genotypes with new colours and colour combinations, releasing much genetic diversity.Hybridization has also been responsible for transgressive segregation, particularly in length and breadth of staminodia and luxuriance, affecting not only plant height but also flower size. Perhaps the most important single factor responsible for the evolution of ornamental cannas has been the repeated cycles of hybridization which have led to the breakage of size and other barriers; this seems to have been exploited continuously until very large flower size was built up and combined with other useful vegetative and floral characters such as colour and number of flowers per inflorescence, extended blooming period, cold resistance, etc. The efficient vegetative propagation made fixing of the useful genotypes no problem, although they may contain a high degree of heterozygosity and sexual sterility.Along these lines, Année (hybrids between C. indica and C. glauca) and Ehemann (hybrids between C. iridiflora and C. warscwiczii) cannas came into being in 1848 and 1863 respectively. Although both were a distinct improvement over the original species, they were still relatively small-flowered and major improvements came roundabout 1868, when Crozy, Gladiolus or French Dwarf cannas (C. X generalis Bailey) were released. This group arose from hybrids and back crosses of the first two groups and contains diploids

  17. The evolutionary origins of the southern ocean Philobryid bivalves: hidden biodiversity, ancient persistence.

    Directory of Open Access Journals (Sweden)

    Jennifer A Jackson

    Full Text Available Philobryids (Bivalvia: Arcoida are one of the most speciose marine bivalve families in the Southern Ocean and are common throughout the Southern Hemisphere. Considering this diversity and their brooding reproductive mode (limiting long-distance dispersal, this family may have been present in the Southern Ocean since its inception. However Philobrya and Adacnarca appear only in the Quaternary fossil record of the Antarctic, suggesting a much more recent incursion. Molecular dating provides an independent means of measuring the time of origin and radiation of this poorly known group. Here we present the first combined molecular and morphological investigation of the Philobryidae in the Southern Ocean. Two nuclear loci (18S and 28S were amplified from 35 Southern Ocean Adacnarca and Philobrya specimens, with a combined sequence length of 2,282 base pairs (bp. Adacnarca specimens (A. nitens and A. limopsoides were resolved as a strongly supported monophyletic group. Genus Philobrya fell into two strongly supported groups ('sublaevis' and 'magellanica/wandelensis', paraphyletic with Adacnarca. The A. nitens species complex is identified as at least seven morpho-species through morphological and genetic analysis of taxon clustering. Phylogenetic analyses resolve Philobryidae as a strongly supported monophyletic clade and sister taxon to the Limopsidae, as anticipated by their classification into the superfamily Limopsoidea. Bayesian relaxed clock analyses of divergence times suggest that genus Adacnarca radiated in the Southern Ocean from the Early Paleogene, while P. sublaevis and P. wandelensis clades radiated in the late Miocene, following the formation of the Antarctic Circumpolar Current.

  18. Cytogenetic rogue cells: what is their frequency, origin, and evolutionary significance

    Energy Technology Data Exchange (ETDEWEB)

    Awa, A.A.; Neel, J.V.

    1986-02-01

    Among 102,170 cultured lymphocytes obtained from 9818 individuals from Hiroshima, Japan, aged 9 to 37 years and scored for chromosomal abnormalities, 24 cells that exhibited an extreme degree of damage were encountered. The damage consists of multiple dicentric and even tricentric chromosomes, as well as numerous fragments, many with the appearance of double minutes. The occurrence of these cells was not correlated with parental exposure to the atomic bomb, age, sex, year, or season. They were nonrandomly distributed by individual. Such cells were originally described in South American Indians and have also been recorded in inhabitants of the United States and the United Kingdom; this appears to be a world-wide phenomenon. Their cause remains unknown, and it is not known whether they occur in other somatic and germ-line cells. Should the latter be the case and should the least damaged of these cells occasionally successfully complete mitosis and meiosis, the possible role of such cells in oncogenesis and evolution must be considered.

  19. Massive Structures of Galaxies at High Redshifts in the Great Observatories Origins Deep Survey Fields

    CERN Document Server

    Kang, Eugene

    2016-01-01

    If the Universe is dominated by cold dark matter and dark energy as in the currently popular LCDM cosmology, it is expected that large scale structures form gradually, with galaxy clusters of mass M > ~10^14 Msun appearing at around 6 Gyrs after the Big Bang (z ~ 1). Here, we report the discovery of 59 massive structures of galaxies with masses greater than a few x 10^13 Msun at redshifts between z=0.6 and 4.5 in the Great Observatories Origins Deep Survey fields. The massive structures are identified by running top-hat filters on the two dimensional spatial distribution of magnitude-limited samples of galaxies using a combination of spectroscopic and photometric redshifts. We analyze the Millennium simulation data in a similar way to the analysis of the observational data in order to test the LCDM cosmology. We find that there are too many massive structures (M > 7 x 10^13 Msun) observed at z > 2 in comparison with the simulation predictions by a factor of a few, giving a probability of < 1/2500 of the ob...

  20. Deep Brain Stimulation for Movement Disorders of Basal Ganglia Origin: Restoring Function or Functionality?

    Science.gov (United States)

    Wichmann, Thomas; DeLong, Mahlon R

    2016-04-01

    Deep brain stimulation (DBS) is highly effective for both hypo- and hyperkinetic movement disorders of basal ganglia origin. The clinical use of DBS is, in part, empiric, based on the experience with prior surgical ablative therapies for these disorders, and, in part, driven by scientific discoveries made decades ago. In this review, we consider anatomical and functional concepts of the basal ganglia relevant to our understanding of DBS mechanisms, as well as our current understanding of the pathophysiology of two of the most commonly DBS-treated conditions, Parkinson's disease and dystonia. Finally, we discuss the proposed mechanism(s) of action of DBS in restoring function in patients with movement disorders. The signs and symptoms of the various disorders appear to result from signature disordered activity in the basal ganglia output, which disrupts the activity in thalamocortical and brainstem networks. The available evidence suggests that the effects of DBS are strongly dependent on targeting sensorimotor portions of specific nodes of the basal ganglia-thalamocortical motor circuit, that is, the subthalamic nucleus and the internal segment of the globus pallidus. There is little evidence to suggest that DBS in patients with movement disorders restores normal basal ganglia functions (e.g., their role in movement or reinforcement learning). Instead, it appears that high-frequency DBS replaces the abnormal basal ganglia output with a more tolerable pattern, which helps to restore the functionality of downstream networks.

  1. The origin of layered gabbros from the mid lower ocean crust, Hess Deep, East Pacific Rise

    Science.gov (United States)

    Cheadle, M. J.; Brown, T. C.; Ceuleneer, G.; Meyer, R.

    2014-12-01

    IODP Exp. 345 Holes U1415 I & J cored a ~30m thick unit of conspicuously layered gabbroic rocks from the lower plutonic crust at Hess Deep. These rocks likely come from >1500m below the dike gabbro transition and thus provide an unique opportunity to study the origin of layering and the formation of relatively deep, fast spread plutonic crust formed at the EPR. Here we report the initial results of a comprehensive high-resolution petrologic, geochemical and petrographic study of this unit, which focuses on a fairly continuous 1.5m long section recovered at Hole I. The rocks consist of opx-bearing olivine gabbro, olivine gabbro and gabbro and exhibit 1-10cm scale modal layering. Some layers host spectacular 2-3 cm diameter cpx oikocrysts encapsulating partially resorbed plagioclase laths. Downhole variations in mineral chemistry are complicated. Olivine, cpx and opx Mg#'s partly reflect equilibration and show a subtle metre-scale variation (1-2 Mg#), whereas, for example, plagioclase anorthite, and cpx TiO2 contents reveal a more complicated 10-20 cm-scale variation (2-4 An, and 0.2 TiO2). Mineral zonation, for all but Mg# in equilibrated olivine, is of higher magnitude than downhole variations in average mineral compositions. Trace element geochemistry reveals rather homogeneous plagioclase and opx compositions; however cpx exhibits variation at the mineral scale. Cpx shows an increased range of, and highest REE concentrations, in the more olivine rich, near cotectic, composition gabbros, whereas the more plagioclase rich, cumulates show no variation of, and low REE, concentrations.Plagioclase fabrics are moderate to weak and partially modally controlled, but the strength of the plagioclase crystallographic preferred orientation (CPO) varies dramatically, within the 1.5m core showing a significant part of the variation recorded by Oman ophiolite plutonic crust. Plagioclase shape preferred orientation and CPO match well suggesting that diffusion enabled compaction

  2. The evolutionary origin of the turtle shell and its dependence on the axial arrest of the embryonic rib cage.

    Science.gov (United States)

    Hirasawa, Tatsuya; Pascual-Anaya, Juan; Kamezaki, Naoki; Taniguchi, Mari; Mine, Kanako; Kuratani, Shigeru

    2015-05-01

    Turtles are characterized by their possession of a shell with dorsal and ventral moieties: the carapace and the plastron, respectively. In this review, we try to provide answers to the question of the evolutionary origin of the carapace, by revising morphological, developmental, and paleontological comparative analyses. The turtle carapace is formed through modification of the thoracic ribs and vertebrae, which undergo extensive ossification to form a solid bony structure. Except for peripheral dermal elements, there are no signs of exoskeletal components ontogenetically added to the costal and neural bones, and thus the carapace is predominantly of endoskeletal nature. Due to the axial arrest of turtle rib growth, the axial part of the embryo expands laterally and the shoulder girdle becomes encapsulated in the rib cage, together with the inward folding of the lateral body wall in the late phase of embryogenesis. Along the line of this folding develops a ridge called the carapacial ridge (CR), a turtle-specific embryonic structure. The CR functions in the marginal growth of the carapacial primordium, in which Wnt signaling pathway might play a crucial role. Both paleontological and genomic evidence suggest that the axial arrest is the first step toward acquisition of the turtle body plan, which is estimated to have taken place after the divergence of a clade including turtles from archosaurs. The developmental relationship between the CR and the axial arrest remains a central issue to be solved in future. © 2014 Wiley Periodicals, Inc.

  3. Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae

    Science.gov (United States)

    Marcelino, Vanessa Rossetto; Verbruggen, Heroen

    2016-01-01

    Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. We used a cost-effective protocol and a combination of markers (tufA, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton samples. We identified a wide range of prokaryotic and eukaryotic organisms, many never reported in corals before. We additionally investigated the phylogenetic diversity of the green algae—the most abundant eukaryotic member of this community, for which previous literature recognizes only a handful of endolithic species. We found more than 120 taxonomic units (near species level), including six family-level lineages mostly new to science. The results suggest that the existence of lineages with an endolithic lifestyle predates the existence of modern scleractinian corals by ca. 250my, and that this particular niche was independently invaded by over 20 lineages in green algae evolution. These results highlight the potential of the multi-marker approach to assist in species discovery and, when combined with a phylogenetic framework, clarify the evolutionary origins of host-microbiota associations. PMID:27545322

  4. A Middle Triassic thoracopterid from China highlights the evolutionary origin of overwater gliding in early ray-finned fishes.

    Science.gov (United States)

    Xu, Guang-Hui; Zhao, Li-Jun; Shen, Chen-Chen

    2015-01-01

    Gliding adaptations in thoracopterid flying fishes represent a remarkable case of convergent evolution of overwater gliding strategy with modern exocoetid flying fishes, but the evolutionary origin of this strategy was poorly known in the thoracopterids because of lack of transitional forms. Until recently, all thoracopterids, from the Late Triassic of Austria and Italy and the Middle Triassic of South China, were highly specialized 'four-winged' gliders in having wing-like paired fins and an asymmetrical caudal fin with the lower caudal lobe notably larger than the upper lobe. Here, we show that the new genus Wushaichthys and the previously alleged 'peltopleurid' Peripeltopleurus, from the Middle Triassic (Ladinian, 235-242 Ma) of South China and near the Ladinian/Anisian boundary of southern Switzerland and northern Italy, respectively, represent the most primitive and oldest known thoracopterids. Wushaichthys, the most basal thoracopterid, shows certain derived features of this group in the skull. Peripeltopleurus shows a condition intermediate between Wushaichthys and Thoracopterus in having a slightly asymmetrical caudal fin but still lacking wing-like paired fins. Phylogenetic studies suggest that the evolution of overwater gliding of thoracopterids was gradual in nature; a four-stage adaption following the 'cranial specialization-asymmetrical caudal fin-enlarged paired fins-scale reduction' sequence has been recognized in thoracopterid evolution. Moreover, Wushaichthys and Peripeltopleurus bear hooklets on the anal fin of supposed males, resembling those of modern viviparious teleosts. Early thoracopterids probably had evolved a live-bearing reproductive strategy.

  5. Evolutionary origin of the mitochondrial cholesterol transport machinery reveals a universal mechanism of steroid hormone biosynthesis in animals.

    Directory of Open Access Journals (Sweden)

    Jinjiang Fan

    Full Text Available Steroidogenesis begins with the transport of cholesterol from intracellular stores into mitochondria via a series of protein-protein interactions involving cytosolic and mitochondrial proteins located at both the outer and inner mitochondrial membranes. In adrenal glands and gonads, this process is accelerated by hormones, leading to the production of high levels of steroids that control tissue development and function. A hormone-induced multiprotein complex, the transduceosome, was recently identified, and is composed of cytosolic and outer mitochondrial membrane proteins that control the rate of cholesterol entry into the outer mitochondrial membrane. More recent studies unveiled the steroidogenic metabolon, a bioactive, multimeric protein complex that spans the outer-inner mitochondrial membranes and is responsible for hormone-induced import, segregation, targeting, and metabolism of cholesterol by cytochrome P450 family 11 subfamily A polypeptide 1 (CYP11A1 in the inner mitochondrial membrane. The availability of genome information allowed us to systematically explore the evolutionary origin of the proteins involved in the mitochondrial cholesterol transport machinery (transduceosome, steroidogenic metabolon, and signaling proteins, trace the original archetype, and predict their biological functions by molecular phylogenetic and functional divergence analyses, protein homology modeling and molecular docking. Although most members of these complexes have a history of gene duplication and functional divergence during evolution, phylogenomic analysis revealed that all vertebrates have the same functional complex members, suggesting a common mechanism in the first step of steroidogenesis. An archetype of the complex was found in invertebrates. The data presented herein suggest that the cholesterol transport machinery is responsible for steroidogenesis among all vertebrates and is evolutionarily conserved throughout the entire animal kingdom.

  6. Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome

    Directory of Open Access Journals (Sweden)

    Valerio Alejandro

    2011-10-01

    evolutionary dynamics of these domains support the early origin of the acidocalcisome organelle. In particular, the universality of volutin granules and presence of a functional V-H+PPase domain in the three superkingdoms of life reveals that the acidocalcisomes may have appeared earlier than the divergence of the superkingdoms. This result is remarkable and highlights the possibility that a high degree of cellular compartmentalization could already have been present in the LUCA. Reviewers This article was reviewed by Anthony Poole, Lakshminarayan Iyer and Daniel Kahn

  7. Subduction recycling of continental sediments and the origin of geochemically enriched reservoirs in the deep mantle

    Energy Technology Data Exchange (ETDEWEB)

    Rapp, R.P.; Irifune, T.; Shimizu, N.; Nishiyama, N.; Norman, M.D.; Inoue, T. (Ehime U); (WHOI); (UC); (ANU)

    2008-10-08

    Isotopic and trace element geochemical studies of ocean island basalts (OIBs) have for many years been used to infer the presence of long-lived ({approx} 1-2 Ga old) compositional heterogeneities in the deep mantle related to recycling of crustal lithologies and marine and terrigenous sediments via subduction [e.g., Zindler, A., Hart, S.R., 1986. Chemical geodynamics. Annu. Rev. Earth Planet. Sci. 14, 493-571; Weaver, B.L., 1991. The origin of ocean island basalt end-member compositions: trace element and isotopic constraints. Earth Planet. Sci. Lett. 104, 381-397; Chauvel, C., Hofmann, A.W., Vidal, P., 1992. HIMU-EM: the French Polynesian connection. Earth Planet. Sci. Lett. 110, 99-119; Hofmann, A.W., 1997. Mantle geochemistry: the message from oceanic volcanism. Nature 385, 219-229; Willbold, M., Stracke, A., 2006. Trace element composition of mantle end-members: Implications for recycling of oceanic and upper and lower continental crust. Geochem. Geophys. Geosyst. Q04004. 7, doi:10.1029/2005GC001005]. In particular, models for the EM-1 type ('enriched mantle') OIB reservoir have invoked the presence of subducted, continental-derived sediment to explain high {sup 87}Sr/{sup 86}Sr ratios, low {sup 143}Nd/{sup 144}Nd and {sup 206}Pb/{sup 204}Pb ratios, and extreme enrichments in incompatible elements observed in OIB lavas from, for example, the Pitcairn Island group in the South Pacific [Woodhead, J.D., McCulloch, M.T., 1989; Woodhead, J.D., Devey, C.W., 1993. Geochemistry of the Pitcairn seamounts, I: source character and temporal trends. Earth Planet. Sci. Lett. 116, 81-99; Eisele, J., Sharma, M., Galer, S.J.G., Blichert-Toft, J., Devey, C.W., Hofmann, A.W., 2002. The role of sediment recycling in EM-1 inferred from Os, Pb, Hf, Nd, Sr isotope and trace element systematics of the Pitcairn hotspot. Earth Planet. Sci. Lett. 196, 197-212]. More recently, ultrapotassic, mantle-derived lavas (lamproites) from Gaussberg, Antarctica have been interpreted as

  8. Origin and assessment of deep groundwater inflow in the Ca' Lita landslide using hydrochemistry and in situ monitoring

    Directory of Open Access Journals (Sweden)

    F. Cervi

    2012-06-01

    Full Text Available Changes in soil water content, groundwater flow and a rise in pore water pressure are well-known causal or triggering factors for hillslope instability. Rainfall and snowmelt are generally assumed as the only sources of groundwater recharge. This assumption neglects the role of deep water inflow in highly tectonized areas, a factor that can influence long-term pore-pressure regimes and play a role on local slope instability.

    This paper aims to assess the origin of groundwater in the Ca' Lita landslide (northern Italian Apennines and to qualify and quantify the aliquot attributable to deep water inflow. The research is essentially based on in situ monitoring and hydrochemical analyses. It involved 5 yr of continuous monitoring of groundwater levels, electrical conductivity and temperature, and with groundwater sampling followed by determination of major ions, tracers (such as Boron and Strontium, and isotopes (Oxygen, Deuterium, Tritium. Leaching experiments on soil samples and water recharge estimation were also carried out.

    Results show that the groundwater balance in the Ca' Lita landslide must take into account an inflow of highly mineralized Na-SO4 water (more than 9500 μS cm−1 with non-negligible amounts of Chloride (up to 800 mg l−1. The deep water inflow recharges the aquifer hosted in the bedrock underlying the sliding surface (at a rate of about 7800–17 500 m3 yr−1. It also partly recharges the landslide body, where the hydrochemical imprint of deep water mixed with rainfall and snowmelt water was observed. This points to a probable influence of deep water inflow on the mobility of the Ca' Lita landslide, a finding that could be applicable to other large landslides occurring in highly tectonized areas in the northern Apennines or in other mountain chains.

  9. The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis.

    Science.gov (United States)

    Komiyama, Tomoyoshi; Ikeo, Kazuho; Gojobori, Takashi

    2004-05-26

    Chickens with exceptionally long crow are often favored all over the world, and connoisseur breeders have bred certain types of chicken exclusively for this trait. In Japan, three chicken varieties have been specifically bred to develop an exceptionally long crow of over 15 s. Although these three long-crowing chickens, Naganakidori, are honored as heritage varieties of Japan, the domestication process and genealogical origin of long-crowing chickens remain unclear. The purpose of this study is to clarify these issues using nucleotide sequences of the mitochondrial DNA D-loop region. Blood samples from a total of nine long-crowing chickens and 74 chickens from 11 Japanese native varieties were collected. DNA sequence data of two Junglefowl species were also collected from the International DNA database (DDBJ /EMBL/GenBank) for use as the outgroup. A phylogenetic tree was then constructed revealing that all three Naganakidori varieties were monophyletic and originated from a fighting cock, a Shamo, for cockfighting. These results suggest that these three long-crowing chickens share a common origin in spite of their conspicuously different characters, and that human cultures favoring long-crowing chickens might have been preceded by a tradition of cockfighting. Moreover, these long-crowing varieties first separated from the fighting cocks of Okinawa, which is geographically closer to Southern China and Indochina than Mainland Japan (Honshu/Kyushu). This implies that Japanese long-crowing chickens were first brought to Mainland Japan as fighting cocks from the surrounding regions of Southern China or Indochina and through Okinawa.

  10. Plagiogranites from Markov Deep, Mid-Atlantic Ridge (MAR): physical conditions and alternative modes of origin

    Science.gov (United States)

    Aranovich, Leonid

    2010-05-01

    Very fresh samples of plagiogranites (PG) hosted by gabbro and peridotite, were collected from the slopes of slow spreading MAR within the Markov Deep area. The PG form pockets, lenses and veins ranging in size from a few mm to first few cm, and are structurally very similar to the migmatites found in ophiolite complexes. The PG veinlets in peridotite contain no quartz (Qtz) and are separated from the host by clearly seen reaction zones. Their bulk composition (56-58 wt.% SiO2) plots at the extreme SiO2-poor end of the PG compositional range from literature, what could be related to the consumption of SiO2 due to reaction with the host. The PG hosted by gabbro are characterized by the presence of Qtz, and, correspondingly, much higher bulk SiO2 (70-76 wt.%). Some PG-containing gabbro samples show textures indicative of the incipient felsic melt formation via partial melting of the host. In both gabbroic and peridotite samples certain textural and mineral composition changes point to interaction with the PG melt. Pressure (P)-temperature (T) estimates for the melt-forming conditions based on the microprobe analyses of coexisting minerals and multi-mineral thermobarometry approach (TWQ; Berman, 1990) along with the Berman and Aranovich (1996) thermodynamic data set correspond to 2-2.5 kbar and 800-830оС. The consistent (in the sense of TWQ) results could be obtained only taking into account a decreased silica activity in the rocks, which was estimated (relative to the beta-Qtz standard state) at a(SiO2)=0.7 for gabbro and at a(SiO2)=0.5 for peridotite. Under these P-T, generation of felsic melt is only possible in the presence of a water-rich fluid phase. Water activity values (aН2О) were evaluated with two independent methods: (1) TWQ calculations (at a constant P=2.2 kbar and a(SiO2)=0.5) employing compositions of orthopyroxene, clinopyroxene and pargasitic amphibole coexisting in the reaction zones between the PG veinlets and peridotite; (2) model granite melt

  11. Chemistry and origin of deep ground water in crystalline rocks; Kemi och genes av djupa grundvatten i kristallint berg

    Energy Technology Data Exchange (ETDEWEB)

    Lagerblad, B. [Swedish Cement and Concrete Research Inst., Stockholm (Sweden)

    1995-11-01

    This report discusses the interactions between water and crystalline rocks and its consequences for the chemical composition of the water. It also treats how flows of different types of water are modified by the rock, and the possible consequences for the ground water near a nuclear waste repository. The focus of the work is the changes in composition that ground water gets at deep levels in the rock. Data from Finnsjoen and Aespoe in Sweden show higher salinity in deep rock, which has been interpreted as a result of marine inflow of water during glaciation. Data from other, deeper boreholes in Finland, Canada, Russia, England and Sweden show that the increasing salinity is a rule and very high at great depths, higher than marine water can produce. Therefore, the deep waters from Finnsjoen and Aespoe are probably very old, and the high salinity a result from geological processes. Differing cation and isotopic composition than seawater also indicate geologic water. Differing theories on the origin of the ground water should be regarded in the safety analysis for a repository. 36 refs, 3 figs, 1 tab.

  12. New evidence of microbe origin for ferromanganese nodules from the East Pacific deep sea floor

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Using a fluorescence microscope and EPMA,abundant microbe "bodies" and clear microbic fluorescent microstructure are determined in the ferromanganese nodules recently collected from the East Pacific deep sea floor.The microbic fluorescent structure shows a close relation to the formation of the ferromanganese nodules.According to their morphological features,the microbes are classified into two types:one is named clumpy microbe,which takes a bar-shaped manganese mineral as a pillar and grows like fasciculate coral,resulting in irregular cauliflorate nodules with rough surfaces; the other is called filamentous microbe,which grows in very thin arcuate and/or concentric circular laminae composed of a microbe layer and a metal (manganese and iron)-rich layer,leading to potato-shaped nodules with relatively smooth surfaces.It also can be seen that the two types of microbes are intergrown together,resulting in nodules complicated in compositions and shapes.

  13. New evidence of microbe origin for ferromanganese nodules from the East Pacific deep sea floor

    Institute of Scientific and Technical Information of China (English)

    胡文宣; 周怀阳; 顾连兴; 张文兰; 陆现彩; 符琦; 潘建明; 张海生

    2000-01-01

    Using a fluorescence microscope and EPMA, abundant microbe "bodies" and clear mi-crobic fluorescent microstructure are determined in the ferromanganese nodules recently collected from the East Pacific deep sea floor. The microbic fluorescent structure shows a close relation to the formation of the ferromanganese nodules. According to their morphological features, the microbes are classified into two types: one is named clumpy microbe, which takes a bar-shaped manganese mineral as a pillar and grows like fasciculate coral, resulting in irregular cauliflorate nodules with rough surfaces; the other is called filamentous microbe, which grows in very thin arcuate and/or concentric circular laminae composed of a microbe layer and a metal (manganese and iron)-rich layer, leading to potato-shaped nodules with relatively smooth surfaces. It also can be seen that the two types of microbes are intergrown together, resulting in nodules complicated in compositions and shapes.

  14. A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems.

    Science.gov (United States)

    Meng, Fanfeng; Dong, Xuan; Hu, Tao; Chang, Shuang; Fan, Jianhua; Zhao, Peng; Cui, Zhizhong

    2016-12-19

    As a typical retrovirus, the evolution of Avian leukosis virus subgroup J (ALV-J) in different infectious ecosystems is not characterized, what we know is there are a cloud of diverse variants, namely quasispecies with considerable genetic diversity. This study is to explore the selection of infectious ecosystems on dominant variants and their evolutionary dynamics of ALV-J between DF1 cells and specific-pathogen-free (SPF) chickens. High-throughput sequencing platforms provide an approach for detecting quasispecies diversity more fully. An average of about 20,000 valid reads were obtained from two variable regions of gp85 gene and LTR-U3 region from each sample in different infectious ecosystems. The top 10 dominant variants among ALV-J from chicken plasmas, DF1 cells and liver tumor were completely different from each other. Also there was a difference of shannon entropy and global selection pressure values (ω) in different infectious ecosystems. In the plasmas of two chickens, a large portion of quasispecies contained a 3-peptides "LSD" repeat insertion that was only less than 0.01% in DF1 cell culture supernatants. In parallel studies, the LTR-U3 region of ALV-J from the chicken plasmas demonstrated more variants with mutations in their transcription regulatory elements than those from DF1 cells. Our data taken together suggest that the molecular epidemiology based on isolated ALV-J in cell culture may not represent the true evolution of virus in chicken flocks in the field. The biological significance of the "LSD" insert and mutations in LTR-U3 needs to be further studied.

  15. Deep origin and hot melting of an Archaean orogenic peridotite massif in Norway.

    Science.gov (United States)

    Spengler, Dirk; van Roermund, Herman L M; Drury, Martyn R; Ottolini, Luisa; Mason, Paul R D; Davies, Gareth R

    2006-04-13

    The buoyancy and strength of sub-continental lithospheric mantle is thought to protect the oldest continental crust (cratons) from destruction by plate tectonic processes. The exact origin of the lithosphere below cratons is controversial, but seems clearly to be a residue remaining after the extraction of large amounts of melt. Models to explain highly melt-depleted but garnet-bearing rock compositions require multi-stage processes with garnet and clinopyroxene possibly of secondary origin. Here we report on orogenic peridotites (fragments of cratonic mantle incorporated into the crust during continent-continent plate collision) from Otrøy, western Norway. We show that the peridotites underwent extensive melting during upwelling from depths of 350 kilometres or more, forming a garnet-bearing cratonic root in a single melting event. These peridotites appear to be the residue after Archaean aluminium depleted komatiite magmatism.

  16. Investigating the merger origin of Early-Type Galaxies using ultra-deep optical images

    CERN Document Server

    Duc, P -A; Alatalo, K; Blitz, L; Bois, M; Bournaud, F; Bureau, M; Cappellari, M; Cote, P; Davies, R L; Davis, T A; de Zeeuw, P T; Emsellem, E; Ferrarese, L; Ferriere, E; Gwyn, S; Khochfar, S; Krajnovic, D; Kuntschner, H; Lablanche, P -Y; MacArthur, L; McDermid, R M; Michel-Dansac, L; Morganti, R; Naab, T; Oosterloo, T; Sarzi, M; Scott, N; Serra, P; Weijmans, A; Young, L M

    2011-01-01

    The mass assembly of galaxies leaves various imprints on their surroundings, such as shells, streams and tidal tails. The frequency and properties of these fine structures depend on the mechanism driving the mass assembly: e.g. a monolithic collapse, rapid cold-gas accretion followed by violent disk instabilities, minor mergers or major dry / wet mergers. Therefore, by studying the outskirts of galaxies, one can learn about their main formation mechanism. I present here our on-going work to characterize the outskirts of Early-Type Galaxies (ETGs), which are powerful probes at low redshift of the hierarchical mass assembly of galaxies. This work relies on ultra-deep optical images obtained at CFHT with the wide-field of view MegaCam camera of field and cluster ETGs obtained as part of the Atlas-3D and NGVS projects. State of the art numerical simulations are used to interpret the data. The images reveal a wealth of unknown faint structures at levels as faint as 29 mag arcsec-2 in the g-band. Initial results fo...

  17. Japanese monkeys (Macaca fuscata) quickly detect snakes but not spiders: Evolutionary origins of fear-relevant animals.

    Science.gov (United States)

    Kawai, Nobuyuki; Koda, Hiroki

    2016-08-01

    Humans quickly detect the presence of evolutionary threats through visual perception. Many theorists have considered humans to be predisposed to respond to both snakes and spiders as evolutionarily fear-relevant stimuli. Evidence supports that human adults, children, and snake-naive monkeys all detect pictures of snakes among pictures of flowers more quickly than vice versa, but recent neurophysiological and behavioral studies suggest that spiders may, in fact, be processed similarly to nonthreat animals. The evidence of quick detection and rapid fear learning by primates is limited to snakes, and no such evidence exists for spiders, suggesting qualitative differences between fear of snakes and fear of spiders. Here, we show that snake-naive Japanese monkeys detect a single snake picture among 8 nonthreat animal pictures (koala) more quickly than vice versa; however, no such difference in detection was observed between spiders and pleasant animals. These robust differences between snakes and spiders are the most convincing evidence that the primate visual system is predisposed to pay attention to snakes but not spiders. These findings suggest that attentional bias toward snakes has an evolutionary basis but that bias toward spiders is more due to top-down, conceptually driven effects of emotion on attention capture. (PsycINFO Database Record

  18. Evolution in Mind: Evolutionary Dynamics, Cognitive Processes, and Bayesian Inference.

    Science.gov (United States)

    Suchow, Jordan W; Bourgin, David D; Griffiths, Thomas L

    2017-07-01

    Evolutionary theory describes the dynamics of population change in settings affected by reproduction, selection, mutation, and drift. In the context of human cognition, evolutionary theory is most often invoked to explain the origins of capacities such as language, metacognition, and spatial reasoning, framing them as functional adaptations to an ancestral environment. However, evolutionary theory is useful for understanding the mind in a second way: as a mathematical framework for describing evolving populations of thoughts, ideas, and memories within a single mind. In fact, deep correspondences exist between the mathematics of evolution and of learning, with perhaps the deepest being an equivalence between certain evolutionary dynamics and Bayesian inference. This equivalence permits reinterpretation of evolutionary processes as algorithms for Bayesian inference and has relevance for understanding diverse cognitive capacities, including memory and creativity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.

    Directory of Open Access Journals (Sweden)

    Adam Ameur

    2011-03-01

    Full Text Available Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading-deficient mtDNA polymerase (mtDNA mutator mice have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life.

  20. Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria.

    Science.gov (United States)

    Criscuolo, Alexis; Gribaldo, Simonetta

    2011-11-01

    The emergence of photosynthetic eukaryotes has played a crucial role in evolution and has strongly modified earth's ecology. Several phylogenetic analyses have established that primary plastids arose from a cyanobacterium through endosymbiosis. However, the question of which present-day cyanobacterial lineage is most closely related to primary plastids has been unclear. Here, we have performed an extensive phylogenomic investigation on the origin of primary plastids based on the analysis of up to 191 protein markers and over 30,000 aligned amino acid sites from 22 primary photosynthetic eukaryotes and 61 cyanobacteria representing a wide taxonomic sampling of this phylum. By using a number of solutions to circumvent a large range of systematic errors, we have reconstructed a robust global phylogeny of cyanobacteria and studied the placement of primary plastids within it. Our results strongly support an early emergence of primary plastids within cyanobacteria, prior to the diversification of most present-day cyanobacterial lineages for which genomic data are available.

  1. New materials of the steppe mammoth, Mammuthus trogontherii, with discussion on the origin and evolutionary patterns of mammoths

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Recently found materials indicate that the steppe mammoth, Mammuthus trogontherii, survived in northern China into the late Pleistocene. East Asia is the key area of mammoth evolution after the initial radiation of early forms out of Africa and into Eurasia at the beginning of the late Pliocene (c. 3.5–3.0 Ma). M. rumanus, M. meridionalis, M. trogontherii, and M. primige- nius probably formed a continuous and transitional evolutionary lineage within the pan-Eurasian mammoth radiation in East Asia. Each speciation event of the Eurasian mammoths was followed by a rapid and large-scale dispersal event: out of East Asia. Allopatric speciation is the main speciation pattern of Mammuthus. The climatic vacillation was severe and frequent in East Asia from the early part of early Pleistocene (c. 2.6 Ma) onward, which probably brought about successive speciation in East Asia and the subsequent dispersal of the mammoths.

  2. Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene.

    Science.gov (United States)

    Tee, Kok Keng; Lam, Tommy Tsan-Yuk; Chan, Yoke Fun; Bible, Jon M; Kamarulzaman, Adeeba; Tong, C Y William; Takebe, Yutaka; Pybus, Oliver G

    2010-04-01

    Human enterovirus 71 (EV-71) is one of the major etiologic causes of hand, foot, and mouth disease (HFMD) among young children worldwide, with fatal instances of neurological complications becoming increasingly common. Global VP1 capsid sequences (n = 628) sampled over 4 decades were collected and subjected to comprehensive evolutionary analysis using a suite of phylogenetic and population genetic methods. We estimated that the common ancestor of human EV-71 likely emerged around 1941 (95% confidence interval [CI], 1929 to 1952), subsequently diverging into three genogroups: B, C, and the now extinct genogroup A. Genealogical analysis revealed that diverse lineages of genogroup B and C (subgenogroups B1 to B5 and C1 to C5) have each circulated cryptically in the human population for up to 5 years before causing large HFMD outbreaks, indicating the quiescent persistence of EV-71 in human populations. Estimated phylogenies showed a complex pattern of spatial structure within well-sampled subgenogroups, suggesting endemicity with occasional lineage migration among locations, such that past HFMD epidemics are unlikely to be linked to continuous transmission of a single strain of virus. In addition, rises in genetic diversity are correlated with the onset of epidemics, driven in part by the emergence of novel EV-71 subgenogroups. Using subgenogroup C1 as a model, we observe temporal strain replacement through time, and we investigate the evidence for positive selection at VP1 immunogenic sites. We discuss the consequences of the evolutionary dynamics of EV-71 for vaccine design and compare its phylodynamic behavior with that of influenza virus.

  3. [Evolutionary history of Metazoa, ancestral status of the bilateria clonal reproduction, and semicolonial origin of the mollusca].

    Science.gov (United States)

    Martynov, A V

    2013-01-01

    Evolutionary history of any metazoan group is a history of the entire ontogenetic cycles instead of separate stages and genes only. Ontogeny in the most objective way links two key components of the biological systematics: historically-independent characters attribution and phylogeny itself. A general theory encompassing "static" traditional taxonomy and dynamic evolutionary process, based on the ontogenetic transformation of the organisms' shape is suggested here to term as ontogenetic systematics. As an important practical implication of the ontogenetic systematics, a new model of the bilaterian metazoans evolution is suggested. The new model considers asexual clonal reproduction as a central feature of the ancestral ontogenetic cycles of basal Bilateria. The new scenario resolves several notable contradictions, e.g. morphological, ontogenetic and molecular similarities of Pogonophora, Vestimentifera, Phoronida simultaneously to protostomian Spiralia (Lophotrochozoa) and Deuterostomia. The suggested model implies individuation (possibly multiple) of ancestral semicolonial sedentary group as a major factor of the basal Bilateria diversification. In the late Ediacaran and early Cambrian thus existed ancestral bilaterian group that shared characters of both Spiralia and Deuterostomia and possessed polyp-shape body and cephalic secretory shield (like in modern Pterobranchia and Vestimentifera), that later on reduced in various lines. This ancestral taxon in rank of supraphylum is suggested to term as Carmaphora (shield-bearers). Presence of the enigmatic sedentary fossil of the genus Cloudina with vestimentiferan-like tubes and evident clonal reproduction already in the late Ediacaran, and most recent found of an unquestionable pterobranch already in the early Cambrian support the new model of Bilateria evolution.

  4. Evolutionary medicine.

    Science.gov (United States)

    Swynghedauw, B

    2004-04-01

    Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.

  5. On the origin of framboidal pyrite in sediments of the Suakin Deep (Red Sea)Sur l'origine de la pyrite framboïdale dans les sédiments de la fosse Suakin (mer Rouge)

    Science.gov (United States)

    Pierret, Marie-Claire; Blanc, Gérard; Clauer, Norbert

    2000-01-01

    Suakin Deep is one of the southern depressions of the Red Sea, with sediments containing up to 20 % of pyrite. Although metalliferous sediments result from hydrothermal activity in most deeps, those of Suakin have different characteristics. Pyrite is framboïdal and the REE patterns of its sediments are similar to those of biodetrital sediments. The sediments seem to be of biodetritic origin and to have undergone diagenetic changes without hydrothermal activity.

  6. Origin and assessment of deep groundwater inflow in the Ca' Lita landslide using hydrochemistry and in situ monitoring

    Directory of Open Access Journals (Sweden)

    F. Cervi

    2012-11-01

    Full Text Available Changes in soil water content, groundwater flow and a rise in pore water pressure are well-known causal or triggering factors for hillslope instability. Rainfall and snowmelt are generally assumed as the main sources of groundwater recharge. This assumption neglects the role of deep water inflow in highly tectonized areas, a factor that can influence long-term pore-pressure regimes and play a role on local slope instability.

    This paper aims to assess the origin of groundwater in the Ca' Lita landslide (northern Italian Apennines and to qualify and quantify the aliquot attributable to deep water inflow. The research is essentially based on in situ monitoring and hydrochemical analyses. It involved 5 yr of continuous monitoring of groundwater levels, electrical conductivity and temperature and with groundwater sampling followed by determination of major ions (Na+, K+, Mg2+, Ca2+, Cl, HCO3, SO42−, tracers (such as Btot and Sr2+, and isotopes (δ18O, δ2H and 3H. Leaching experiments on soil samples, hydrochemical modelling and water recharge estimation were also carried out.

    Results show that the groundwater balance in the Ca' Lita landslide must take into account an inflow of deep and highly mineralised Na-SO4 water (more than 9500 μS cm−1 with non-negligible amounts of Cl (up to 800 mg l−1. The chemical and isotopic fingerprint of this water points to oilfield water hosted at large depths in the Apennine chain and that uprises through a regional fault line crossing the landslide area. It recharges the aquifer hosted in the bedrock underlying the sliding surface (at a rate of about 49 000–85 700 m3 yr−1 and it also partly recharges the landslide body. In both the aquifers, the hydrochemical

  7. An evolutionary scenario for the origin of pentaradial echinoderms-implications from the hydraulic principles of form determination.

    Science.gov (United States)

    Gudo, Michael

    2005-01-01

    The early evolutionary history of echinoderms was reconstructed on the basis of structural-functional considerations and application of the quasi-engineering approach of 'Konstruktions-Morphologie'. According to the presented evolutionary scenario, a bilaterally symmetrical ancestor, such as an enteropneust-like organism, became gradually modified into a pentaradial echinoderm by passing through an intermediate pterobranch-like stage. The arms of a pentaradial echinoderm are identified as hydraulic outgrowths from the central coelomic cavity of the bilateral ancestor which developed due to a shortening of the body in length but widening in the diameter. The resulting pentaradial symmetry is a consequence of mechanical laws that dictate minimal contact surface areas among hydraulic pneumatic entities. These developed in the coelomic cavity (metacoel) in the bilaterally symmetrical ancestor, when from the already U-shaped mesentery with the intestinal tract two additional U-shaped bows developed directly or subsequently. During the subsequent development tensile chords of the mesentery 'sewed' the gut with the body wall first in three and secondly in five 'seams'. During the direct development five 'seams' between tensile chords and body wall developed straightly. These internal tensile chords subdivide the body coelom into five hydraulic subsystems ('pneus'), which eventually arrange in a pentaradial pattern. The body could then enlarge only between the tensile chords, which means that five hydraulic bulges developed. These bulges initially supported the tentacles and finally each of them enclosed the tentacle until only the feather-like appendages of the tentacles projected over the surface. The tentacles with their feathers were transformed into the ambulacral system, and the bulges become the arms. These morphological transformations were accompanied and partly determined by specific histological modifications, such as the development of mutable connective

  8. Evolutionary developmental perspective for the origin of turtles: the folding theory for the shell based on the developmental nature of the carapacial ridge.

    Science.gov (United States)

    Kuratani, Shigeru; Kuraku, Shigehiro; Nagashima, Hiroshi

    2011-01-01

    The body plan of the turtle represents an example of evolutionary novelty for acquisition of the shell. Unlike similar armors in other vertebrate groups, the turtle shell involves the developmental repatterning of the axial skeleton and exhibits an unusual topography of musculoskeletal elements. Thus, the turtle provides an ideal case study for understanding changes in the developmental program associated with the morphological evolution of vertebrates. In this article, the evolution of the turtle-specific body plan is reviewed and discussed. The key to understanding shell patterning lies in the modification of the ribs, for which the carapacial ridge (CR), a turtle-specific embryonic anlage, is assumed to be responsible. The growth of the ribs is arrested in the axial part of the body, allowing dorsal and lateral oriented growth to encapsulate the scapula. Although the CR does not appear to induce this axial arrest per se, it has been shown to support the fan-shaped patterning of the ribs, which occurs concomitant with marginal growth of the carapace along the line of the turtle-specific folding that takes place in the lateral body wall. During the process of the folding, some trunk muscles maintain their ancestral connectivities, whereas the limb muscles establish new attachments specific to the turtle. The turtle body plan can thus be explained with our knowledge of vertebrate anatomy and developmental biology, consistent with the evolutionary origin of the turtle suggested by the recently discovered fossil species, Odontochelys. © 2011 Wiley Periodicals, Inc.

  9. The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record.

    Science.gov (United States)

    Hsiang, Allison Y; Field, Daniel J; Webster, Timothy H; Behlke, Adam D B; Davis, Matthew B; Racicot, Rachel A; Gauthier, Jacques A

    2015-05-20

    The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group - approximated by the Coniophis node - is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K

  10. Evolutionary reversion of editing sites of ndh genes suggests their origin in the Permian-Triassic, before the increase of atmospheric CO2

    Directory of Open Access Journals (Sweden)

    Mercedes eMartin

    2015-07-01

    Full Text Available The plastid ndh genes have hovered frequently on the edge of dispensability. They are absent in the plastid DNA of many algae and certain higher plants and present editing sites requiring C-to-U corrections of primary transcripts. The evolutionary origin of editing sites and their loss due to C-to-T reversions at the DNA level are unknown and must be related to the dispensability of the ndh genes in specific environments. In order to better understand the evolution of ndh gene editing sites, we have created expandable data banks with the 12 editing sites of the ndhB gene (600 GenBank sequences and both editing sites of the ndhF gene (1,600 GenBank sequences. Since their origin via T-to-C mutations that probably occurred between 300 and 200 Myr BP (Permian-Triassic, ndh editing sites have undergone independent and random C-to-T reversions in the different angiosperm lineages. Some of these reversions appear early in angiosperm diversification. Old C-to-T reversions can be traced back to radiation steps that gave origin to main classes, orders and some families.

  11. The TOPOMOD-ITN project: unravel the origin of Earth's topography from modelling deep-surface processes

    Science.gov (United States)

    Faccenna, C.; Funiciello, F.

    2012-04-01

    EC-Marie Curie Initial Training Networks (ITN) projects aim to improve the career perspectives of young generations of researchers. Institutions from both academic and industry sectors form a collaborative network to recruit research fellows and provide them with opportunities to undertake research in the context of a joint research training program. In this frame, TOPOMOD - one of the training activities of EPOS, the new-born European Research Infrastructure for Geosciences - is a funded ITN project designed to investigate and model how surface processes interact with crustal tectonics and mantle convection to originate and develop topography of the continents over a wide range of spatial and temporal scales. The multi-disciplinary approach combines geophysics, geochemistry, tectonics and structural geology with advanced geodynamic numerical/analog modelling. TOPOMOD involves 8 European research teams internationally recognized for their excellence in complementary fields of Earth Sciences (Roma TRE, Utrecht, GFZ, ETH, Cambridge, Durham, Rennes, Barcelona), to which are associated 5 research institutions (CNR-Italy, Univ. Parma, Univ. Lausanne, Univ. Montpellier, Univ. Mainz) , 3 high-technology enterprises (Malvern Instruments, TNO, G.O. Logical Consulting) and 1 large multinational oil and gas company (ENI). This unique network places emphasis in experience-based training increasing the impact and international visibility of European research in modeling. Long-term collaboration and synergy are established among the overmentioned research teams through 15 cross-disciplinary research projects that combine case studies in well-chosen target areas from the Mediterranean, the Middle and Far East, west Africa, and South America, with new developments in structural geology, geomorphology, seismology, geochemistry, InSAR, laboratory and numerical modelling of geological processes from the deep mantle to the surface. These multidisciplinary projects altogether aim to

  12. An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin

    OpenAIRE

    Thiergart, T.; Landan, G; Schenk, M.; Dagan, T.; Martin, W F

    2012-01-01

    To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the a...

  13. An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.

    Science.gov (United States)

    Thiergart, Thorsten; Landan, Giddy; Schenk, Marc; Dagan, Tal; Martin, William F

    2012-01-01

    To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the archaebacteria, euryarchaeote genomes most frequently harbored the sister to the eukaryotic nuclear gene, whereas among eubacteria, the α-proteobacteria were most frequently represented within the sister group. Only 3 genes out of 571 gave a 3-domain tree. Homologues from α-proteobacterial genomes that branched as the sister to nuclear genes were found more frequently in genomes of facultatively anaerobic members of the rhiozobiales and rhodospirilliales than in obligate intracellular ricketttsial parasites. Following α-proteobacteria, the most frequent eubacterial sister lineages were γ-proteobacteria, δ-proteobacteria, and firmicutes, which were also the prokaryote genomes least frequently found as monophyletic groups in our trees. Although all 22 higher prokaryotic taxa sampled (crenarchaeotes, γ-proteobacteria, spirochaetes, chlamydias, etc.) harbor genes that branch as the sister to homologues present in the eukaryotic common ancestor, that is not evidence of 22 different prokaryotic cells participating at eukaryote origins because prokaryotic "lineages" have laterally acquired genes for more than 1.5 billion years since eukaryote origins. The data underscore the archaebacterial (host) nature of the eukaryotic informational genes and the eubacterial (mitochondrial) nature of eukaryotic energy metabolism. The network linking genes of the eukaryote ancestor to contemporary homologues distributed across prokaryotic genomes elucidates eukaryote gene origins in a dialect

  14. Deep Reaching Gas-permeable Tectonic Faults of the Early Earth as Habitats for the Origin of Life

    Science.gov (United States)

    Schreiber, U.; Mayer, C.

    2012-04-01

    The discussion on the origin of life encounters difficulties when it comes to estimate the conditions of the early earth and to define plausible environments for the development of the first complex organic molecules. Until now, the role of the earth's crust has been more or less ignored. First continental crustal cores may have been developed some tens to hundreds of million years after formation of earth. Due to tectonic stress the proto continents were sheared by vertical strike-slip faults at an early stage. These deep-reaching open, interconnected tectonic faults may provide possible reaction habitats ranging from nano- to centimetre and even larger dimensions that sum up to several cubic kilometres for the formation of prebiotic molecules. Their fillings consist of supercritical and subcritical waters and supercritical and subcritical gases. Here, all necessary raw materials including phosphate for the development of prebiotic molecules exist in variable concentrations and in sufficient quantities. Furthermore, there are periodically changing pressure and temperature conditions, varying pH-values, metallic surfaces, clay minerals and a large number of catalysts. While cosmic and UV-radiation are excluded, nuclear radiation intervenes the chemical evolution of the molecules inside the crust. Carbon dioxide (CO2) is of crucial importance. It can be present in an almost pure form as a supercritical fluid (scCO2) in a crustal depth less than 1 km (critical point of pure CO2: 74 bar; 31°C). Inside strike-slip faults, a two-phase system formed by supercritical CO2 in liquid water provides the environment for condensation and polymerisation of hydrogen cyanide, nucleobases, nucleotides and amino acids. ScCO2 is a non-polar solvent that is widely used in "green chemistry" (Anastas and Kirchhoff 2002) and enables the dissolution of non-polar reactants and their reactions normally occurring in the absence of water. Under the influence of periodically changing

  15. Origin of Ultra-Deep Diamonds: Chemical Interaction of Ca-CARBONATE and the Earth's Lower Mantle Minerals

    Science.gov (United States)

    Spivak, A. V.; Dubrovinsky, L. S.; Litvin, Yu. A.

    2012-04-01

    The main goal of the work is experimental study of physicochemical conditions of origin of ultra-deep diamonds in the substance of the Earth's lower mantle (LM) based on the experimental criterium of syngenesis of diamond and primary inclusions of LM mineral. Magnesiowustite (Mg,Fe)O, Mg-Fe perovskite (Mg,Fe)(Si,Al)O3 and Ca-perovskite CaSiO3 mainly present the LM substance and are frequently disclosed as primary inclusions in ultra-deep diamonds together with Ca-, (Ca, Mg, Fe)-, Na-Ca-carbonates. For the upper mantle conditions, the mantle-carbonatite conception of diamond genesis was developed based on the effects of congruent melting of carbonates and complete liquid miscibility of carbonate-silicate melts. Melting of Ca-carbonate and CaCO3 - (Mg,Fe)O, CaCO3 - (Mg,Fe)(Si,Al)O3 systems, stability of the melts and their decomposition were studied in static high pressure experiments at pressures of 16 to 55 GPa and temperatures of 1600 to 3900 K using diamond anvil cell technique with laser heating. It was determined that melting of Ca-carbonate is congruent at the PT-conditions of the lower mantle and characterized by an expanded field of liquid Ca-carbonate phase. We observed formation of graphite (below 16 GPa) and diamond (between 16 and 43 GPa) on decomposition of the CaCO3 melt at temperatures above 3400 K. At temperatures below 3400 K congruent melting of calcium carbonate was confirmed. Also it was shown that CaCO3 - (Mg,Fe)O - (Mg,Fe)(Si,Al)O3 system is capable to form diamonds together with Ca-carbonate, magnesiowustite and perovskite as syngenesis minerals at PT-conditions of the lower mantle. We observed formation diamond (between 40 and 55 GPa) on decomposition of the CaCO3 from CaCO3 - (Mg,Fe)(Si,Al)O3 melt at temperatures above 2000 K. The experimental data on phase relations at the melting and decomposition of CaCO3 and CaCO3-(Mg,Fe)O-(Mg,Fe)(Si,Al)O3 system as well as diamond crystallization are applied to the problem of formation of natural ultra-deep

  16. A fundamental plant evolutionary problem: the origin of land-plant sporophyte; is a new hypothesis possible?

    Science.gov (United States)

    Bennici, Andrea

    2005-01-01

    The origin of the sporophyte in land plants represents a fundamental phase in the plant evolution. Today this subject is controversial and, in my opinion, scarcely considered in our textbooks and journals of botany, in spite of its importance. There are two conflicting theories concerning the origin of the alternating generations in land plants: the "antithetic" and the "homologous" theory. These have never been fully resolved. The antithetic theory maintains that the sporophyte and gametophyte generations are fundamentally dissimilar and that the sporophyte originated in an ancestor organism with haplontic cycle by the zygote dividing mitotically rather than meiotically, and with a developmental pattern not copying the developmental events of the gametophyte. The sporophyte generation was an innovation of critical significance for the land-plant evolution. By contrast, the homologous theory simply stated that a mass of cells forming mitotically from the zygote adopted the same developmental plan of the gametophyte, but giving origin to a diploid sporophyte. In this context, a very important question concerns the possible ancestor or ancestors of the land plants. Considerable evidences at morphological, cytological, ultrastructural, biochemical and, especially, molecular level, strongly suggest that the land plants or Embryophyta (both vascular and non-vascular) evolved from green algal ancestor(s), similar to those belonging to the genus Coleochaete, Chara and Nitella, living today. Their organism is haploid for most of their life cycle, and diploid only in the zygote phase (haplontic cycle). On the contrary, the land plants are characterized by a diplo-haplontic life cycle. Several questions are implied in these theories, and numerous problems remain to be solved, such as, for example, the morphological difference between gametophyte and sporophyte (heteromorphism, already present in the first land plants, the bryophytes), and the strong gap existing between

  17. Origins.

    Science.gov (United States)

    Online-Offline, 1999

    1999-01-01

    Provides an annotated list of resources dealing with the theme of origins of life, the universe, and traditions. Includes Web sites, videos, books, audio materials, and magazines with appropriate grade levels and/or subject disciplines indicated; professional resources; and learning activities. (LRW)

  18. Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Punita Sharma

    2015-12-01

    Full Text Available In prokaryotes, horizontal gene transfer (HGT has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito, Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito.

  19. Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion.

    Science.gov (United States)

    Sun, Yongshuai; Abbott, Richard J; Li, Lili; Li, Long; Zou, Jiabin; Liu, Jianquan

    2014-02-01

    Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai-Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, P. likiangensis and P. wilsonii, are unclear. To clarify them, we surveyed sequence variation within and between them for 11 nuclear loci, three chloroplast (cp) and two mitochondrial (mt) DNA fragments, and examined their ecological requirements using ecological niche modelling. Initial analyses based on 11 nuclear loci rejected a close relationship between P. schrenkiana and P. purpurea. BP&P tests and ecological niche modelling indicated substantial divergence between the remaining three species and supported the species status of P. purpurea, which contained many private alleles as expected for a well-established species. Sequence variation for cpDNA and mtDNA suggested a close relationship between P. purpurea and P. wilsonii, while variation at the nuclear se1364 gene suggested P. purpurea was more closely related to P. likiangensis. Analyses of genetic divergence, Bayesian clustering and model comparison using approximate Bayesian computation (ABC) of nuclear (nr) DNA variation all supported the hypothesis that P. purpurea originated by homoploid hybrid speciation from P. wilsonii and P. likiangensis. The ABC analysis dated the origin of P. purpurea at the Pleistocene, and the estimated hybrid parameter indicated that 69% of its nuclear composition was contributed by P. likiangensis and 31% by P. wilsonii. Our results further suggested that during or immediately following its formation, P. purpurea was subject to organelle DNA introgression from P. wilsonii such that it came to possess both mtDNA and cpDNA of P. wilsonii. The estimated parameters indicated that following its origin, P. purpurea underwent an

  20. Evolutionary computer programming of protein folding and structure predictions.

    Science.gov (United States)

    Nölting, Bengt; Jülich, Dennis; Vonau, Winfried; Andert, Karl

    2004-07-07

    In order to understand the mechanism of protein folding and to assist the rational de-novo design of fast-folding, non-aggregating and stable artificial enzymes it is very helpful to be able to simulate protein folding reactions and to predict the structures of proteins and other biomacromolecules. Here, we use a method of computer programming called "evolutionary computer programming" in which a program evolves depending on the evolutionary pressure exerted on the program. In the case of the presented application of this method on a computer program for folding simulations, the evolutionary pressure exerted was towards faster finding deep minima in the energy landscape of protein folding. Already after 20 evolution steps, the evolved program was able to find deep minima in the energy landscape more than 10 times faster than the original program prior to the evolution process.

  1. Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria and Nematoda possibly originating from ancient (inland seas.

    Directory of Open Access Journals (Sweden)

    Gaetan eBorgonie

    2015-08-01

    Full Text Available Stalactites (CaCO3 and salt from water seeps are frequently encountered in ceilings of mine tunnels whenever they intersect water-bearing faults or fractures. To determine whether stalactites could be mineralized traps for indigenous fracture water microorganisms, we analyzed stalactites collected from three different mines ranging in depth from 1.3 to 3.1 km. During sampling in Beatrix gold mine (1.4 km beneath the surface, central South Africa, CaCO3 stalactites growing on the mine tunnel ceiling were collected and discovered, in two cases, to contain a living obligate brackish water/marine nematode species, Monhystrella parvella. After sterilization of the outer surface, mineral layers were physically removed from the outside to the interior, the DNA extracted. Based upon 16S and 18S rRNA gene sequencing, Archaea, Bacteria and Eukarya in different combinations were detected for each layer. . Using CT scan and electron microscopy the inner structure of CaCO3 and salt stalactites were analyzed. CaCO3 stalactites show a complex pattern of lamellae carrying bacterially precipitated mineral structures. Nematoda were clearly identified between these layers confirming that bacteria and nematodes live inside the stalactites and not only in the central straw. Salt stalactites exhibit a more uniform internal structure. Surprisingly, several Bacteria showing highest sequence identities to marine Bacteria were identified. This, together with the observation that the nematode M. parvella recovered from Beatrix gold mine stalactite can only survive in a salty environment makes the origin of the deep subsurface colonization enigmatic. The possibility of a Permian origin is discussed. Our results indicate stalactites are suitable for biodiversity recovery and act as natural traps for microorganisms in the fissure water long after the water that formed the stalactite stopped flowing.

  2. Investigating the timing of origin and evolutionary processes shaping regional species diversity: Insights from simulated data and neotropical butterfly diversification rates.

    Science.gov (United States)

    Matos-Maraví, Pável

    2016-07-01

    Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence.

  3. Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system.

    Science.gov (United States)

    Vieira, Filipe G; Rozas, Julio

    2011-01-01

    Chemoreception is a biological process essential for the survival of animals, as it allows the recognition of important volatile cues for the detection of food, egg-laying substrates, mates, or predators, among other purposes. Furthermore, its role in pheromone detection may contribute to evolutionary processes, such as reproductive isolation and speciation. This key role in several vital biological processes makes chemoreception a particularly interesting system for studying the role of natural selection in molecular adaptation. Two major gene families are involved in the perireceptor events of the chemosensory system: the odorant-binding protein (OBP) and chemosensory protein (CSP) families. Here, we have conducted an exhaustive comparative genomic analysis of these gene families in 20 Arthropoda species. We show that the evolution of the OBP and CSP gene families is highly dynamic, with a high number of gains and losses of genes, pseudogenes, and independent origins of subfamilies. Taken together, our data clearly support the birth-and-death model for the evolution of these gene families with an overall high gene turnover rate. Moreover, we show that the genome organization of the two families is significantly more clustered than expected by chance and, more important, that this pattern appears to be actively maintained across the Drosophila phylogeny. Finally, we suggest the homologous nature of the OBP and CSP gene families, dating back their most recent common ancestor after the terrestrialization of Arthropoda (380--450 Ma) and we propose a scenario for the origin and diversification of these families.

  4. A common evolutionary origin for the ON- and OFF-edge motion detection pathways of the Drosophila visual system

    Directory of Open Access Journals (Sweden)

    Kazunori eShinomiya

    2015-07-01

    Full Text Available Synaptic circuits for identified behaviors in the Drosophila brain have typically been considered from either a developmental or functional perspective without reference to how the circuits might have been inherited from ancestral forms. For example, two candidate pathways for ON- and OFF-edge motion detection in the visual system act via circuits that use respectively either T4 or T5, two cell types of the fourth neuropil, or lobula plate, that exhibit narrow-field direction-selective responses and provide input to wide-field tangential neurons. T4 or T5 both have four subtypes that terminate one each in the four strata of the lobula plate. Representatives are reported in a wide range of Diptera, and both cell types exhibit various similarities in: 1 the morphology of their dendritic arbors; 2 their four morphological and functional subtypes; 3 their cholinergic profile in Drosophila; 4 their input from the pathways of L3 cells in the first neuropil, or lamina, and by one of a pair of lamina cells, L1 (to the T4 pathway and L2 (to the T5 pathway; and 5 their innervation by a single, wide-field contralateral tangential neuron from the central brain. Progenitors of both also express the gene atonal early in their proliferation from the inner anlage of the developing optic lobe, being alone among many other cell type progeny to do so. Yet T4 receives input in the second neuropil, or medulla, and T5 in the third neuropil or lobula. Here we suggest that these two cell types were originally one, that their ancestral cell population duplicated and split to innervate separate medulla and lobula neuropils, and that a fiber crossing – the internal chiasma – arose between the two neuropils. The split most plausibly occurred, we suggest, with the formation of the lobula as a new neuropil that formed when it separated from its ancestral neuropil to leave the medulla, suggesting additionally that medulla input neurons to T4 and T5 may also have had a

  5. Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies.

    Science.gov (United States)

    Aardema, Matthew L; Andolfatto, Peter

    2016-08-01

    Many distantly related insect species are specialized feeders of cardenolide-containing host plants such as milkweed (Asclepias spp.). Previous studies have revealed frequent, parallel substitution of a functionally important amino acid substitution (N122H) in the alpha subunit of Na(+) ,K(+) -ATPase in a number of these species. This substitution facilitates the ability of these insects to feed on their toxic hosts and sequester cardenolides for their own use in defense. Among milkweed butterflies of the genus Danaus, the previously established phylogeny for this group suggests that N122H arose independently and fixed in two distinct lineages. We reevaluate this conclusion by examining Danaus phylogenetic relationships using >400 orthologous gene sequences assembled from transcriptome data. Our results indicate that the three Danaus species known to harbor the N122H substitution are more closely related than previously thought, consistent with a single, common origin for N122H. However, we also find evidence of both incomplete lineage sorting and post-speciation genetic exchange among these butterfly species, raising the possibility of collateral evolution of cardenolide-insensitivity in this species group.

  6. The Cockroach Origin of the Termite Gut Microbiota: Patterns in Bacterial Community Structure Reflect Major Evolutionary Events

    Science.gov (United States)

    Dietrich, Carsten; Köhler, Tim

    2014-01-01

    Termites digest wood and other lignocellulosic substrates with the help of their intestinal microbiota. While the functions of the symbionts in the digestive process are slowly emerging, the origin of the bacteria colonizing the hindgut bioreactor is entirely unknown. Recently, our group discovered numerous representatives of bacterial lineages specific to termite guts in a closely related omnivorous cockroach, but it remains unclear whether they derive from the microbiota of a common ancestor or were independently selected by the gut environment. Here, we studied the bacterial gut microbiota in 34 species of termites and cockroaches using pyrotag analysis of the 16S rRNA genes. Although the community structures differed greatly between the major host groups, with dramatic changes in the relative abundances of particular bacterial taxa, we found that the majority of sequence reads belonged to bacterial lineages that were shared among most host species. When mapped onto the host tree, the changes in community structure coincided with major events in termite evolution, such as acquisition and loss of cellulolytic protists and the ensuing dietary diversification. UniFrac analysis of the core microbiota of termites and cockroaches and construction of phylogenetic tree of individual genus level lineages revealed a general host signal, whereas the branching order often did not match the detailed phylogeny of the host. It remains unclear whether the lineages in question have been associated with the ancestral cockroach since the early Cretaceous (cospeciation) or are diet-specific lineages that were independently acquired from the environment (host selection). PMID:24487532

  7. Bilaterian Giant Ankyrins Have a Common Evolutionary Origin and Play a Conserved Role in Patterning the Axon Initial Segment

    Science.gov (United States)

    Jegla, Timothy; Nguyen, Michelle M.; Feng, Chengye; Goetschius, Daniel J.; van Rossum, Damian B.; Pisupati, Aditya; Milner, Elliott S.

    2016-01-01

    In vertebrate neurons, the axon initial segment (AIS) is specialized for action potential initiation. It is organized by a giant 480 Kd variant of ankyrin G (AnkG) that serves as an anchor for ion channels and is required for a plasma membrane diffusion barrier that excludes somatodendritic proteins from the axon. An unusually long exon required to encode this 480Kd variant is thought to have been inserted only recently during vertebrate evolution, so the giant ankyrin-based AIS scaffold has been viewed as a vertebrate adaptation for fast, precise signaling. We re-examined AIS evolution through phylogenomic analysis of ankyrins and by testing the role of ankyrins in proximal axon organization in a model multipolar Drosophila neuron (ddaE). We find giant isoforms of ankyrin in all major bilaterian phyla, and present evidence in favor of a single common origin for giant ankyrins and the corresponding long exon in a bilaterian ancestor. This finding raises the question of whether giant ankyrin isoforms play a conserved role in AIS organization throughout the Bilateria. We examined this possibility by looking for conserved ankyrin-dependent AIS features in Drosophila ddaE neurons via live imaging. We found that ddaE neurons have an axonal diffusion barrier proximal to the cell body that requires a giant isoform of the neuronal ankyrin Ank2. Furthermore, the potassium channel shal concentrates in the proximal axon in an Ank2-dependent manner. Our results indicate that the giant ankyrin-based cytoskeleton of the AIS may have evolved prior to the radiation of extant bilaterian lineages, much earlier than previously thought. PMID:27911898

  8. Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C.

    Directory of Open Access Journals (Sweden)

    Ujjwal Neogi

    Full Text Available BACKGROUND: India has the third largest HIV-1 epidemic with 2.4 million infected individuals. Molecular epidemiological analysis has identified the predominance of HIV-1 subtype C (HIV-1C. However, the previous reports have been limited by sample size, and uneven geographical distribution. The introduction of HIV-1C in India remains uncertain due to this lack of structured studies. To fill the gap, we characterised the distribution pattern of HIV-1 subtypes in India based on data collection from nationwide clinical cohorts between 2007 and 2011. We also reconstructed the time to the most recent common ancestor (tMRCA of the predominant HIV-1C strains. METHODOLOGY/PRINCIPAL FINDINGS: Blood samples were collected from 168 HIV-1 seropositive subjects from 7 different states. HIV-1 subtypes were determined using two or three genes, gag, pol, and env using several methods. Bayesian coalescent-based approach was used to reconstruct the time of introduction and population growth patterns of the Indian HIV-1C. For the first time, a high prevalence (10% of unique recombinant forms (BC and A1C was observed when two or three genes were used instead of one gene (p<0.01; p = 0.02, respectively. The tMRCA of Indian HIV-1C was estimated using the three viral genes, ranged from 1967 (gag to 1974 (env. Pol-gene analysis was considered to provide the most reliable estimate [1971, (95% CI: 1965-1976]. The population growth pattern revealed an initial slow growth phase in the mid-1970s, an exponential phase through the 1980s, and a stationary phase since the early 1990s. CONCLUSIONS/SIGNIFICANCE: The Indian HIV-1C epidemic originated around 40 years ago from a single or few genetically related African lineages, and since then largely evolved independently. The effective population size in the country has been broadly stable since the 1990s. The evolving viral epidemic, as indicated by the increase of recombinant strains, warrants a need for continued molecular

  9. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation.

    Science.gov (United States)

    Wang, Lu; Peng, Qian; Zhao, Jianbo; Ren, Fei; Zhou, Hui; Wang, Wei; Liao, Liao; Owiti, Albert; Jiang, Quan; Han, Yuepeng

    2016-05-01

    Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.

  10. Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa.

    Science.gov (United States)

    Jacquet, François; Denys, Christiane; Verheyen, Erik; Bryja, Josef; Hutterer, Rainer; Kerbis Peterhans, Julian C; Stanley, William T; Goodman, Steven M; Couloux, Arnaud; Colyn, Marc; Nicolas, Violaine

    2015-04-23

    This study aims to reconstruct the evolutionary history of African shrews referred to the Crocidura olivieri complex. We tested the respective role of forest retraction/expansion during the Pleistocene, rivers (allopatric models), ecological gradients (parapatric model) and anthropogenic factors in explaining the distribution and diversification within this species complex. We sequenced three mitochondrial and four nuclear markers from 565 specimens encompassing the known distribution of the complex, i.e. from Morocco to Egypt and south to Mozambique. We used Bayesian phylogenetic inference, genetic structure analyses and divergence time estimates to assess the phylogenetic relationships and evolutionary history of these animals. The C. olivieri complex (currently composed of C. olivieri, C. fulvastra, C. viaria and C. goliath) can be segregated into eight principal geographical clades, most exhibiting parapatric distributions. A decrease in genetic diversity was observed between central and western African clades and a marked signal of population expansion was detected for a broadly distributed clade occurring across central and eastern Africa and portions of Egypt (clade IV). The main cladogenesis events occurred within the complex between 1.37 and 0.48 Ma. Crocidura olivieri sensu stricto appears polyphyletic and C. viaria and C. fulvastra were not found to be monophyletic. Climatic oscillations over the Pleistocene probably played a major role in shaping the genetic diversity within this species complex. Different factors can explain their diversification, including Pleistocene forest refuges, riverine barriers and differentiation along environmental gradients. The earliest postulated members of the complex originated in central/eastern Africa and the first radiations took place in rain forests of the Congo Basin. A dramatic shift in the ecological requirements in early members of the complex, in association with changing environments, took place sometime after

  11. Evolutionary origin of eukaryotic cells.

    Science.gov (United States)

    Kostianovsky, M

    2000-01-01

    This article reviews literature on the transition from rudimentary prokaryotic life to eukaryotes. An overview of the differences between these organisms and theories of eukaryogenesis are reviewed. Various methods of investigating the transformation from prokaryotes to eukaryotes are elaborated, including the fossil, the molecular and living records, and examples are given. Lastly, the recent molecular studies and the impact on phylogenetic classification for the tree of life, based on molecular evolution, are discussed.

  12. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells.

    Science.gov (United States)

    Francis, Brian R

    2015-02-11

    Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and

  13. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

    Directory of Open Access Journals (Sweden)

    Brian R. Francis

    2015-02-01

    Full Text Available Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid. Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of

  14. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

    Science.gov (United States)

    Francis, Brian R.

    2015-01-01

    Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and

  15. Remembering the evolutionary Freud.

    Science.gov (United States)

    Young, Allan

    2006-03-01

    Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

  16. 比目鱼类的眼睛移位和不对称的进化起源%The eye migration and evolutionary origin of flatfish asymmetry

    Institute of Scientific and Technical Information of China (English)

    鲍宝龙

    2012-01-01

    Asymmetry of flatfish has already caught people’s eye over one century.The research on eye migration is introducted as five sections in this review: diversity and distribution of Pleuronectiformes,the mechanical force driving eye migration,thyroid hormone-dependent signalling pathway in regulating eye migration,the relationship between eye migration and the left/right asymmetry of visceral organs,and evolutionary origin of flatfish asymmetry.My lab’s findings on the genetic mechanism behind eye migration are introducted extensively,such as our important finding that eye migration is driven by proliferating cells in suborbital skin and the twist of frontal bone is dependent upon eye migration,which corrected some mistakes of previous hypothesis.Thyroid hormone-dependent signalling pathway was investigated extensively as well.T3 distribution and expressional location of type 2 deiodinase and thyroid hormone receptor(TRαA and TRβ1) in the skin around both eyes displayed left/right and dorsal/ventral asymmetry pattern,which is similar as observed pattern of proliferating cells in same area in previous study.The TH-dependent signalling pathway in regulating eye migration might be T4-Dio2-T3-TRαA/TRβ1.Finally,we propose a hypothesis on evolutionary origin of flatfish asymmetry,and hope that this could arouse further discussion on the flatfish evolution.%比目鱼类外形不对称产生的机制引起人们兴趣已逾一个多世纪。从比目鱼类(鲽形目)的类群和分布、变态过程中眼睛移位机械力的来源、甲状腺激素调控眼睛移位的信号通路、比目鱼类外形左右不对称与内脏左右不对称两者调控机制之间的关系以及比目鱼类眼睛左右不对称的进化起源等5个方面,系统地介绍了比目鱼类变态发育过程中眼睛移位的研究历史。重点介绍了本实验室提出的关于眼睛移位的组织学模型,以及眼睛移位信号调控途径的最新研究进展。发现并证

  17. Recent Advances in Evolutionary Computation

    Institute of Scientific and Technical Information of China (English)

    Xin Yao; Yong Xu

    2006-01-01

    Evolutionary computation has experienced a tremendous growth in the last decade in both theoretical analyses and industrial applications. Its scope has evolved beyond its original meaning of "biological evolution" toward a wide variety of nature inspired computational algorithms and techniques, including evolutionary, neural, ecological, social and economical computation, etc., in a unified framework. Many research topics in evolutionary computation nowadays are not necessarily "evolutionary". This paper provides an overview of some recent advances in evolutionary computation that have been made in CERCIA at the University of Birmingham, UK. It covers a wide range of topics in optimization, learning and design using evolutionary approaches and techniques, and theoretical results in the computational time complexity of evolutionary algorithms. Some issues related to future development of evolutionary computation are also discussed.

  18. The deep hydrogeologic flow system underlying the Oak Ridge Reservation -- Assessing the potential for active groundwater flow and origin of the brine

    Energy Technology Data Exchange (ETDEWEB)

    Nativ, R. [Hebrew Univ. of Jerusalem (Israel). Dept. of Soil and Water Sciences; Halleran, A.; Hunley, A. [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.

    1997-08-01

    The deep hydrogeologic system underlying the Oak Ridge Reservation (ORR) contains contaminants such as radionuclides, heavy metals, nitrates, and organic compounds. The groundwater in the deep system is saline and has been considered to be stagnant in previous studies. This study was designed to address the following questions: is groundwater in the deep system stagnant; is contaminant migration controlled by diffusion only or is advection a viable mechanism; where are the potential outlet points? On the basis of existing and newly collected data, the nature of saline groundwater flow and potential discharge into shallow, freshwater systems was assessed. Data used for this purpose included (1) spatial and temporal pressures and hydraulic heads measured in the deep system, (2) hydraulic parameters of the formations in question, (3) spatial and temporal temperature variations at depth, and (4) spatial and temporal chemical and isotopic composition of the saline groundwater. The observations suggest that the saline water contained at depth is old but not isolated (in terms of recharge and discharge) from the overlying active, freshwater-bearing units. Influx of recent water does occur. Groundwater volumes involved in this flow are likely to be small. The origin of the saline groundwater was assessed by using existing and newly acquired chemical and isotopic data. The proposed model that best fits the data is modification of residual brine from which halite has been precipitated. Other models, such as ultrafiltration and halite dissolution, were also evaluated.

  19. Origin and assessment of deep groundwater inflow in the Ca' Lita landslide using hydrochemistry and in situ monitoring

    NARCIS (Netherlands)

    Cervi, F.; Ronchetti, F.; Martinelli, G.; Bogaard, T.A.; Corsini, A.

    2012-01-01

    Changes in soil water content, groundwater flow and a rise in pore water pressure are well-known causal or triggering factors for hillslope instability. Rainfall and snowmelt are generally assumed as the main sources of groundwater recharge. This assumption neglects the role of deep water inflow in

  20. The Great Observatories Origins Deep Survey VLT/FORS2 spectroscopy in the GOODS-South Field

    NARCIS (Netherlands)

    Vanzella, E; Cristiani, S; Dickinson, M; Kuntschner, H; Moustakas, LA; Nonino, M; Rosati, P; Stern, D; Cesarsky, C; Ettori, S; Ferguson, HC; Fosbury, RAE; Giavalisco, M; Haase, J; Renzini, A; Rettura, A; Serra, P

    2005-01-01

    We present the first results of the ESO/ GOODS program of spectroscopy of faint galaxies in the Chandra Deep Field South ( CDF- S). 399 spectra of 303 unique targets have been obtained in service mode with the FORS2 spectrograph at the ESO/ VLT, providing 234 redshift determinations ( the median of

  1. Origin and assessment of deep groundwater inflow in the Ca' Lita landslide using hydrochemistry and in situ monitoring

    NARCIS (Netherlands)

    Cervi, F.; Ronchetti, F.; Martinelli, G.; Bogaard, T.A.; Corsini, A.

    2012-01-01

    Changes in soil water content, groundwater flow and a rise in pore water pressure are well-known causal or triggering factors for hillslope instability. Rainfall and snowmelt are generally assumed as the main sources of groundwater recharge. This assumption neglects the role of deep water inflow in

  2. 'Deep is the well of the past': Reconsidering the origins of the Exodus motif in its cultural context

    Directory of Open Access Journals (Sweden)

    Raik Heckl

    2013-09-01

    Full Text Available The article shows, that the stories of the Patriarchs as well as the Exodus-story are allochthonous traditions of origin. We find comparable stories in the neighboring cultures of Israel. Egypt as origin of human culture was of utmost importance in the Levant. Herodotus reports a myth of origin of the Phoenicians which is of particular interest in this respect. As far as it can be seen there are affinities between this tradition and the Exodus motif from the Hebrew Bible. This raises the question if we should read the Biblical traditions as part of the comprehensive cultural context of the Levant.

  3. A possible in situ 3H and 3He source in Earth's interior: an alternative explanation of origin of 3He in deep Earth.

    Science.gov (United States)

    Jiang, Songsheng; Liu, Jing; He, Ming

    2010-07-01

    Origin of (3)He in the Earth is a mystery. Lacking a production mechanism, scientists assume (3)He was trapped in the Earth, when the Earth was formed. In contrast to this assumption, we have found (3)He and (3)H concentrations in excess of the atmospheric values in the deep waters of the volcanic Lakes Pavin (France), Laacher (Germany) and Nemrut (Turkey). This paper reports the result of finding (3)H in these three volcanic lakes that appear to originate from the mantle. Because (3)H has a half-life of 12.3 years, this (3)H and the resulting (3)He must have formed recently in the mantle and not be part of a primordial reservoir. The nuclear reactions that generate tritium might be a source of "missing" energy in the interior of the Earth.

  4. The deep Earth origin of the Iceland plume and its effects on regional surface uplift and subsidence

    Science.gov (United States)

    Barnett-Moore, Nicholas; Hassan, Rakib; Flament, Nicolas; Müller, Dietmar

    2017-02-01

    The present-day seismic structure of the mantle under the North Atlantic Ocean indicates that the Iceland hotspot represents the surface expression of a deep mantle plume, which is thought to have erupted in the North Atlantic domain during the Palaeocene. The spatial and temporal evolution of the plume since its eruption is still highly debated, and little is known about its deep mantle history. Here, we use palaeogeographically constrained global mantle flow models to investigate the evolution of deep Earth flow beneath the North Atlantic since the Jurassic. The models show that over the last ˜ 100 Myr a remarkably stable pattern of convergent flow has prevailed in the lowermost mantle near the tip of the African Large Low-Shear Velocity Province (LLSVP), making it an ideal plume nucleation site. We extract model dynamic topography representative of a plume beneath the North Atlantic region since eruption at ˜ 60 Ma to present day and compare its evolution to available offshore geological and geophysical observations across the region. This comparison confirms that a widespread episode of Palaeocene transient uplift followed by early Eocene anomalous subsidence can be explained by the mantle-driven effects of a plume head ˜ 2500 km in diameter, arriving beneath central eastern Greenland during the Palaeocene. The location of the model plume eruption beneath eastern Greenland is compatible with several previous models. The predicted dynamic topography is within a few hundred metres of Palaeocene anomalous subsidence derived from well data. This is to be expected given the current limitations involved in modelling the evolution of Earth's mantle flow in 3-D, particularly its interactions with the base of a heterogeneous lithosphere as well as short-wavelength advective upper mantle flow, not captured in the presented global models.

  5. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary...

  6. Commentary on "The Evolutionary Origin of Female Orgasm" by M. Pavlicev and G. Wagner, 2016, J. Exp. Zool. (Mol. Dev. Evol.) 326(6):326-337.

    Science.gov (United States)

    Komisaruk, Barry R

    2016-12-01

    Evidence is presented as an alternative to the authors' claims that in the course of evolution, a link between orgasm and ovulation has been lost in women, that evolutionary changes in clitoral anatomy underlie this loss, and that women's orgasm plays no significant role in reproduction.

  7. Origin and distribution of the organic matter in the distal lobe of the Congo deep-sea fan - A Rock-Eval survey

    Science.gov (United States)

    Baudin, François; Stetten, Elsa; Schnyder, Johann; Charlier, Karine; Martinez, Philippe; Dennielou, Bernard; Droz, Laurence

    2017-08-01

    The Congo River, the second largest river in the world, is a major source of organic matter for the deep Atlantic Ocean because of the connection of its estuary to the deep offshore area by a submarine canyon which feeds a vast deep-sea fan. The lobe zone of this deep-sea fan is the final receptacle of the sedimentary inputs presently channelled by the canyon and covers an area of 2500 km². The quantity and the source of organic matter preserved in recent turbiditic sediments from the distal lobe of the Congo deep-sea fan were assessed using Rock-Eval pyrolysis analyses. Six sites, located at approximately 5000 m water-depth, were investigated. The mud-rich sediments of the distal lobe contain high amounts of organic matter ( 3.5 to 4% Corg), the origin of which is a mixture of terrestrial higher-plant debris, soil organic matter and deeply oxidized phytoplanktonic material. Although the respective contribution of terrestrial and marine sources of organic matter cannot be precisely quantified using Rock-Eval analyses, the terrestrial fraction is dominant according to similar hydrogen and oxygen indices of both suspended and bedload sediments from the Congo River and that deposited in the lobe complex. The Rock-Eval signature supports the 70% to 80% of the terrestrial fraction previously estimated using C/N and δ13Corg data. In the background sediment, the organic matter distribution is homogeneous at different scales, from a single turbiditic event to the entire lobe, and changes in accumulation rates only have a limited effect on the quantity and quality of the preserved organic matter. Peculiar areas with chemosynthetic bivalves and/or bacterial mats, explored using ROV Victor 6000, show a Rock-Eval signature similar to background sediment. This high organic carbon content associated to high sedimentation rates (> 2 to 20 mm.yr-1) in the Congo distal lobe complex implies a high burial rate for organic carbon. Consequently, the Congo deep-sea fan represents an

  8. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness...

  9. The phylogeny of a species-level tendency: species heritability and possible deep origins of Bergmann's rule in tetrapods.

    Science.gov (United States)

    De Queiroz, Alan; Ashton, Kyle G

    2004-08-01

    One of the most widely recognized generalizations in biology is Bergmann's rule, the observation that, within species of birds and mammals, body size tends to be inversely related to ambient temperature. Recent studies indicate that turtles and salamanders also tend to follow Bergmann's rule, which hints that this species-level tendency originated early in tetrapod history. Furthermore, exceptions to Bergmann's rule are concentrated within squamate reptiles (lizards and snakes), suggesting that the tendency to express a Bergmann's rule cline may be heritable at the species level. We evaluated species-level heritability and early origination of Bergmann's rule by mapping size-latitude relationships for 352 species onto a tetrapod phylogeny. When the largest available dataset is used, Bergmann's rule shows significant phylogenetic signal, indicating species-level heritability. This represents one of the few demonstrations of heritability for an emergent species-level property and the first for an ecogeographic rule. When species are discretely coded as showing either Bergmann's rule or its converse, parsimony reconstructions suggest that: (1) the tendency to follow Bergmann's rule is ancestral for tetrapods, and (2) most extant species that express the rule have retained this tendency from that ancient ancestor. The first inference also generally holds when the discrete data or size-latitude correlation coefficients are analyzed using maximum likelihood, although the results are only statistically significant for some versions of the discrete analyses. The best estimates of ancestral states suggest that the traditional adaptive explanation for Bergmann's rule-conservation of metabolic heat-was not involved in the origin of the trait since that origin predates the evolution of endothermy. A more general thermoregulatory hypothesis could apply to endotherms and some ectotherms, but fails to explain why salamanders have retained Bergmann's rule. Thus, if

  10. Origin of arc-like continental basalts: Implications for deep-Earth fluid cycling and tectonic discrimination

    Science.gov (United States)

    Wang, Xuan-Ce; Wilde, Simon A.; Xu, Bei; Pang, Chong-Jin

    2016-09-01

    Continental basalts generally display enrichment of fluid-mobile elements and depletion of high-field-strength elements, similar to those that evolved in the subduction environment, but different from oceanic basalts. Based on the continental flood basalt database for six large igneous provinces, together with rift-related basalt data from the Basin and Range Province, this study aimed to test the validity of geochemical tectonic discrimination diagrams in distinguishing arc-like intra-continental basalts from arc basalts and to further investigate the role of deep-Earth water cycling in producing arc-like signatures in large-scale intra-continental basalts. Our evaluation shows that arc-like intra-continental basalts can be distinguished from arc basalts by integrating the following factors: (1) the FeO, MgO, and Al2O3 concentrations of the primary melt; (2) Tisbnd V, Zrsbnd Zr/Y, Zrsbnd Ti, and Ti/Vsbnd Zr/Smsbnd Sr/Nd discrimination diagrams; (3) the coexistence of arc-like and OIB-like subtype basalts within the same province; (4) primitive mantle-normalized trace element distribution patterns. The similarity of enrichment in fluid-mobile elements (Ba, Rb, Sr, U, and K) between arc-like and true arc basalts suggests the importance of water flux melting in producing arc-like signatures in continental basalts. Experimentally determined liquid lines of descent (LLD) imply high magma water concentrations for continental flood basalts (CFBs) and the Basin and Range basalts. Furthermore, estimates based on the Al2O3-LLD method indicates 4.0-5.0 wt% pre-eruptive magma H2O concentration for CFBs and the Basin and Range basalts. The tight relationships between H2O/Ce and Ba/La, Ba/Nb and Rb/Nb based on global arc basalt data were further used to estimate the primary H2O concentrations. With the exception of the Emeishan CFBs (mainly containing 4.0-5.6 wt% H2O), all other CFBs investigated have similar estimated primary H2O contents, with values ranging from 1.0 to 2

  11. The Origin of Voluminous Dacite (vs. Andesite) at Mature, Thick Continental Arcs: A Reflection of Processes in the Deep Crust

    Science.gov (United States)

    Lange, R. A.

    2013-12-01

    An outstanding question is why some continental arc segments are characterized by voluminous eruptions of dacite (65-70 wt% SiO2), whereas others erupt more andesite (58-64 wt% SiO2) than any other magma type. An example of the former is the Altiplano-Puna region of the central Andean arc, which has erupted a predominance of dacite over all magma types 10-1 Ma (de Silva, 1989). In contrast, a 200-km arc segment of the Mexican volcanic arc (Michoacán-Guanajuato arc segment) has erupted ~75% andesite, ~26% basaltic andesite and 20%) of hornblende-rich (~40%) gabbronorite in the deep crust, driven by mantle-derived basalt intrusions at depths of 30-40 km. The absence of any dacite or rhyolite along this arc segment indicates that interstitial liquid from crystal-rich andesites never segregated to form eruptible magma. Thus, little upper-crust differentiation occurred along this arc segment. On the basis of phase-equilibrium experiments in the literature (e.g., Sisson et al., 2005), it is proposed that rhyolite and dacite did form during partial melting of the lower arc crust, but at melt fractions too low (≤15%) to permit efficient transport to the upper crust (Vigneresse and Tikoff, 1999). It is further proposed that the reason why dacite is so abundant at mature thick continental arcs (e.g., Altiplano-Puno complex) may be because mantle-derived basalts are primarily emplaced at similar depths (~30-40 km) in continental arc crustal columns. If so, in the central Andean arc, a depth of 30-40 km is within the middle dioritic crust (Graeber and Asch, 1999). Partial melts of hornblende diorite (vs. hornblende gabbro) are predicted to be dacitic (vs. andesitic) at melt fractions of 20-25%, which permits transport to the upper crust. It is therefore proposed that it is deep crustal processes that determine whether andesite or dacite is the most voluminous magma type emplaced into the upper crust and erupted at arcs.

  12. Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases

    Directory of Open Access Journals (Sweden)

    Aravind L

    2003-01-01

    Full Text Available Abstract Background The eukaryotic RNA-dependent RNA polymerase (RDRP is involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing. This enzyme is highly conserved in most eukaryotes but is missing in archaea and bacteria. No evolutionary relationship between RDRP and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery. Results Using extensive sequence profile searches, we identified bacteriophage homologs of the eukaryotic RDRP. The comparison of the eukaryotic RDRP and their homologs from bacteriophages led to the delineation of the conserved portion of these enzymes, which is predicted to harbor the catalytic site. Further, detailed sequence comparison, aided by examination of the crystal structure of the DNA-dependent RNA polymerase (DDRP, showed that the RDRP and the β' subunit of DDRP (and its orthologs in archaea and eukaryotes contain a conserved double-psi β-barrel (DPBB domain. This DPBB domain contains the signature motif DbDGD (b is a bulky residue, which is conserved in all RDRPs and DDRPs and contributes to catalysis via a coordinated divalent cation. Apart from the DPBB domain, no similarity was detected between RDRP and DDRP, which leaves open two scenarios for the origin of RDRP: i RDRP evolved at the onset of the evolution of eukaryotes via a duplication of the DDRP β' subunit followed by dramatic divergence that obliterated the sequence similarity outside the core catalytic domain and ii the primordial RDRP, which consisted primarily of the DPBB domain, evolved from a common ancestor with the DDRP at a very early stage of evolution, during the RNA world era. The latter hypothesis implies that RDRP had been subsequently eliminated from cellular life forms and might have been reintroduced into the eukaryotic genomes through a bacteriophage. Sequence and structure analysis of the DDRP led to further insights into the

  13. The Great Observatories Origins Deep Survey - VLT/FORS2 Spectroscopy in the GOODS-South Field

    CERN Document Server

    Vanzella, E; Dickinson, M; Kuntschner, H; Moustakas, L A; Nonino, M; Rosati, P; Stern, D; Césarsky, C J; Ettori, S; Ferguson, H C; Fosbury, R A E; Giavalisco, M; Haase, J; Renzini, A; Rettura, A; Serra, P

    2004-01-01

    We present the first results of the ESO/GOODS program of spectroscopy of faint galaxies in the Chandra Deep Field South (CDF-S). 399 spectra of 303 unique targets have been obtained in service mode with the FORS2 spectrograph at the ESO/VLT, providing 234 redshift determinations (the median of the redshift distribution is at 1.04). The typical redshift uncertainty is estimated to be sig(z) ~ 0.001. Galaxies have been color selected in a way that the resulting redshift distribution typically spans from z=0.5 to 2. The reduced spectra and the derived redshifts are released to the community through the ESO web page http://www.eso.org/science/goods/ Large scale structure is clearly detected at z ~ 0.67, 0.73, 1.10 and 1.61. Three Lyman-break galaxies have also been included as targets and are confirmed to have redshifts z=4.800, 4.882 and 5.828. In a few cases, we observe clear [OII]3727 rotation curves, even at the relatively low resolution (R = 860) of the present observations. Assuming that the observed veloci...

  14. The Great Observatories Origins Deep Survey VLT/FORS2 Spectroscopy in the GOODS-South Field: Part II

    CERN Document Server

    Vanzella, E; Dickinson, M; Kuntschner, H; Nonino, M; Rettura, A; Rosati, P; Vernet, J; Césarsky, C J; Ferguson, H C; Fosbury, R A E; Giavalisco, M; Haase, J; Moustakas, L A; Popesso, P; Renzini, A; Stern, D; Team, the GOODS

    2006-01-01

    We present the second campaign of the ESO/GOODS program of spectroscopy of faint galaxies in the Chandra Deep Field South (CDF-S). Objects were selected as candidates for VLT/FORS2 observations primarily based on the expectation that the detection and measurement of their spectral features would benefit from the high throughput and spectral resolution of FORS2. The reliability of the redshift estimates is assessed using diagnostic diagrams and comparing the results with public data. 807 spectra of 652 individual targets have been obtained in service mode with the FORS2 spectrograph at the ESO/VLT, providing 501 redshift determinations. The typical redshift uncertainty is estimated to be sigma_z ~ 0.0009. Galaxies have been color selected in a way that the resulting redshift distribution typically spans two redshift domains: from z=0.5 to 2 and z=3.5 to 6.2. In particular, 94 B435-,V606-,i775-"dropout" Lyman break galaxies have been observed, yielding redshifts for 64 objects in the interval 3.4

  15. Sample classification for improved performance of PLS models applied to the quality control of deep-frying oils of different botanic origins analyzed using ATR-FTIR spectroscopy.

    Science.gov (United States)

    Kuligowski, Julia; Carrión, David; Quintás, Guillermo; Garrigues, Salvador; de la Guardia, Miguel

    2011-01-01

    The selection of an appropriate calibration set is a critical step in multivariate method development. In this work, the effect of using different calibration sets, based on a previous classification of unknown samples, on the partial least squares (PLS) regression model performance has been discussed. As an example, attenuated total reflection (ATR) mid-infrared spectra of deep-fried vegetable oil samples from three botanical origins (olive, sunflower, and corn oil), with increasing polymerized triacylglyceride (PTG) content induced by a deep-frying process were employed. The use of a one-class-classifier partial least squares-discriminant analysis (PLS-DA) and a rooted binary directed acyclic graph tree provided accurate oil classification. Oil samples fried without foodstuff could be classified correctly, independent of their PTG content. However, class separation of oil samples fried with foodstuff, was less evident. The combined use of double-cross model validation with permutation testing was used to validate the obtained PLS-DA classification models, confirming the results. To discuss the usefulness of the selection of an appropriate PLS calibration set, the PTG content was determined by calculating a PLS model based on the previously selected classes. In comparison to a PLS model calculated using a pooled calibration set containing samples from all classes, the root mean square error of prediction could be improved significantly using PLS models based on the selected calibration sets using PLS-DA, ranging between 1.06 and 2.91% (w/w).

  16. [Schizophrenia and evolutionary psychopathology].

    Science.gov (United States)

    Kelemen, Oguz; Kéri, Szabolcs

    2007-01-01

    Evolution can shape any characteristic appearing as a phenotype that is genetically rooted and possesses a long history. The stress-diathesis model suggests that psychiatric disorders have some genetic roots, and therefore the theory of evolution may be relevant for psychiatry. Schizophrenia is present in every human culture with approximately the same incidence. The great evolutionary paradox is: how can such illness persist despite fundamental reproductive disadvantages? Since the 1960s, several evolutionary explanations have been raised to explain the origins of schizophrenia. This article reviews all the major evolutionary theories about the possible origins of this disease. On the one hand, some researchers have proposed that schizophrenia is an evolutionary disadvantageous byproduct of human brain evolution (e.g. the evolution of hemispheric specialization, social brain or language skills). On the other hand, others have suggested that a compensatory advantage must exist either in the biological system of patients with schizophrenia (e.g. resistance against infectious diseases), or within the social domain (e.g. greater creativity of the relatives). According to some theories, shamanism and religion demonstrate some similarities to psychosis and provide clues regarding the origins of schizophrenia. At the end of this article we discuss this last theory in detail listing arguments for and against.

  17. Deep XMM Observations of Draco rule out a dark matter decay origin for the 3.5 keV line

    CERN Document Server

    Jeltema, Tesla E

    2015-01-01

    We searched for an X-ray line at energies around 3.5 keV in deep, ~1.6 Msec XMM-Newton observations of the dwarf spheroidal galaxy Draco. No line was found. The data in this energy range are completely consistent with a simple power law X-ray background, dominated by particle background, plus instrumental lines; the addition of a ~3.5 keV line feature gives no improvement to the fit. The corresponding upper limit on the line flux rules out a dark matter decay origin for the 3.5 keV line found in observations of clusters of galaxies and in the Galactic Center at greater than 99% C.L..

  18. Impact of weathering on the geomechanical properties of rocks along thermal metamorphic contact belts and morpho-evolutionary processes: The deep-seated gravitational slope deformations of Mt. Granieri Salincriti (Calabria Italy)

    Science.gov (United States)

    Pellegrino, A.; Prestininzi, A.

    2007-06-01

    Numerous Deep-Seated Gravitational Slope Deformations (DSGSDs) occur throughout Italy, that originate from particular tectono-stratigraphic settings, relief, seismicity, deglaciation, as well as from intense and deep processes of chemico-physical weathering of crystalline-metamorphic rocks. These DSGSDs are particularly widespread in the Calabrian mountains. This study is focused on the Mt. Granieri-Salincriti slope, on the Ionian side of the Serre Massif, where granites and granodiorites (Stilo Unit, Palaeozoic) are in contact with metamorphites through a thermal-metamorphic aureole. This setting generates deep geochemical processes, inducing intense chemical weathering. These processes are mainly due to the interaction between groundwater and the sulphides that are contained in the local pegmatitic-hydrothermal intrusions, especially along the thermal-metamorphic contact belt. The Mt. Granieri-Salincriti slope has an important DSGSD, which is associated with many active and/or quiescent landslides. Among these landslides, the Salincriti rock avalanche-debris flow (about 2 M m 3) represents the paroxysmal and terminal stage of the deep creep deformations of Mt. Granieri, typifying a geological setting that is common in the Calabrian Arc. This multi-disciplinary study assessed the weathering susceptibility of the local crystalline-metamorphic rocks, especially those lying along thermal-metamorphic contact belts, by characterising the weathering horizons and the spatial distribution of weathering in the rock mass. The study was also aimed at identifying the relations between weathering, above all deep geochemical processes, effects on rocks and slope morphodynamics. The methodology was based on detailed geological data, geological-engineering surveys, geomorphology and surface hydrogeology analyses, as well as physico-mechanical laboratory tests. These investigations, supported by a monitoring program, led to the development of an engineering-geological model of the

  19. Origin and age of deep waters of the Paris Basin; Origine et age des eaux profondes du bassin de Paris par l`utilisation des traceurs chimiques et isotopiques

    Energy Technology Data Exchange (ETDEWEB)

    Matray, J.M.; Chery, L. [Bureau de Recherches Geologiques et Minieres (BRGM), 45 - Orleans (France)

    1998-12-31

    The origin and age of deep waters of the Paris Basin are considered on the basis of chemical and isotopic analyses carried out on almost 150 water samples collected from geothermal wells, oil wells, and Middle Jurassic and LATE Triassic aquifers. The studies reveal that currently only Cl, Br, {sup 2}H and {sup 18}O species are present in the three aquifers, although one of the original waters previously enriched in oxygen- 18 probably due to a temperature effect. The combination of Cl/Br ratios and stable isotopes reveals the complex origin of these aqueous solutions that result from the mixing of two distinct secondary brines formed by the dissolution of Triassic salt by meteoric water. The first brine was derived from an ancient meteoric water that had undergone oxygen- 18 enrichment. The second brine has the same origin as the first, but its isotopic composition has remained constant since infiltration. The evolution of these waters within the framework of the geological history of the Paris Basin suggests that the first generation of brine is sequential to exposure of the reservoir rocks in the east at the beginning of the Cenozoic, and that it is older that the general cooling of the basin at the end of the Oligocene. Vertical fluid transfer along faults also took place during this period which also explains the presence of hydrocarbons and late carbonate cements in the Dogger aquifer. The maximum outcropping in the east initiated the formation of the second brine which mixed with the already existing brine, traces of which can only be detected in the deepest parts of the Triassic aquifers. The addition of meteoric water, unaffected by salt dissolution, is responsible for the present salinity distribution in the three aquifers. (authors) 21 refs.

  20. Evolutionary embryology resurrected in Japan with a new molecular basis: Nori Satoh and the history of ascidian studies originating in Kyoto during the 20th century.

    Science.gov (United States)

    Kuratani, Shigeru; Wada, Hiroshi; Kusakabe, Rie; Agata, Kiyokazu

    2006-01-01

    This article briefly summarizes the scientific contributions of Nori Satoh, the winner of the 2005 edition of the Kowalevsky Medal, to Developmental Biology and especially to Evo-Devo with his 30 years of research on tunicates - a primitive chordate species. His research began with his pure developmental interest in the clock mechanism of cell differentiation and later expanded into various aspects of evolutionary and developmental phenomena. He is not only known as a founder of molecular biology-based tunicate studies, but also for his world-wide service to education and his prestigious publications in international scientific journals.

  1. A comparative examination of neural circuit and brain patterning between the lamprey and amphioxus reveals the evolutionary origin of the vertebrate visual center.

    Science.gov (United States)

    Suzuki, Daichi G; Murakami, Yasunori; Escriva, Hector; Wada, Hiroshi

    2015-02-01

    Vertebrates are equipped with so-called camera eyes, which provide them with image-forming vision. Vertebrate image-forming vision evolved independently from that of other animals and is regarded as a key innovation for enhancing predatory ability and ecological success. Evolutionary changes in the neural circuits, particularly the visual center, were central for the acquisition of image-forming vision. However, the evolutionary steps, from protochordates to jaw-less primitive vertebrates and then to jawed vertebrates, remain largely unknown. To bridge this gap, we present the detailed development of retinofugal projections in the lamprey, the neuroarchitecture in amphioxus, and the brain patterning in both animals. Both the lateral eye in larval lamprey and the frontal eye in amphioxus project to a light-detecting visual center in the caudal prosencephalic region marked by Pax6, which possibly represents the ancestral state of the chordate visual system. Our results indicate that the visual system of the larval lamprey represents an evolutionarily primitive state, forming a link from protochordates to vertebrates and providing a new perspective of brain evolution based on developmental mechanisms and neural functions. © 2014 Wiley Periodicals, Inc.

  2. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

    Full Text Available In this article, we advance the concept of “evolutionary awareness,” a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities—which we refer to as “intergenerational extended phenotypes”—by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  3. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  4. Evolutionary awareness.

    Science.gov (United States)

    Gorelik, Gregory; Shackelford, Todd K

    2014-08-27

    In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  5. The origin of life near deep-sea hydrothermal systems during the Cambrian explosion: data from the Kyzyl Tashtyg sulphide deposit (Central Asia)

    Science.gov (United States)

    Simonov, Vladimir; Terleev, Alexander; Safonova, Inna; Kotlyarov, Alexey; Stupakov, Sergey; Tokarev, Dmitry

    2015-04-01

    On Earth the solar radiation and the hydrothermal circulation both affect life evolution. Recent extensive studies of the World Ocean have shown that the biodiversity of Earth is linked with hydrothermal activity on the oceanic floor. These deep-sea ecosystems use chemical energy, not solar radiation. In the last quarter of the XX century, a new type of hydrothermal systems, so-called black smokers, was discovered in mid-oceanic ridges. As black smokers form sulfide ores and are surrounded by abundant bio-oases or symbioses, identification of their analogues in ancient orogenic belts is necessary for studying life origin and evolution. Of special importance are problems of life associated with deep-sea hydrothermal systems acted at the Precambrian-Cambrian boundary - the time of Cambrian explosion (Maruyama et al., 2013). During that explosion life significantly evolved and diversified due to dramatic changes of Earth's environment. Consequently, the early Cambrian - late Precambrian Kyzyl Tashtyg sulphide deposit of East Tuva in the Central Asian Orogenic Belt is of special interest. This deposit was formed on the bottom of ancient back-arc deep-sea basin as a result of black smoker hydrothermal activity and is hosted by volcanogenic-sedimentary rocks altered by the high temperature solutions. The altered Kyzyl Tashtyg basalts have an amygdules (filled by albite, epidote and carbonates), contain brown-green microfossils, often attached to their walls. The microfossils are thin tubes 5 to 25 microns in diameter and 500 microns long. This tubes are empty and have straight, curved or branching shape. Chemically, the tube material is close to epidote. In consideration of microscopic dimensions, simple morphology and similarity with modern tubular microorganisms, the studied tube-shaped microfossils can be related to cyanobacteria. Almost the same fossils, associated with oceanic basalt complexes, were described earlier (Furnes et al., 2007; Mcloughlin et al., 2007

  6. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover......, they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical...... expectations emphasizes not only that causal structure changes are common in social systems but also that causal structures in social systems, and expectations about them, develop together....

  7. Evolution Born of Moisture: Analogies and Parallels Between Anaximander's Ideas on Origin of Life and Man and Later Pre-Darwinian and Darwinian Evolutionary Concepts.

    Science.gov (United States)

    Kočandrle, Radim; Kleisner, Karel

    2013-01-01

    This study focuses on the origin of life as presented in the thought of Anaximander of Miletus but also points to some parallel motifs found in much later conceptions of both the pre-Darwinian German romantic science and post-Darwinian biology. According to Anaximander, life originated in the moisture associated with earth (mud). This moist environment hosted the first living creatures that later populated the dry land. In these descriptions, one can trace the earliest hints of the notion of environmental adaptation. The origin of humans was seen as connected in some way with fish: ancient humans were supposed to have developed inside fish-like animals. Anaximander took into account changes in the development of living creatures (adaptations) and speculated on the origins of humans. Similar ideas are found also in the writings of much later, eighteenth and nineteenth century authors who were close to the tradition of German romantic science. We do not argue that these later concepts are in any way directly linked with those of the pre-Socratics, but they show surprising parallels in, e.g., the hypothesis that life originated in a moist environment or the supposition that human developed from fish-like ancestors. These transformations are seen as a consequence of timeless logic rather than as evolution in historical terms. Despite the accent on the origin of living things, both Anaximander and the later Naturphilosophen lack in their notions the element most characteristic of Darwin's thought, that is, the emphasis on historicity and uniqueness of all that comes into being.

  8. Deep trees: Woodfall biodiversity dynamics in present and past oceans

    Science.gov (United States)

    Sigwart, Julia D.

    2017-03-01

    Marine deposits of sunken wood provide an important habitat for deep-sea biota, including an extensive wood-endemic invertebrate fauna. These habitats are important in their own right; many species on organic falls are not able to survive in other deep sea ecosystems. Evolutionary transitions of species among various chemosynthesis-based ecosystems does not proceed deliberately from organic falls toward hydrothermal vents. Polyplacophoran molluscs (chitons) are generally rare in deep-sea systems but are found in comparatively high diversity and abundance on tropical sunken wood. A new time-calibrated phylogeny for the predominantly deep-sea order Lepidopleurida shows the chiton lineages found in sunken wood habitats do not comprise a single clade or radiation, but represents a minimum of three independent radiations in the Pacific alone. Most marine invertebrate groups diversified in the deep sea following the end Cretaceous extinction event; by contrast, sunken-wood chitons may have persisted in these habitats for longer than other animals. Fossil chitons from the early Carboniferous (ca. 350 Mya) have strong similarities to modern wood-endemic taxa, yet the common ancestor of living Lepidopleurida occurred much later in the Triassic and did not apparently rely on woodfall. Clades within Lepidopleurida that occupy wood habitats in the tropical Pacific probably arose in the Jurassic, which corresponds to evidence from the fossil record, but with an additional separate colonisation more recently in the early Paleogene. Wood-endemic chiton species encompass multiple independent evolutionary origins of co-occurring wood species, and these separate lineages correspond to differences in micohabitat and feeding strategies. These patterns demonstrate the ongoing evolutionary linkages between terrestrial and deep marine environments, and the opportunistic adaptations of deep-sea organisms.

  9. They Came From the Deep in the Supernova: The Origin of TiC and Metal Subgrains in Presolar Graphite Grains

    CERN Document Server

    Lodders, K

    2006-01-01

    A new formation scenario for TiC and Fe,Ni-metal inclusions in presolar graphite grains of supernova origin is described. The mineralogy and chemistry require condensation of (Fe,Ni)-titanides from Fe, Ni, and Ti-rich gaseous ejecta, subsequent carburization to make TiC and metal, and encapsulation into graphite. Titanides only condense if Si is depleted relative to heavier mass elements, which requires alpha-rich freeze-out and a deep mass-cut for the supernova ejecta. This Si-poor core material must remain unmixed with other supernova zones until the titanides condensed. This can be accomplished by transport of core ejecta in bipolar jets through the major expanding supernova zone ejecta. If the jets stall in regions dominated by C-rich ejecta such as C-He zone where graphite condenses, thermochemically favored in situ carburization of the titanides - either before or during encapsulation into condensing graphite - leads to a TiC and metal composite. This scenario agrees with theoretical models and observat...

  10. The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates

    Directory of Open Access Journals (Sweden)

    Pesole Graziano

    2007-11-01

    Full Text Available Abstract Background When orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such as the identification of the forces that shape gene structure during evolution, although the functional constraints involved may vary in different genes and lineages. Results We identified and annotated in the MitoComp2 dataset the orthologs of 68 nuclear genes controlling oxidative phosphorylation in 11 Drosophilidae species and in five non-Drosophilidae insects, and compared them with each other and with their counterparts in three vertebrates (Fugu rubripes, Danio rerio and Homo sapiens and in the cnidarian Nematostella vectensis, taking into account conservation of gene structure and regulatory motifs, and preservation of gene paralogs in the genome. Comparative analysis indicates that the ancestral insect OXPHOS genes were intron rich and that extensive intron loss and lineage-specific intron gain occurred during evolution. Comparison with vertebrates and cnidarians also shows that many OXPHOS gene introns predate the cnidarian/Bilateria evolutionary split. The nuclear respiratory gene element (NRG has played a key role in the evolution of the insect OXPHOS genes; it is constantly conserved in the OXPHOS orthologs of all the insect species examined, while their duplicates either completely lack the element or possess only relics of the motif. Conclusion Our observations reinforce the notion that the common ancestor of most animal phyla had intron-rich gene, and suggest that changes in the pattern of expression of the gene facilitate the fixation of duplications in the genome and the development of novel genetic functions.

  11. The great struggles of life: Darwin and the emergence of evolutionary psychology.

    Science.gov (United States)

    Buss, David M

    2009-01-01

    Darwin envisioned a scientific revolution for psychology. His theories of natural and sexual selection identified two classes of struggles--the struggle for existence and the struggle for mates. The emergence of evolutionary psychology and related disciplines signals the fulfillment of Darwin's vision. Natural selection theory guides scientists to discover adaptations for survival. Sexual selection theory illuminates the sexual struggle, highlighting mate choice and same-sex competition adaptations. Theoretical developments since publication of On the Origin of Species identify important struggles unknown to Darwin, notably, within-families conflicts and conflict between the sexes. Evolutionary psychology synthesizes modern evolutionary biology and psychology to penetrate some of life's deep mysteries: Why do many struggles center around sex? Why is social conflict pervasive? And what are the mechanisms of mind that define human nature? 2009 APA, all rights reserved

  12. Oxygen isotopes and volatile contents of the Gorgona komatiites, Colombia: A confirmation of the deep mantle origin of H2O

    Science.gov (United States)

    Gurenko, Andrey A.; Kamenetsky, Vadim S.; Kerr, Andrew C.

    2016-11-01

    values for melt inclusions also support the deep mantle origin of H2O (and probably other volatiles) in the Gorgona mafic and ultramafic magmas.

  13. Evolutionary thinking

    OpenAIRE

    Hunt, Tam

    2015-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this de...

  14. 昆虫孤雌生殖起源的遗传机制和进化意义%Genetic mechanism and evolutionary significance of the origin of parthenogenetic insects

    Institute of Scientific and Technical Information of China (English)

    王成业

    2011-01-01

    孤雌生殖在昆虫纲中有很高的发生比例,昆虫的孤雌生殖能力是造成农林灾害的一个重要而常被忽视的因素.孤雌生殖物种的存在和维持在进化生物学领域是个令人困惑的话题.在一些物种中孤雌生殖的细胞学机制得到了研究和解释,但是对于从两性生殖转换到孤雌生殖的遗传机制却知之甚少.了解孤雌生殖起源的遗传机制和进化意义对于预防农林虫害有着重要的意义.因此,该文就近年来对昆虫孤雌生殖起源的遗传和进化意义的研究做以综述,并就可能的利用前景进行简单讨论.%There is a high proportion of parthenogenesis in insecta, and the parthenogenetic potential of insects is an important but often ignored threaten factor for the agricultural and forestry production. The maintenance of parthenogenetic species is a puzzling issue in evolutionary biology. In recent years, although the cellular mechanisms during parthenogenesis in some species have been well studied, the underlying genetic mechanisms that cause the switch from sexual reproduction to parthenogenesis have not been defined. While, understanding the genetic mechanism and evolutionary significance of the origin of parthenogenetic insects is crucial for preventing the pests in agricultural and forestry production. Here we summarized recent studies aimed at identifying the underlying genetic mechanism of parthenogenesis in insects, and briefly discussed its potential application in this filed.

  15. Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation.

    Science.gov (United States)

    Laumer, Christopher E; Hejnol, Andreas; Giribet, Gonzalo

    2015-03-12

    Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked 'microturbellarian' groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.

  16. A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code

    Directory of Open Access Journals (Sweden)

    Higgs Paul G

    2009-04-01

    Full Text Available Abstract Background The arrangement of the amino acids in the genetic code is such that neighbouring codons are assigned to amino acids with similar physical properties. Hence, the effects of translational error are minimized with respect to randomly reshuffled codes. Further inspection reveals that it is amino acids in the same column of the code (i.e. same second base that are similar, whereas those in the same row show no particular similarity. We propose a 'four-column' theory for the origin of the code that explains how the action of selection during the build-up of the code leads to a final code that has the observed properties. Results The theory makes the following propositions. (i The earliest amino acids in the code were those that are easiest to synthesize non-biologically, namely Gly, Ala, Asp, Glu and Val. (ii These amino acids are assigned to codons with G at first position. Therefore the first code may have used only these codons. (iii The code rapidly developed into a four-column code where all codons in the same column coded for the same amino acid: NUN = Val, NCN = Ala, NAN = Asp and/or Glu, and NGN = Gly. (iv Later amino acids were added sequentially to the code by a process of subdivision of codon blocks in which a subset of the codons assigned to an early amino acid were reassigned to a later amino acid. (v Later amino acids were added into positions formerly occupied by amino acids with similar properties because this can occur with minimal disruption to the proteins already encoded by the earlier code. As a result, the properties of the amino acids in the final code retain a four-column pattern that is a relic of the earliest stages of code evolution. Conclusion The driving force during this process is not the minimization of translational error, but positive selection for the increased diversity and functionality of the proteins that can be made with a larger amino acid alphabet. Nevertheless, the code that results is one

  17. Do Deep Nets Really Need to be Deep?

    OpenAIRE

    Ba, Lei Jimmy; Caruana, Rich

    2013-01-01

    Currently, deep neural networks are the state of the art on problems such as speech recognition and computer vision. In this extended abstract, we show that shallow feed-forward networks can learn the complex functions previously learned by deep nets and achieve accuracies previously only achievable with deep models. Moreover, in some cases the shallow neural nets can learn these deep functions using a total number of parameters similar to the original deep model. We evaluate our method on th...

  18. Origin of the deep fluids in the paleosubduction zones in western Tianshan: Evidence from Pb- and Sr-isotope compositions of high-pressure veins and host rocks

    Institute of Scientific and Technical Information of China (English)

    HUANG; Dezhi; GAO; Jun; DAI; Tageng; ZOU; Haiyang; XIONG; X

    2005-01-01

    Fluids in the deep subduction zones play an important role in crust-mantle exchange related to the subduction process. Identification of fluids origin, internal or external, can help us to evaluate the contribution of crust materials to mantle during this process. High-pressure veins, which developed in the western Tianshan HP-metamorphic belt extensively, are the direct products of the fluids in subduction zones. In western Tianshan, high-pressure veins and host rocks have overall Pb- and Sr-isotope compositions. At t = 340 Ma, the high-pressure metamorphic time, the ratios of 206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb and 87Sr/86Sr of high pressure veins are 17.122―18.431, 15.477―15.611, 37.432―38.689 and 0.70529―0.70705, and are 17.605―17.834, 15.508―15.564, 37.080―38.145 and 0.70522―0.70685 for host rocks. However, high-pressure veins show a much larger variation in Pb-isotope compositions than host rocks. Plots of samples are distributed roughly along a line parallel to and far away from the Northern Hemisphere reference line (NHRL) on the plot of 206Pb/204Pb vs 207Pb/204Pb. On the plot of 206Pb/204Pb vs 208Pb/204Pb, plots of data are distributed nearby mid-ocean-ridge basalts (MORB) area or along a line parallel to and not far away from NHRL, which shows that the data plots are farther away from MORB and ocean island basalts (OIB) areas on the plot of 206Pb/204Pb vs 207Pb/204Pb than on the plot of 206Pb/204Pb vs 208Pb/204Pb. The compositions of Pb- and Sr-isotopes of these high-pressure metamorphic rocks are between that of enriched mantle 1(EMI) and of sediments or upper crust. A notable characteristic can be seen from plots of Pb-isotope ratio vs Pb-isotope ratio and 206Pb/204Pb vs 87Sr/86Sr that array of plots shows an evident tendency of mixture of two end members. Ratios of Rb/Ba, Ce/Pb, Nb/U and Ta/U of high-pressure veins and host rocks are between that of OIB or MORB and that of continental crust, which indicates that continental crust

  19. An introduction to comparative evolutionary psychology.

    Science.gov (United States)

    Vonk, Jennifer; Shackelford, Todd K

    2013-07-18

    Previously we (Vonk and Shackelford, 2012, in press) proposed an integration of comparative psychology and evolutionary psychology into a new field of "comparative evolutionary psychology." This integrative discipline incorporates principles from ethology, ecology, biology, anthropology, and psychology, broadly defined. We present in this special issue a collection of original empirical and theoretical review articles in which leading researchers propose ways to successfully integrate comparative and evolutionary approaches within their particular areas of study. We showcase the key contributions of these articles and highlight several empirical and theoretical challenges, as well as key future directions, for comparative evolutionary psychology.

  20. An Introduction to Comparative Evolutionary Psychology

    Directory of Open Access Journals (Sweden)

    Jennifer Vonk

    2013-07-01

    Full Text Available Previously we (Vonk and Shackelford, 2012, in press proposed an integration of comparative psychology and evolutionary psychology into a new field of “comparative evolutionary psychology.” This integrative discipline incorporates principles from ethology, ecology, biology, anthropology, and psychology, broadly defined. We present in this special issue a collection of original empirical and theoretical review articles in which leading researchers propose ways to successfully integrate comparative and evolutionary approaches within their particular areas of study. We showcase the key contributions of these articles and highlight several empirical and theoretical challenges, as well as key future directions, for comparative evolutionary psychology.

  1. The major synthetic evolutionary transitions

    Science.gov (United States)

    Solé, Ricard

    2016-01-01

    Evolution is marked by well-defined events involving profound innovations that are known as ‘major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These ‘synthetic’ transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431528

  2. Evolutionary Information Theory

    OpenAIRE

    Mark Burgin

    2013-01-01

    Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we const...

  3. The evolutionary history of protein domains viewed by species phylogeny

    National Research Council Canada - National Science Library

    Yang, Song; Bourne, Philip E

    2009-01-01

    .... The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins...

  4. Evolutionary developmental psychology

    National Research Council Canada - National Science Library

    King, Ashley C; Bjorklund, David F

    2010-01-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection...

  5. Evolutionary origins of human brain and spirituality.

    Science.gov (United States)

    Henneberg, Maciej; Saniotis, Arthur

    2009-12-01

    Evolving brains produce minds. Minds operate on imaginary entities. Thus they can create what does not exist in the physical world. Spirits can be deified. Perception of spiritual entities is emotional--organic. Spirituality is a part of culture while culture is an adaptive mechanism of human groups as it allows for technology and social organization to support survival and reproduction. Humans are not rational, they are emotional. Most of explanations of the world, offered by various cultures, involve an element of "fiat", a will of a higher spiritual being, or a reference to some ideal. From this the rules of behaviour are deduced. These rules are necessary to maintain social peace and allow a complex unit consisting of individuals of both sexes and all ages to function in a way ensuring their reproductive success and thus survival. There is thus a direct biological benefit of complex ideological superstructure of culture. This complex superstructure most often takes a form of religion in which logic is mixed with appeals to emotions based on images of spiritual beings. God is a consequence of natural evolution. Whether a deity is a cause of this evolution is difficult to discover, but existence of a deity cannot be questioned.

  6. Evolutionary origin of rhizobium Nod factor signaling

    NARCIS (Netherlands)

    Streng, A.; Camp, Op den R.; Bisseling, T.; Geurts, R.

    2011-01-01

    For over two decades now, it is known that the nodule symbiosis between legume plants and nitrogen fixing rhizobium bacteria is set in motion by the bacterial signal molecule named nodulation (Nod) factor.1 Upon Nod factor perception a signaling cascade is activated that is also essential for endomy

  7. On the Evolutionary Origins of Executive Functions

    Science.gov (United States)

    Ardila, Alfredo

    2008-01-01

    In this paper it is proposed that the prefrontal lobe participates in two closely related but different executive function abilities: (1) "metacognitive executive functions": problem solving, planning, concept formation, strategy development and implementation, controlling attention, working memory, and the like; that is, executive functions as…

  8. A new genus of Nanaloricidae (Loricifera) from deep-sea sediments of volcanic origin in the Kilinailau Trench north of Papua New Guinea

    Science.gov (United States)

    Gad, Gunnar

    2004-02-01

    A new genus and species of Nanaloricidae (Loricifera), Phoeniciloricus simplidigitatus, is described inhabiting fine sand covered by a layer of volcanic ash at a water depth of 1,813 m in the New Ireland Basin near the Kilinailau Trench (north of Papua New Guinea). The described specimen is a postlarva enclosed in a larval exuvium. This is the first report of a species belonging to the Nanaloricidae from the deep sea. This occurrence is surprising, because Nanaloricidae are typical inhabitants of coarse sands in the intertidal or littoral zone. Preference for these shallow water habitats is reflected in many morphological features which characterize the Nanaloricidae, and are not normally found in Loricifera inhabiting fine-grained, clayish, deep-sea bottoms. The postlarva of the new species is characterized by a long narrow mouth tube, an urn-shaped lorica divided into ten plates, and 13 small lorica spikes. Distinguishing features of the Higgins-larva include short spinose toes lacking mucros but having small and slightly enlarged bases, short scalids on the introvert, many thoracic plates arranged in 6-8 rows, numerous small papillate flosculi in the collar and caudal regions, and three pairs of filiform, short locomotory appendages on the ventral side. Some features of the new species, especially of the Higgins-larva, are discussed as adaptations to the deep-sea environment.

  9. Evolutionary Information Theory

    Directory of Open Access Journals (Sweden)

    Mark Burgin

    2013-04-01

    Full Text Available Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we construct and study universal evolutionary machines and automata, which form the base for evolutionary information theory. The first class of measures introduced and studied in this paper is evolutionary information size of symbolic objects relative to classes of automata or machines. In particular, it is proved that there is an invariant and optimal evolutionary information size relative to different classes of evolutionary machines. As a rule, different classes of algorithms or automata determine different information size for the same object. The more powerful classes of algorithms or automata decrease the information size of an object in comparison with the information size of an object relative to weaker4 classes of algorithms or machines. The second class of measures for evolutionary information in symbolic objects is studied by introduction of the quantity of evolutionary information about symbolic objects relative to a class of automata or machines. To give an example of applications, we briefly describe a possibility of modeling physical evolution with evolutionary machines to demonstrate applicability of evolutionary information theory to all material processes. At the end of the paper, directions for future research are suggested.

  10. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms

    Directory of Open Access Journals (Sweden)

    Achal Rastogi

    2015-07-01

    Full Text Available Recent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epigenetic features found in mammals and plants suggesting their ancient origin. Phaeodactylum tricornutum and Thalassiosira pseudonana, pennate and centric diatoms, respectively, emerged as model species to address questions on the evolution of epigenetic phenomena such as what has been lost, retained or has evolved in contemporary species. In the present work, we will discuss how the study of non-model or emerging model organisms, such as diatoms, helps understand the evolutionary history of epigenetic mechanisms with a particular focus on DNA methylation and histone modifications.

  11. Why religious human beings need evolutionary epistemology! A theological and evolutionary viewpoint of 'why humans need to embrace evolutionary epistemology'

    Directory of Open Access Journals (Sweden)

    Johan A. van Rooyen

    2016-03-01

    Full Text Available I put forward an understanding of evolutionary epistemology that rescues something of the old and venerable idea of freedom, and it means that we as theologians should grasp our very nature realistically, beyond any illusionism and utopian dreams. The author feels that scholars, especially theologians, should firstly take evolution seriously and secondly regard evolutionary epistemology as important as evolution itself, the reason being theologians should know that it is of paramount importance for their systematic-theological intradisciplinary and/or interdisciplinary implications, which is embarking on a way of thinking that regards evolutionary epistemology as a friend in their accommodation of their respective theological fields of interest. This accommodation is substantial as it will enhance their respective theological disciplines as �an exhilarating vision of God�. Evolutionary epistemology takes a pragmatic view of humans. Evolutionary epistemologists question how humans really behave and what the true origin of their behaviour is. In contrast to this programme, many conceptions of humans are based on an idealisation of our species.Intradisciplinary and/or interdisciplinary implications: Evolutionary epistemology takes a pragmatic view of humans. Evolutionary epistemologists question how humans really behave and what the true origin of their behaviour is. In contrast to this programme, many conceptions of humans are based on an idealisation of our species. I then put forward my own understanding of evolutionary epistemology and conclude that evolutionary epistemology recues something of the old and venerable idea of freedom, and it means that we should grasp our very nature realistically, beyond any illusionism and utopian dreams.Keywords: Evolutionary epistemology

  12. High origin of the deep femoral artery: a case report and literature review Origem alta da artéria femoral profunda: relato de caso e revisão da literatura

    Directory of Open Access Journals (Sweden)

    Vishal Kumar

    2011-09-01

    Full Text Available Arterial variations of the femoral triangle are rarely reported in the literature. In the present article, we have reported a case of high origin of the deep femoral artery, which was originating just lower to the inguinal ligament. It was also observed that the lateral circumflex femoral artery arose directly from the femoral artery instead from the deep femoral artery. We have discussed the anatomy, embryological basis, and clinical implications of these variations along with relevant literature review. The importance of knowledge about these variations in therapeutic and diagnostic interventions is discussed.Variações arteriais no triângulo femoral têm sido pouco relatadas na literatura. No presente artigo, relatou-se um caso de origem alta da artéria femoral profunda, que estava se originando pouco abaixo do ligamento inguinal. Também foi observado que a artéria femoral circunflexa originava-se diretamente da artéria femoral, ao invés de ser originada da artéria femoral profunda. Discutiu-se sobre anatomia, base embriológica e implicações clínicas dessas variações junto com uma revisão da literatura pertinente. A importância do conhecimento sobre essas variações no quadro das intervenções diagnósticas e terapêuticas é discutida.

  13. An Introduction to Comparative Evolutionary Psychology

    OpenAIRE

    Jennifer Vonk; Todd K. Shackelford

    2013-01-01

    Previously we (Vonk and Shackelford, 2012, in press) proposed an integration of comparative psychology and evolutionary psychology into a new field of “comparative evolutionary psychology.” This integrative discipline incorporates principles from ethology, ecology, biology, anthropology, and psychology, broadly defined. We present in this special issue a collection of original empirical and theoretical review articles in which leading researchers propose ways to successfully integrate compara...

  14. Evolutionary history of anglerfishes (Teleostei: Lophiiformes: a mitogenomic perspective

    Directory of Open Access Journals (Sweden)

    Shimazaki Mitsuomi

    2010-02-01

    Full Text Available Abstract Background The teleost order Lophiiformes, commonly known as the anglerfishes, contains a diverse array of marine fishes, ranging from benthic shallow-water dwellers to highly modified deep-sea midwater species. They comprise 321 living species placed in 68 genera, 18 families and 5 suborders, but approximately half of the species diversity is occupied by deep-sea ceratioids distributed among 11 families. The evolutionary origins of such remarkable habitat and species diversity, however, remain elusive because of the lack of fresh material for a majority of the deep-sea ceratioids and incompleteness of the fossil record across all of the Lophiiformes. To obtain a comprehensive picture of the phylogeny and evolutionary history of the anglerfishes, we assembled whole mitochondrial genome (mitogenome sequences from 39 lophiiforms (33 newly determined during this study representing all five suborders and 17 of the 18 families. Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation. Results Partitioned maximum likelihood analysis confidently recovered monophyly for all of the higher taxa (including the order itself with the exception of the Thaumatichthyidae (Lasiognathus was deeply nested within the Oneirodidae. The mitogenomic trees strongly support the most basal and an apical position of the Lophioidei and a clade comprising Chaunacoidei + Ceratioidei, respectively, although alternative phylogenetic positions of the remaining two suborders (Antennarioidei and Ogcocephaloidei with respect to the above two lineages are statistically indistinguishable. While morphology-based intra-subordinal relationships for relatively shallow, benthic dwellers (Lophioidei, Antennarioidei, Ogcocephaloidei, Chaunacoidei are either congruent with or statistically indistinguishable from the present mitogenomic tree, those of the principally deep

  15. Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

    Science.gov (United States)

    Shackelford, Todd K; Liddle, James R

    2014-05-01

    The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

  16. Deep Integration: Letting the Epigenome out of the Bottle without Losing Sight of the Structural Origins of Population Health and Disease

    OpenAIRE

    Geronimus, Arline T

    2013-01-01

    Investigators are applying advances in stress physiology and molecular dynamics to illuminate US population health inequalities. As examples, the “weathering” hypothesis posits that socially structured, repeated stress process activation across the life course increases disease vulnerability and accelerates aging in marginalized groups. The developmental origins of health and disease (DOHaD) hypothesis posits that a limiting uterine environment programs the fetus for later life disease via re...

  17. Deep Near-Infrared Imaging of the rho Oph Cloud Core: Clues to the Origin of the Lowest-Mass Brown Dwarfs

    CERN Document Server

    Marsh, Kenneth A; Kirkpatrick, J Davy; Lowrance, Patrick J; Cutri, Roc M; Velusamy, Thangasamy

    2010-01-01

    A search for young substellar objects in the rho Oph cloud core region has been made using the deep-integration Combined Calibration Scan images of the 2MASS extended mission in J, H and Ks bands, and Spitzer IRAC images at 3.6, 4.5, 5.8 and 8.0 microns. The field of view of the combined observations was 1 deg x 9.3 arcmin, and the 5 sigma limiting magnitude at J was 20.5. Comparison of the observed SEDs with the predictions of the COND and DUSTY models, for an assumed age of 1 Myr, supports the identification of many of the sources with brown dwarfs, and enables the estimation of effective temperature, Teff. The cluster members are then readily distinguishable from background stars by their locations on a plot of flux density versus Teff. The range of estimated Teff extends down to ~ 750 K, suggesting the presence of objects of sub-Jupiter mass. The results also suggest that the mass function for the rho Oph cloud resembles that of the sigma Orionis cluster based on a recent study, with both rising towards l...

  18. The Great Observatories Origins Deep Survey: Constraints on the Lyman Continuum Escape Fraction Distribution of Lyman--Break Galaxies at 3.4

    CERN Document Server

    Vanzella, E; Inoue, A; Nonino, M; Fontanot, F; Cristiani, S; Grazian, A; Dickinson, M; Stern, D; Tozzi, P; Giallongo, E; Ferguson, H; Spinrad, H; Boutsia, K; Fontana, A; Rosati, P

    2010-01-01

    We use ultra-deep ultraviolet VLT/VIMOS intermediate-band and VLT/FORS1 narrow-band imaging in the GOODS Southern field to derive limits on the distribution of the escape fraction (f_esc) of ionizing radiation for L >~ L*(z=3) Lyman Break Galaxies (LBGs) at redshift 3.4--4.5. Only one LBG, at redshift z=3.795, is detected in its Lyman continuum (LyC; S/N~5.5), the highest redshift galaxy currently known with a direct detection. Its ultraviolet morphology is quite compact (R_eff=0.8, kpc physical). Three out of seven AGN are also detected in their LyC, including one at redshift z=3.951 and z850 = 26.1. From stacked data (LBGs) we set an upper limit to the average f_esc in the range 5%--20%, depending on the how the data are selected (e.g., by magnitude and/or redshift). We undertake extensive Monte Carlo simulations that take into account intergalactic attenuation, stellar population synthesis models, dust extinction and photometric noise in order to explore the moments of the distribution of the escaping radi...

  19. Age constraints on the origin and growth history of a deep-water coral mound in the northeast Atlantic drilled during Integrated Ocean Drilling Program Expedition 307

    Science.gov (United States)

    Kano, Akihiro; Ferdelman, Timothy G.; Williams, Trevor; Henriet, Jean-Pierre; Ishikawa, Tsuyoshi; Kawagoe, Noriko; Takashima, Chiduru; Kakizaki, Yoshihiro; Abe, Kohei; Sakai, Saburo; Browning, Emily L.; Li, Xianghui; Ocean Drilling Program Expedition 307 Scientists

    2007-11-01

    Sr isotope stratigraphy provides a new age model for the first complete section drilled through a deep-water coral mound. The 155-m-long section from Challenger Mound in the Porcupine Sea-bight, southwest of Ireland, is on Miocene siliciclastics and consists entirely of sediments bearing well-preserved cold-water coral Lophelia pertusa. The 87Sr/86Sr values of 28 coral specimens from the mound show an upward-increasing trend, correspond to ages from 2.6 to 0.5 Ma, and identify a significant hiatus from ca. 1.7 to 1.0 Ma at 23.6 m below seafloor. The age of the basal mound sediments coincides with the intensification of Northern Hemisphere glaciations that set up the modern stratification of the northeast Atlantic and enabled coral growth. Mound growth persisted throughout glacial-interglacial fluctuations, reached a maximum rate (24 cm/k.y.) ca. 2.0 Ma, and ceased at 1.7 Ma. Unlike other buried mounds in Porcupine Seabight, Challenger Mound was only partly covered during its growth interruption, and growth restarted ca. 1.0 Ma.

  20. A major merger origin for the high fraction of galaxies at 2Deep Survey

    CERN Document Server

    Ribeiro, B; Cassata, P; Garilli, B; Lemaux, B C; Maccagni, D; Schaerer, D; Tasca, L A M; Zamorani, G; Zucca, E; Amorín, R; Bardelli, S; Hathi, N P; Koekemoer, A; Pforr, J

    2016-01-01

    (Abridged) The properties of stellar clumps in star forming galaxies and their evolution over the redshift range $2\\lesssim z \\lesssim 6$ are presented and discussed in the context of the build-up of massive galaxies at early cosmic times. We use HST/ACS images of galaxies with spectroscopic redshifts from the VIMOS Ultra Deep Survey (VUDS) to identify clumps within a 20 kpc radius. We find that the population of galaxies with more than one clump is dominated by galaxies with two clumps, representing $\\sim21-25$\\% of the population, while the fraction of galaxies with 3, or 4 and more, clumps is 8-11 and 7-9\\%, respectively. The fraction of clumpy galaxies is in the range $\\sim35-55\\%$ over $2

  1. The Atlas-3D project - IX. The merger origin of a fast and a slow rotating Early-Type Galaxy revealed with deep optical imaging: first results

    CERN Document Server

    Duc, Pierre-Alain; Serra, Paolo; Michel-Dansac, Leo; Ferriere, Etienne; Alatalo, Katherine; Blitz, Leo; Bois, Maxime; Bournaud, Frederic; Bureau, Martin; Cappellari, Michele; Davies, Roger L; Davis, Timothy A; de Zeeuw, P T; Emsellem, Eric; Khochfar, Sadegh; Krajnovic, Davor; Kuntschner, Harald; Lablanche, Pierre-Yves; McDermid, Richard M; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Weijmans, Anne-Marie; Young, Lisa M

    2011-01-01

    The mass assembly of galaxies leaves imprints in their outskirts, such as shells and tidal tails. The frequency and properties of such fine structures depend on the main acting mechanisms - secular evolution, minor or major mergers - and on the age of the last substantial accretion event. We use this to constrain the mass assembly history of two apparently relaxed nearby Early-Type Galaxies (ETGs) selected from the Atlas-3D sample, NGC 680 and NGC 5557. Our ultra deep optical images obtained with MegaCam on the Canada-France-Hawaii Telescope reach 29 mag/arcsec^2 in the g-band. They reveal very low-surface brightness (LSB) filamentary structures around these ellipticals. Among them, a gigantic 160 kpc long tail East of NGC 5557 hosts gas-rich star-forming objects. NGC 680 exhibits two major diffuse plumes apparently connected to extended HI tails, as well as a series of arcs and shells. Comparing the outer stellar and gaseous morphology of the two ellipticals with that predicted from models of colliding galax...

  2. Deep multi-scale location-aware 3D convolutional neural networks for automated detection of lacunes of presumed vascular origin

    Directory of Open Access Journals (Sweden)

    Mohsen Ghafoorian

    2017-01-01

    In this paper, we propose an automated two-stage method using deep convolutional neural networks (CNN. We show that this method has good performance and can considerably benefit readers. We first use a fully convolutional neural network to detect initial candidates. In the second step, we employ a 3D CNN as a false positive reduction tool. As the location information is important to the analysis of candidate structures, we further equip the network with contextual information using multi-scale analysis and integration of explicit location features. We trained, validated and tested our networks on a large dataset of 1075 cases obtained from two different studies. Subsequently, we conducted an observer study with four trained observers and compared our method with them using a free-response operating characteristic analysis. Shown on a test set of 111 cases, the resulting CAD system exhibits performance similar to the trained human observers and achieves a sensitivity of 0.974 with 0.13 false positives per slice. A feasibility study also showed that a trained human observer would considerably benefit once aided by the CAD system.

  3. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  4. Exaptation, adaptation, and evolutionary psychology.

    Science.gov (United States)

    Schulz, Armin

    2013-01-01

    One of the most well known methodological criticisms of evolutionary psychology is Gould's claim that the program pays too much attention to adaptations, and not enough to exaptations. Almost as well known is the standard rebuttal of that criticism: namely, that the study of exaptations in fact depends on the study of adaptations. However, as I try to show in this paper, it is premature to think that this is where this debate ends. First, the notion of exaptation that is commonly used in this debate is different from the one that Gould and Vrba originally defined. Noting this is particularly important, since, second, the standard reply to Gould's criticism only works if the criticism is framed in terms of the former notion of exaptation, and not the latter. However, third, this ultimately does not change the outcome of the debate much, as evolutionary psychologists can respond to the revamped criticism of their program by claiming that the original notion of exaptation is theoretically and empirically uninteresting. By discussing these issues further, I also seek to determine, more generally, which ways of approaching the adaptationism debate in evolutionary biology are useful, and which not.

  5. Deep source gas

    Energy Technology Data Exchange (ETDEWEB)

    1985-02-01

    Three separate emplacement concepts could explain the occurrence of gas at extreme depths: abiogenesis (a primordial, nonbiologic origin source); subducted, organic-origin gas (involving the deep, tectonic subduction emplacement of hydrocarbon-generating ocean sediments); and deep sedimentary basin gas (the more conventional emplacement of sedimentary rocks by deep downwarping of the Earth's crust). Of these concepts, Deep Source Gas research focuses on the subducted, organic-origin concept. The purpose of Deep Source Gas research is to verify natural gas arising from depths in excess of 30,000 feet, to relate these occurrences to conceptual models, to define the limits of target areas, to quantify the resource, and to determine the significance of the gas to the nation's reserves. The research emphasizes an Earth science study (geology, geochemistry, and geophysics) of the Cordilleran Geologic Province of western North America. This area is considered a prospective source largely because of known and suspected plate tectonic structures and their youthful emplacement, which increase the likelihood of a timely entrapment of deep-source generated hydrocarbons. Detailed geochemical studies indicate that the deep-source-gas generating capacity of the Aleutian Trench area of southern Alaska is high. Furthermore, geophysical studies show that an apparent fossil subduction zone exists in western Washington. This zone appears to have very thick sedimentary rock units, the existence of which will be evaluated through a more detailed seismic study and possibly through drilling activities. Structural observations made in the northern Brooks Range and central Alaskan Range indicate that overthrusting and compressional features may serve as large-scale target areas for deep source gas generation and occurrence. 12 figures, 2 tables.

  6. Silicification of pelitic schist in the Iwakuni-Yanai area of the Ryoke belt, southwest Japan: Origin of competent layers in the deep crust

    Science.gov (United States)

    Terabayashi, M.; Yamamoto, H.

    2003-12-01

    Bright-layer reflections have been imaged at about 15-20 km depth in fore-arc region of southwest Japan, and most of the epicenter distributes above the bright-layer (Ito, 1999). To understand the cause of a seismic bright-layer with the mechanism of large inland earthquake, we studied the low-P/T metamorphic rocks in the Ryoke belt, southwest Japan. The Ryoke belt in the Iwakuni-Yanai area is underlain by Jurassic accretionary complex and their metamorphosed equivalents. They were intruded by Cretaceous granitic rocks. Five metamorphic zones can be difined by mineral assemblages of pelitic rocks as a regional metamorphism before the intrusion; chlorite, chlorite-biotite, biotite, cordierite and sillimanite zones from north to south (Ikeda, 1993). Silicified rocks have been found in pelitic schist of the biotite zone and northernmost part of the cordierite zone. The pelitic schist is dark in color but silicification turned it to be pale gray or milky white. Silicified pelitic schist is mainly composed of fine-grained quartz and minor muscovite and biotite. The silicified pelitic schist forms layers or lenticular bodies several to fifty meters in thickness. The boundary between silicified rock layer and underlying pelitic schist is fairly distinct but that between the overlying pelitic schist is gradual. Quartz veins crossing high angles with schistosity were preferentially developed in the silicified rock layers, while schistosity-parallel quartz veins, which underwent plastic flow, were observed in the pelitic schist. En echelon quartz vein and fishnet-like quartz veins are characteristic of silicified rock layers. This mode of occurrence of quartz veins indicates competence of silicified rock layers relative to pelitic schist. Rock boundary with high competence contrast is probably a good reflector of seismic waves. Bright-layer reflections would arise from silicified rock layers if those are distributed in the deep crust to a considerable extent.

  7. Anomalous origin of the deep brachial artery (profunda brachii observed in bilateral arms: case report Origem anômala da artéria braquial profunda (profunda brachii observada em braços bilaterais: relato de caso

    Directory of Open Access Journals (Sweden)

    Rafael Cisne de Paula

    2013-03-01

    Full Text Available During an ordinary dissection, a cadaver showed a bilateral anomalous origin of the deep brachial artery, where this vessel appeared like a branching of the subscapular artery with common trunk, which included the posterior circumflex humeral artery. The course and distribution of the deep brachial artery in the back compartment were relatively consistent with previous reports. Arterial variations can be damaged through iatrogenic means if not properly documented. The knowledge of this case is very important in clinical medicine and in surgeries in this compartment to prevent any injury.Durante dissecação em prática usual, um cadáver apresentou origem anômala da artéria braquial profunda, na qual este vaso apareceu como um ramo da artéria subescapular com um tronco comum, que incluiu a artéria circunflexa posterior do úmero. O curso e a distribuição da artéria braquial profunda no compartimento posterior foram relativamente coincidentes com relatos prévios. Variações arteriais podem ser danificadas de maneira iatrogênica se não forem adequadamente documentadas. O conhecimento desse caso é muito importante na prática clínica e em cirurgias nesse compartimento para prevenção de qualquer injúria.

  8. The Evolutionary History of Protein Domains Viewed by Species Phylogeny

    OpenAIRE

    Song Yang; Philip E. Bourne

    2009-01-01

    BACKGROUND: Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. METHODOLOGY/PRINCIPAL FINDINGS: A methodology is presented for providing a parsimon...

  9. Contribution and constraints by deep geophysics to earthquakes origin and distribution in the Italian peninsula; Contributi e vincoli dalla geofisica profonda all'origine e distribuzione dei terremoti nella penisola italiana

    Energy Technology Data Exchange (ETDEWEB)

    Morelli, C.

    1998-07-01

    The static structural features of the italian peninsula have been obscured for decades by the over thrusts, centrifugal from the Ligurian-Tyrrhenian area. These difficulties have been surpassed for the upper part (0-10 Km) with the integrated application of the advanced geophysical methodologies (reflection 3D seismic, aero magnetism gravity), calibrated on many thousands of drill-holes. In the same time (last 30 year) more then 30000 Km of deep refraction and reflection seismic sponsored by CNR have revealed a structural model with an Adriatic crust of normal thickness (30-35 Km), rigid and stable and a Ligurian-Tyrrhenian thinned crust (20-25 Km), heated and fractured, with mantellic windows in the SE-Tyrrhenian. The contact between the two crusts is a strongly tectonized suture, to which at the surface corresponds a band of seismicity maxima on the peninsula, 30-60 Km wide (large to the North and narrower to the South), separated in Central Italy by an area of more spread deformations and rotations. These data, derived from the ING seismic network, allowed also to demonstrate that the seismic release in the peninsular Italy is only weakly connected with the Africa-Europe convergence, but is better explained with the activity of two subduction/collision areas (Northern Appennines and Southern Appennines-Calabria-Sicily). The sub horizontal crustal discontinuities revealed by experimental seismic and by high accuracy seismology give the means for understanding other seismicity characteristics and the ramp-tectonics. [Italian] Il quadro statico delle conoscenze strutturali in profondita' e' stato trascurato per decenni su tutta la penisola italiana dai sovrascorrimenti superficiali centrifughi dell'area ligure-tirrena. L'AGIP ha superato le difficolta' per le parti superficiali (0-10 Km) con l'applicazione integrata delle metodiche geofisiche avanzate (sismica a riflessione 3D, aeromagnetismo, gravimetria) tarata su molte migliaia di

  10. Recurrence of Dysplastic Nevi Is Strongly Associated with Extension of the Lesions to the Lateral Margins and into the Deep Margins through the Hair Follicles in the Original Shave Removal Specimens

    Directory of Open Access Journals (Sweden)

    Amin Maghari

    2016-01-01

    Full Text Available Melanocytic nevi, including dysplastic or atypical nevi (DN, can recur or persist following shave removal procedures, and recurrence may resemble melanoma, both clinically and histologically (pseudomelanoma. Recurrence may originate from proliferation of the remaining neoplastic melanocytes following incomplete removal. The present study determines the rate and etiology of this event. A cross-sectional analysis of 110 excision specimens showing histological recurrence was performed, and these specimens were compared to the slides of the original shave specimens showing mildly atypical DN. In the second portion of the study, a retrospective review of 167 cases with biopsy-proven mildly atypical DN which were followed up for at least two years was conducted to determine the rate of recurrence/persistence. When followed up for two years, DN, with positive shave margins, defined by extension or very close extension (≤0.2 mm of the lesions to the lateral margins and into the deep margins through the hair follicles in the shave removal specimens, have a higher probability of recurrence than DN with negative (or clear margins (odds ratio (OR = 158; 95% confidence interval (CI = 36.62–683; P<0.001. The overall rate of histologically confirmed recurrence/persistence was approximately 10%.

  11. New insights into diversity and evolution of deep-sea Mytilidae (Mollusca: Bivalvia).

    Science.gov (United States)

    Lorion, Julien; Buge, Barbara; Cruaud, Corinne; Samadi, Sarah

    2010-10-01

    Bathymodiolinae mussels have been used as a biological model to better understand the evolutionary origin of faunas associated with deep-sea hydrothermal vents and cold seeps. Most studies to date, however, have sampled with a strong bias towards vent and seep species, mainly because of a lack of knowledge of closely related species from organic falls. Here we reassess the species diversity of deep-sea mussels using two genes and a large taxon sample from the South-Western Pacific. This new taxonomic framework serves as a basis for a phylogenetic investigation of their evolutionary history. We first highlight an unexpected allopatric pattern and suggest that mussels usually reported from organic falls are in fact poorly specialized with regard to their environment. This challenges the adaptive scenarios proposed to explain the diversification of the group. Second, we confirm that deep-sea mussels arose from organic falls and then colonized hydrothermal vents and cold seeps in multiple events. Overall, this study constitutes a new basis for further phylogenetic investigations and a global systematic revision of deep-sea mussels. Copyright 2010 Elsevier Inc. All rights reserved.

  12. Deep Neck Infections of Odontogenic Origin and Their Clinical Significance. A Retrospective Study from Hradec Králové, Czech Republic

    Directory of Open Access Journals (Sweden)

    Hana Doležalová

    2015-12-01

    Full Text Available Introduction: Cellulitis remains a very serious disease even today. Mortality, which varied between 10–40%, has been reduced owing to the standard securing of airway patency and use of an appropriate surgical treatment approach. Materials and methods: A total of 195 patients were hospitalised for cellulitis at the University Hospital in Hradec Králové during 2007–2011. The following parameters were evaluated: age, gender, dependence of incidence of the disease on the season of the year, frequency of attacks of the particular areas and their clinical characteristics, aetiology of the inflammation, types of patient complaints, prevalence of current systemic diseases, results of microbiological and selected laboratory analyses, socio-economic status of the patients, and duration of patient stay at the hospital. Statistical analysis was performed by using Pearson’s correlation coefficient, the statistical significance level was p < 0.05. Results: The mean age of the patients was 39.8 years. The group of 195 patients included 108 (55% males and 87 (45% females. The mean time between the first symptoms of the disease and admission to the Department was 5 days. From among the 195 patients, 116 (59.5% were working persons, 79 (40.5% were non-working (children, students, unemployed persons, women on maternity leave, retired people. The odontogenic origin of the disease was verified in 173 (88.7% patients. In total, 65 (33.3% patients had no coinciding complicating systemic disease, 22 (11.3% patients had diabetes mellitus. The most frequent symptom of cellulitis was painful swelling, found in 194 (99.5% patients, followed by jaw contracture, found in 153 (78.5% patients. Conclusion: The results are largely very similar to those of previous studies performed in other countries, except that we found no correlation between the prevalence of cellulitis and the socio-economic status, nor have we confirmed Klebsiella pneumoniae sp. as the cause of

  13. Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

    Science.gov (United States)

    Hunt, Tam

    2014-12-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution-both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place-has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps' book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging "integral" or "evolutionary" cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps.

  14. On evolutionary ray-projection dynamics

    NARCIS (Netherlands)

    Joosten, Reinoud; Roorda, Berend

    2011-01-01

    We introduce the ray-projection dynamics in evolutionary game theory by employing a ray projection of the relative fitness (vector) function, i.e., a projection unto the unit simplex along a ray through the origin. Ray-projection dynamics are weakly compatible in the terminology of Friedman (Econome

  15. Evolutionary Biology: Its Value to Society

    Science.gov (United States)

    Carson, Hampton L.

    1972-01-01

    Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

  16. Evolutionary Biology: Its Value to Society

    Science.gov (United States)

    Carson, Hampton L.

    1972-01-01

    Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

  17. Evolutionary humanoid robotics

    CERN Document Server

    Eaton, Malachy

    2015-01-01

    This book examines how two distinct strands of research on autonomous robots, evolutionary robotics and humanoid robot research, are converging. The book will be valuable for researchers and postgraduate students working in the areas of evolutionary robotics and bio-inspired computing.

  18. Deep learning in neural networks: an overview.

    Science.gov (United States)

    Schmidhuber, Jürgen

    2015-01-01

    In recent years, deep artificial neural networks (including recurrent ones) have won numerous contests in pattern recognition and machine learning. This historical survey compactly summarizes relevant work, much of it from the previous millennium. Shallow and Deep Learners are distinguished by the depth of their credit assignment paths, which are chains of possibly learnable, causal links between actions and effects. I review deep supervised learning (also recapitulating the history of backpropagation), unsupervised learning, reinforcement learning & evolutionary computation, and indirect search for short programs encoding deep and large networks.

  19. Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies

    DEFF Research Database (Denmark)

    Schönherz, Anna A.; Lorenzen, Niels; Guldbrandtsen, Bernt

    2016-01-01

    The high mutation rate of RNA viruses enables the generation of a genetically diverse viral population, termed a quasispecies, within a single infected host. This high in-host genetic diversity enables an RNA virus to adapt to a diverse array of selective pressures such as host immune response....... To better understand the nature of a virus quasispecies related to the evolutionary potential of VHSV, a deep-sequencing protocol specific to VHSV was established and applied to 4 VHSV isolates, 2 originating from rainbow trout and 2 from Atlantic herring. Each isolate was subjected to Illumina paired end...

  20. Origin of microbial biomineralization and magnetotaxis during the Archean.

    Science.gov (United States)

    Lin, Wei; Paterson, Greig A; Zhu, Qiyun; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A; Zhu, Rixiang; Kirschvink, Joseph L; Pan, Yongxin

    2017-02-28

    Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

  1. Origin of microbial biomineralization and magnetotaxis during the Archean

    Science.gov (United States)

    Paterson, Greig A.; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A.; Zhu, Rixiang; Kirschvink, Joseph L.; Pan, Yongxin

    2017-01-01

    Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria. This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth’s dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time. PMID:28193877

  2. Origin of microbial biomineralization and magnetotaxis during the Archean

    Science.gov (United States)

    Lin, Wei; Paterson, Greig A.; Zhu, Qiyun; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A.; Zhu, Rixiang; Kirschvink, Joseph L.; Pan, Yongxin

    2017-02-01

    Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria. This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth’s dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

  3. Deep frying

    NARCIS (Netherlands)

    Koerten, van K.N.

    2016-01-01

    Deep frying is one of the most used methods in the food processing industry. Though practically any food can be fried, French fries are probably the most well-known deep fried products. The popularity of French fries stems from their unique taste and texture, a crispy outside with a mealy soft inter

  4. Deep frying

    NARCIS (Netherlands)

    Koerten, van K.N.

    2016-01-01

    Deep frying is one of the most used methods in the food processing industry. Though practically any food can be fried, French fries are probably the most well-known deep fried products. The popularity of French fries stems from their unique taste and texture, a crispy outside with a mealy soft inter

  5. Deep learning

    CERN Document Server

    Goodfellow, Ian; Courville, Aaron

    2016-01-01

    Deep learning is a form of machine learning that enables computers to learn from experience and understand the world in terms of a hierarchy of concepts. Because the computer gathers knowledge from experience, there is no need for a human computer operator to formally specify all the knowledge that the computer needs. The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones; a graph of these hierarchies would be many layers deep. This book introduces a broad range of topics in deep learning. The text offers mathematical and conceptual background, covering relevant concepts in linear algebra, probability theory and information theory, numerical computation, and machine learning. It describes deep learning techniques used by practitioners in industry, including deep feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling, and practical methodology; and it surveys such applications as natural language proces...

  6. Identification of Two Novel Anti-Fibrotic Benzopyran Compounds Produced by Engineered Strains Derived from Streptomyces xiamenensis M1-94P that Originated from Deep-Sea Sediments

    Directory of Open Access Journals (Sweden)

    Lei Feng

    2013-10-01

    Full Text Available The benzopyran compound obtained by cultivating a mangrove-derived strain, Streptomyces xiamenensis strain 318, shows multiple biological effects, including anti-fibrotic and anti-hypertrophic scar properties. To increase the diversity in the structures of the available benzopyrans, by means of biosynthesis, the strain was screened for spontaneous rifampicin resistance (Rif, and a mutated rpsL gene to confer streptomycin resistance (Str, was introduced into the S. xiamenensis strain M1-94P that originated from deep-sea sediments. Two new benzopyran derivatives, named xiamenmycin C (1 and D (2, were isolated from the crude extracts of a selected Str-Rif double mutant (M6 of M1-94P. The structures of 1 and 2 were identified by analyzing extensive spectroscopic data. Compounds 1 and 2 both inhibit the proliferation of human lung fibroblasts (WI26, and 1 exhibits better anti-fibrotic activity than xiamenmycin. Our study presents the novel bioactive compounds isolated from S. xiamenensis mutant strain M6 constructed by ribosome engineering, which could be a useful approach in the discovery of new anti-fibrotic compounds.

  7. Origins and Evolution of Life

    Science.gov (United States)

    Gargaud, Muriel; López-García, Purificación; Martin, Hervé

    2011-01-01

    Part I. What Is Life?: 1. Problems raised by a definition of life M. Morange; 2. Some remarks about uses of cosmological anthropic 'principles' D. Lambert; 3. Minimal cell: the biologist point of view C. Brochier-Armanet; 4. Minimal cell: the computer scientist point of view H. Bersini; 5. Origins of life: computing and simulation approaches B. Billoud; Part II. Astronomical and Geophysical Context of the Emergence of Life: 6. Organic molecules in interstellar medium C. Ceccarelli and C. Cernicharo; 7. Cosmochemical evolution and the origin of life: insights from meteorites S. Pizzarello; 8. Astronomical constraints on the emergence of life M. Gounelle and T. Montmerle; 9. Formation of habitable planets J. Chambers; 10. The concept of galactic habitable zone N. Prantzos; 11. The young Sun and its influence on planetary atmospheres M. Güdel and J. Kasting; 12. Climates of the Earth G. Ramstein; Part III. Role of Water in the Emergence of Life: 13. Liquid water: a necessary condition to all forms of life K. Bartik, G. Bruylants, E. Locci and J. Reisse; 14. The role of water in the formation and evolution of planets T. Encrenaz; 15. Water on Mars J. P. Bibring; Part IV. From Non-Living Systems to Life: 16. Energetic constraints on prebiotic pathways: application to the emergence of translation R. Pascal and L. Boiteau; 17. Comparative genomics and early cell evolution A. Lazcano; 18. Origin and evolution of metabolisms J. Peretó; Part V. Mechanisms for Life Evolution: 19. Molecular phylogeny: inferring the patterns of evolution E. Douzery; 20. Horizontal gene transfer: mechanisms and evolutionary consequences D. Moreira; 21. The role of symbiosis in eukaryotic evolution A. Latorre, A. Durbán, A. Moya and J. Peretó; Part VI. Life in Extreme Conditions: 22. Life in extreme conditions: Deinococcus radiodurans, an organism able to survive prolonged desiccation and high doses of ionising radiation S. Sommer and M. Toueille; 23. Molecular effects of UV and ionizing

  8. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... topics like the estimation of distribution algorithms, indicator-based selection, etc., are also discussed. An important problem, from a theoretical and practical point of view, of learning classifier systems is presented in depth. Multiobjective evolutionary algorithms, which constitute one of the most...... evolutionary algorithms, such as memetic algorithms, which have emerged as a very promising tool for solving many real-world problems in a multitude of areas of science and technology. Moreover, parallel evolutionary combinatorial optimization has been presented. Search operators, which are crucial in all...

  9. Evolutionary mechanisms for loneliness.

    Science.gov (United States)

    Cacioppo, John T; Cacioppo, Stephanie; Boomsma, Dorret I

    2014-01-01

    Robert Weiss (1973) conceptualised loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organisation than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale.

  10. Rethinking evolutionary individuality.

    Science.gov (United States)

    Ereshefsky, Marc; Pedroso, Makmiller

    2015-08-18

    This paper considers whether multispecies biofilms are evolutionary individuals. Numerous multispecies biofilms have characteristics associated with individuality, such as internal integrity, division of labor, coordination among parts, and heritable adaptive traits. However, such multispecies biofilms often fail standard reproductive criteria for individuality: they lack reproductive bottlenecks, are comprised of multiple species, do not form unified reproductive lineages, and fail to have a significant division of reproductive labor among their parts. If such biofilms are good candidates for evolutionary individuals, then evolutionary individuality is achieved through other means than frequently cited reproductive processes. The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed.

  11. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-01

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps. PMID:23209163

  12. Neurocontroller analysis via evolutionary network minimization.

    Science.gov (United States)

    Ganon, Zohar; Keinan, Alon; Ruppin, Eytan

    2006-01-01

    This study presents a new evolutionary network minimization (ENM) algorithm. Neurocontroller minimization is beneficial for finding small parsimonious networks that permit a better understanding of their workings. The ENM algorithm is specifically geared to an evolutionary agents setup, as it does not require any explicit supervised training error, and is very easily incorporated in current evolutionary algorithms. ENM is based on a standard genetic algorithm with an additional step during reproduction in which synaptic connections are irreversibly eliminated. It receives as input a successfully evolved neurocontroller and aims to output a pruned neurocontroller, while maintaining the original fitness level. The small neurocontrollers produced by ENM provide upper bounds on the neurocontroller size needed to perform a given task successfully, and can provide for more effcient hardware implementations.

  13. Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

    Science.gov (United States)

    Laumer, Christopher E; Hejnol, Andreas; Giribet, Gonzalo

    2015-01-01

    Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked ‘microturbellarian’ groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates. DOI: http://dx.doi.org/10.7554/eLife.05503.001 PMID:25764302

  14. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

    Directory of Open Access Journals (Sweden)

    Jessica eLabonté

    2015-04-01

    Full Text Available A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a three km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32 % of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

  15. Evolutionary Population Synthesis Models of Primeval Galaxies a Critical Appraisal

    CERN Document Server

    Buzzoni, A

    1997-01-01

    A theoretical approach relying on evolutionary population synthesis models could help refining the search criteria in deep galaxy surveys on the basis of a better knowledge of the expected apparent photometric properties of high-redshift objects. The following is a brief discussion reviewing some relevant aspects of the question in order to allow a more critical appraisal to primeval galaxy recognition.

  16. Evolutionary epistemology a multiparadigm program

    CERN Document Server

    Pinxten, Rik

    1987-01-01

    This volume has its already distant origin in an inter­national conference on Evolutionary Epistemology the editors organized at the University of Ghent in November 1984. This conference aimed to follow up the endeavor started at the ERISS (Epistemologically Relevant Internalist Sociology of Science) conference organized by Don Campbell and Alex Rosen­ berg at Cazenovia Lake, New York, in June 1981, whilst in­ jecting the gist of certain current continental intellectual developments into a debate whose focus, we thought, was in danger of being narrowed too much, considering the still underdeveloped state of affairs in the field. Broadly speaking, evolutionary epistemology today con­ sists of two interrelated, yet qualitatively distinct inves­ tigative efforts. Both are drawing on Darwinian concepts, which may explain why many people have failed to discriminate them. One is the study of the evolution of the cognitive apparatus of living organisms, which is first and foremost the province of biologists and...

  17. Evolutionary expansion of the Monogenea.

    Science.gov (United States)

    Kearn, G C

    1994-12-01

    The evolutionary expansion of the monogeneans has taken place in parallel with the diversification of the fish-like vertebrates. In this article the main trends in monogenean evolution are traced from a hypothetical skin-parasitic ancestor on early vertebrates. Special consideration is given to the following topics: early divergence between skin feeders and blood feeders; diversification and specialization of the haptor for attachment to skin; transfer from host to host, viviparity and the success of the gyrodactylids; predation on skin parasites and camouflage; colonization of the buccal and branchial cavities; diversification and specialization of the haptor for attachment to the gills; phoresy in gill parasites; the development of endoparasitism and the origin of the cestodes; the success of dactylogyroidean gill parasites; the uniqueness of the polyopisthocotyleans; ovoviviparity and the colonization of the tetrapods. Host specificity has been the guiding force of coevolution between monogeneans and their vertebrate hosts, but the establishment of monogeneans on unrelated hosts sharing the same environment (host-switching) may have been underestimated. Host-switching has provided significant opportunities for evolutionary change of direction and is probably responsible for the establishment of monogeneans on cephalopod molluscs, on the hippopotamus and possibly on chelonians. There are indications that host-switching may be more common in monogeneans that spread by direct transfer of adults/juveniles from host to host. A limitation on the further expansion of monogeneans is the need for water for the dispersal of the infective larva (oncomiracidium).

  18. Autonomous Evolutionary Information Systems

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Traditional information systems are passive, i.e., data orknowledge is created , retrieved, modified, updated, and deleted only in response to operations issued by users or application programs, and the systems only can execute queries or t ransactions explicitly submitted by users or application programs but have no ab ility to do something actively by themselves. Unlike a traditional information system serving just as a storehouse of data or knowledge and working passively a ccording to queries or transactions explicitly issued by users and application p rograms, an autonomous evolutionary information system serves as an autonomous a nd evolutionary partner of its users that discovers new knowledge from its datab ase or knowledge-base autonomously, cooperates with its users in solving proble m s actively by providing the users with advices, and has a certain mechanism to i mprove its own state of “knowing” and ability of “working”. This paper semi nall y defines what is an autonomous evolutionary information system, explain why aut onomous evolutionary information systems are needed, and presents some new issue s, fundamental considerations, and research directions in design and development of autonomous evolutionary information systems.

  19. Applying evolutionary anthropology.

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

  20. Paleoanthropology and evolutionary theory.

    Science.gov (United States)

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted.

  1. Digging Deep: Exploring College Students' Knowledge of Macroevolutionary Time

    Science.gov (United States)

    Catley, Kefyn M.; Novick, Laura R.

    2009-01-01

    Some ability to comprehend deep time is a prerequisite for understanding macroevolution. This study examines students' knowledge of deep time in the context of seven major historical and evolutionary events (e.g., the age of the Earth, the emergence of life, the appearance of a pre-modern human, "Homo habilis"). The subjects were 126…

  2. New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides

    Directory of Open Access Journals (Sweden)

    Charmet Gilles

    2008-11-01

    Full Text Available Abstract Background Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the Sitopsis section, having Aegilops speltoides (SS, 2n = 14 as the closest identified relative. However molecular relationships based on genomic sequence comparison, including both coding and non-coding DNA, have never been investigated. In an attempt to clarify these relationships, we compared, in this study, sequences of the Storage Protein Activator (SPA locus region of the S genome of Ae. speltoides (2n = 14 to that of the A, B and D genomes co-resident in the hexaploid wheat species (Triticum aestivum, AABBDD, 2n = 42. Results Four BAC clones, spanning the SPA locus of respectively the A, B, D and S genomes, were isolated and sequenced. Orthologous genomic regions were identified as delimited by shared non-transposable elements and non-coding sequences surrounding the SPA gene and correspond to 35 268, 22 739, 43 397 and 53 919 bp for the A, B, D and S genomes, respectively. Sequence length discrepancies within and outside the SPA orthologous regions are the result of non-shared transposable elements (TE insertions, all of which inserted after the progenitors of the four genomes divergence. Conclusion On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, Ae speltoides appears to be more evolutionary related to the B genome of T. aestivum than the A and D genomes. However, the differential insertions of TEs, none of which are conserved between the two genomes led to the conclusion that the S genome of Ae. speltoides has diverged very early from the progenitor of the B genome which remains to be identified.

  3. Deep learning

    Science.gov (United States)

    Lecun, Yann; Bengio, Yoshua; Hinton, Geoffrey

    2015-05-01

    Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.

  4. Evolutionary Computation:ao Overview

    Institute of Scientific and Technical Information of China (English)

    HeZhenya; WeiChengjian

    1997-01-01

    Evolutionary computation is a field of simulating evolution on a computer.Both aspects of it ,the problem solving aspect and the aspect of modeling natural evolution,are important.Simulating evolution on a computer results in stochastic optimization techniques that can outperform classical methods of optimization when applied to difficult real-world problems.There are currently four main avenues of research in simulated evolution:genetic algorithms,evolutionary programming,evolution strategies,and genetic programming.This paper presents a brief overview of thd field on evolutionary computation,including some theoretical issues,adaptive mechanisms,improvements,constrained optimizqtion,constrained satisfaction,evolutionary neural networks,evolutionary fuzzy systems,hardware evolution,evolutionary robotics,parallel evolutionary computation,and co-evolutionary models.The applications of evolutionary computation for optimizing system and intelligent information processing in telecommunications are also introduced.

  5. 47 CFR 32.2424 - Submarine & deep sea cable.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Submarine & deep sea cable. 32.2424 Section 32... Submarine & deep sea cable. (a) This account shall include the original cost of submarine cable and deep sea... defined below, are to be maintained for nonmetallic submarine and deep sea cable and metallic...

  6. Evolutionary Design in Art

    Science.gov (United States)

    McCormack, Jon

    Evolution is one of the most interesting and creative processes we currently understand, so it should come as no surprise that artists and designers are embracing the use of evolution in problems of artistic creativity. The material in this section illustrates the diversity of approaches being used by artists and designers in relation to evolution at the boundary of art and science. While conceptualising human creativity as an evolutionary process in itself may be controversial, what is clear is that evolutionary processes can be used to complement, even enhance human creativity, as the chapters in this section aptly demonstrate.

  7. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    Darwinian evolution by natural selection is driven primarily by differential survival and reproduction among individuals in a population. When the evolutionary interest of an individual is in conflict with the interests of the population, the genes increasing individual fitness at the cost...... of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...

  8. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  9. Evolutionary toxicology: Meta-analysis of evolutionary events in response to chemical stressors.

    Science.gov (United States)

    M Oziolor, Elias; De Schamphelaere, Karel; Matson, Cole W

    2016-12-01

    The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and

  10. Deep Fish.

    Science.gov (United States)

    Ishaq, Omer; Sadanandan, Sajith Kecheril; Wählby, Carolina

    2017-01-01

    Zebrafish ( Danio rerio) is an important vertebrate model organism in biomedical research, especially suitable for morphological screening due to its transparent body during early development. Deep learning has emerged as a dominant paradigm for data analysis and found a number of applications in computer vision and image analysis. Here we demonstrate the potential of a deep learning approach for accurate high-throughput classification of whole-body zebrafish deformations in multifish microwell plates. Deep learning uses the raw image data as an input, without the need of expert knowledge for feature design or optimization of the segmentation parameters. We trained the deep learning classifier on as few as 84 images (before data augmentation) and achieved a classification accuracy of 92.8% on an unseen test data set that is comparable to the previous state of the art (95%) based on user-specified segmentation and deformation metrics. Ablation studies by digitally removing whole fish or parts of the fish from the images revealed that the classifier learned discriminative features from the image foreground, and we observed that the deformations of the head region, rather than the visually apparent bent tail, were more important for good classification performance.

  11. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.

    2016-01-01

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these

  12. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...

  13. Evolutionary developmental psychology.

    Science.gov (United States)

    King, Ashley C; Bjorklund, David F

    2010-02-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection with the study of human development, focusing on the epigenetic effects that occur between humans and their environment in a way that attempts to explain how evolved psychological mechanisms become expressed in the phenotypes of adults. An evolutionary developmental perspective includes an appreciation of comparative research and we, among others, argue that contrasting the cognition of humans with that of nonhuman primates can provide a framework with which to understand how human cognitive abilities and intelligence evolved. Furthermore, we argue that several aspects of childhood (e.g., play and immature cognition) serve both as deferred adaptations as well as imparting immediate benefits. Intense selection pressure was surely exerted on childhood over human evolutionary history and, as a result, neglecting to consider the early developmental period of children when studying their later adulthood produces an incomplete picture of the evolved adaptations expressed through human behavior and cognition.

  14. Optimal Mixing Evolutionary Algorithms

    NARCIS (Netherlands)

    Thierens, D.; Bosman, P.A.N.; Krasnogor, N.

    2011-01-01

    A key search mechanism in Evolutionary Algorithms is the mixing or juxtaposing of partial solutions present in the parent solutions. In this paper we look at the efficiency of mixing in genetic algorithms (GAs) and estimation-of-distribution algorithms (EDAs). We compute the mixing probabilities of

  15. Evolutionary perspectives on ageing.

    Science.gov (United States)

    Reichard, Martin

    2017-05-26

    From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Evolutionary Theories of Detection

    Energy Technology Data Exchange (ETDEWEB)

    Fitch, J P

    2005-04-29

    Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

  17. Evolutionary trends in Heteroptera

    NARCIS (Netherlands)

    Cobben, R.H.

    1968-01-01

    1. This work, the first volume of a series dealing with evolutionary trends in Heteroptera, is concerned with the egg system of about 400 species. The data are presented systematically in chapters 1 and 2 with a critical review of the literature after each family.

    2. Chapter 3 evaluates facts

  18. Learning: An Evolutionary Analysis

    Science.gov (United States)

    Swann, Joanna

    2009-01-01

    This paper draws on the philosophy of Karl Popper to present a descriptive evolutionary epistemology that offers philosophical solutions to the following related problems: "What happens when learning takes place?" and "What happens in human learning?" It provides a detailed analysis of how learning takes place without any direct transfer of…

  19. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.

    2016-01-01

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these o

  20. Molluscan Evolutionary Development

    DEFF Research Database (Denmark)

    Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

    2008-01-01

    Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...

  1. When development matters: From evolutionary psychology to evolutionary developmental psychology

    OpenAIRE

    Hernández Blasi, Carlos; Gardiner, Amy K.; David F. Bjorklund

    2008-01-01

    This article presents evolutionary developmental psychology (EDP) as an emerging field of evolutionary psychology (EP). In describing the core tenets of both approaches and the differences between them, we emphasize the important roles that evolution and development have in understanding human behaviour. We suggest that developmental psychologists should pay more attention to evolutionary issues and, conversely, evolutionary psychologists should take development seriously. Key words: evol...

  2. The Origin of Resources Property Rights and Moral:An Interpretation of Evolutionary Game Theory%资源产权与道德的起源:演化博弈论的诠释

    Institute of Scientific and Technical Information of China (English)

    陈安宁; 朱喆

    2013-01-01

    This article will investigate how resources property rights and moral emerge spontaneously.First it will review the history of property rights briefly,introduce the applied Game Theory,especially the recent research about the emergency of property rights through Evolutionary Game Theory.Then it will point out its deficiency which is too ambiguous about the socio-economic meaning of pay-off to reveal the process of interaction and co-evolution between the Game and its environment.Second,it will expand the concept of fitness from the biological genetics to the analysis of the social evolution; and analyze the constitution of socio-economic fitness which is related to its type of competition.Third,it will introduce the condition equation into the traditional Replicator Dynamic Equation,to explain the interaction between Behavior Game and environment of the Game.Fourth,it will investigate how property rights and moral emerge spontaneously through improved Replicator Dynamic Equation,and point out that both property rights and moral were just the result of human' s intemperate battle and non-restraint multiplication.Finally,it will analyze three deficienies of Locker' s society,and its power to evolve continuously.%论文在一个演化经济学视角下考察资源产权和道德(以下简称为产权和道德)自生自发问题.首先,简略地梳理了产权生发研究的历史;介绍了应用博弈论,特别是演化博弈论研究产权生发问题的近况,并指出其不足之处在于博弈支付的社会经济学含义模糊和无法揭示行为博弈与博弈环境相互作用、共同演化的过程.其次,扩展了生物遗传学中适应度的概念,使其适于社会演化分析;分析了社会经济学适应度的构成及其与竞争类型的关系.第三,为了说明行为博弈与博弈环境之间的相互作用关系,在传统复制者动态方程组中,引入状态方程(或组).第四,采用改进后的复制者动态方程组分析产权和道

  3. Deep history impacts present-day ecology and biodiversity.

    Science.gov (United States)

    Vitt, Laurie J; Pianka, Eric R

    2005-05-31

    Lizards and snakes putatively arose between the early Jurassic and late Triassic; they diversified worldwide and now occupy many different ecological niches, making them ideal for testing theories on the origin of ecological traits. We propose and test the "deep history hypothesis," which claims that differences in ecological traits among species arose early in evolutionary history of major clades, and that present-day assemblages are structured largely because of ancient, preexisting differences. We combine phylogenetic data with ecological data collected over nearly 40 years to reconstruct the evolution of dietary shifts in squamate reptiles. Data on diets of 184 lizard species in 12 families from 4 continents reveal significant dietary shifts at 6 major divergence points, reducing variation by 79.8%. The most striking dietary divergence (27.6%) occurred in the late Triassic, when Iguania and Scleroglossa split. These two clades occupy different regions of dietary niche space. Acquisition of chemical prey discrimination, jaw prehension, and wide foraging provided scleroglossans access to sedentary and hidden prey that are unavailable to iguanians. This cladogenic event may have profoundly influenced subsequent evolutionary history and diversification. We suggest the hypothesis that ancient events in squamate cladogenesis, rather than present-day competition, caused dietary shifts in major clades such that some lizard clades gained access to new resources, which in turn led to much of the biodiversity observed today.

  4. Viruses and mobile elements as drivers of evolutionary transitions

    Science.gov (United States)

    2016-01-01

    The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431520

  5. Evo-Devo: evolutionary developmental mechanisms.

    Science.gov (United States)

    Hall, Brian K

    2003-01-01

    Evolutionary developmental biology (Evo-Devo) as a discipline is concerned, among other things, with discovering and understanding the role of changes in developmental mechanisms in the evolutionary origin of aspects of the phenotype. In a very real sense, Evo-Devo opens the black box between genotype and phenotype, or more properly, phenotypes as multiple life history stages arise in many organisms from a single genotype. Changes in the timing or positioning of an aspect of development in a descendant relative to an ancestor (heterochrony and heterotopy) were two evolutionary developmental mechanisms identified by Ernst Haeckel in the 1870s. Many more have since been identified, in large part because of our enhanced understanding of development and because new mechanisms emerge as development proceeds: the transfer from maternal to zygotic genomic control; cell-to-cell interactions; cell differentiation and cell migration; embryonic inductions; functional interactions at the tissue and organ levels; growth. Within these emergent processes, gene networks and gene cascades (genetic modules) link the genotype with morphogenetic units (cellular modules, namely germ layers, embryonic fields or cellular condensations), while epigenetic processes such as embryonic inductions, tissue interactions and functional integration, link morphogenetic units to the phenotype. Evolutionary developmental mechanisms also include interactions between individuals of the same species, individuals of different species, and species and their biotic and/or abiotic environment. Such interactions link ecological communities. Importantly, there is little to distinguish the causality that underlies these interactions from that which underlies inductive interactions within embryos.

  6. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  7. Evolutionary status of Entamoeba

    Institute of Scientific and Technical Information of China (English)

    DONG Jiuhong; WEN Jianfan; XIN Dedong; LU Siqi

    2004-01-01

    In addition to its medical importance as parasitic pathogen, Entamoeba has aroused people's interest in its evolutionary status for a long time. Lacking mitochondrion and other intracellular organelles common to typical eukaryotes, Entamoeba and several other amitochondrial protozoans have been recognized as ancient pre-mitochondriate eukaryotes and named "archezoa", the most primitive extant eukaryotes. It was suggested that they might be living fossils that remained in a primitive stage of evolution before acquisition of organelles, lying close to the transition between prokaryotes and eukaryotes. However, recent studies revealed that Entamoeba contained an organelle, "crypton" or "mitosome", which was regarded as specialized or reductive mitochondrion. Relative molecular phylogenetic analyses also indicated the existence or the probable existence of mitochondrion in Entamoeba. Our phylogenetic analysis based on DNA topoisomerase II strongly suggested its divergence after some mitchondriate eukaryotes. Here, all these recent researches are reviewed and the evolutionary status of Entamoeba is discussed.

  8. Evolutionary internalized regularities.

    Science.gov (United States)

    Schwartz, R

    2001-08-01

    Roger Shepard's proposals and supporting experiments concerning evolutionary internalized regularities have been very influential in the study of vision and in other areas of psychology and cognitive science. This paper examines issues concerning the need, nature, explanatory role, and justification for postulating such internalized constraints. In particular, I seek further clarification from Shepard on how best to understand his claim that principles of kinematic geometry underlie phenomena of motion perception. My primary focus is on the ecological validity of Shepard's kinematic constraint in the context of ordinary motion perception. First, I explore the analogy Shepard draws between internalized circadian rhythms and the supposed internalization of kinematic geometry. Next, questions are raised about how to interpret and justify applying results from his own and others' experimental studies of apparent motion to more everyday cases of motion perception in richer environments. Finally, some difficulties with Shepard's account of the evolutionary development of his kinematic constraint are considered.

  9. Evolutionary biology of cancer.

    Science.gov (United States)

    Crespi, Bernard; Summers, Kyle

    2005-10-01

    Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease.

  10. New insights into the evolutionary history of biological nitrogen fixation

    Directory of Open Access Journals (Sweden)

    Eric eBoyd

    2013-08-01

    Full Text Available Nitrogenase, which catalyzes the ATP-dependent reduction of dinitrogen (N2 to ammonia (NH3, accounts for roughly half of the bioavailable nitrogen supporting extant life. The fundamental requirement for fixed forms of nitrogen for life on Earth, both at present and in the past, has led to broad and significant interest in the origin and evolution of this fundamental biological process. One key question is whether the limited availability of fixed nitrogen was a factor in life’s origin or whether there were ample sources of fixed nitrogen produced by abiotic processes or delivered through the weathering of bolide impact materials to support this early life. If the latter, the key questions become what were the characteristics of the environment that precipitated the evolution of this oxygen sensitive process, when did this occur, and how was its subsequent evolutionary history impacted by the advent of oxygenic photosynthesis and the rise of oxygen in the Earth’s biosphere. Since the availability of fixed sources of nitrogen capable of supporting early life is difficult to glean from the geologic record, there are limited means to get direct insights into these questions. Indirect insights, however, can be gained by deep phylogenetic studies of nitrogenase structural gene products and additional gene products involved in the biosynthesis of the complex metal-containing prosthetic groups associated with this enzyme complex. Insights gained from such studies, as reviewed herein, challenge traditional models for the evolution of biological nitrogen fixation and provide the basis for the development of new conceptual models that explain the stepwise evolution of this highly complex and life sustaining process.

  11. Evolutionary game design

    CERN Document Server

    Browne, Cameron

    2011-01-01

    The book describes the world's first successful experiment in fully automated board game design. Evolutionary methods were used to derive new rule sets within a custom game description language, and self-play trials used to estimate each derived game's potential to interest human players. The end result is a number of new and interesting games, one of which has proved popular and gone on to be commercially published.

  12. Evolutionary theory of cancer.

    Science.gov (United States)

    Attolini, Camille Stephan-Otto; Michor, Franziska

    2009-06-01

    As Theodosius Dobzhansky famously noted in 1973, "Nothing in biology makes sense except in the light of evolution," and cancer is no exception to this rule. Our understanding of cancer initiation, progression, treatment, and resistance has advanced considerably by regarding cancer as the product of evolutionary processes. Here we review the literature of mathematical models of cancer evolution and provide a synthesis and discussion of the field.

  13. Asymmetric Evolutionary Games.

    Directory of Open Access Journals (Sweden)

    Alex McAvoy

    2015-08-01

    Full Text Available Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

  14. Deep Vein Thrombosis

    Science.gov (United States)

    Deep vein thrombosis, or DVT, is a blood clot that forms in a vein deep in the body. Most deep vein ... the condition is called thrombophlebitis. A deep vein thrombosis can break loose and cause a serious problem ...

  15. From deep-sea volcanoes to human pathogens: a conserved quorum-sensing signal in Epsilonproteobacteria.

    Science.gov (United States)

    Pérez-Rodríguez, Ileana; Bolognini, Marie; Ricci, Jessica; Bini, Elisabetta; Vetriani, Costantino

    2015-05-01

    Chemosynthetic Epsilonproteobacteria from deep-sea hydrothermal vents colonize substrates exposed to steep thermal and redox gradients. In many bacteria, substrate attachment, biofilm formation, expression of virulence genes and host colonization are partly controlled via a cell density-dependent mechanism involving signal molecules, known as quorum sensing. Within the Epsilonproteobacteria, quorum sensing has been investigated only in human pathogens that use the luxS/autoinducer-2 (AI-2) mechanism to control the expression of some of these functions. In this study we showed that luxS is conserved in Epsilonproteobacteria and that pathogenic and mesophilic members of this class inherited this gene from a thermophilic ancestor. Furthermore, we provide evidence that the luxS gene is expressed--and a quorum-sensing signal is produced--during growth of Sulfurovum lithotrophicum and Caminibacter mediatlanticus, two Epsilonproteobacteria from deep-sea hydrothermal vents. Finally, we detected luxS transcripts in Epsilonproteobacteria-dominated biofilm communities collected from deep-sea hydrothermal vents. Taken together, our findings indicate that the epsiloproteobacterial lineage of the LuxS enzyme originated in high-temperature geothermal environments and that, in vent Epsilonproteobacteria, luxS expression is linked to the production of AI-2 signals, which are likely produced in situ at deep-sea vents. We conclude that the luxS gene is part of the ancestral epsilonproteobacterial genome and represents an evolutionary link that connects thermophiles to human pathogens.

  16. Complex cooperative networks from evolutionary preferential attachment.

    Directory of Open Access Journals (Sweden)

    Julia Poncela

    Full Text Available In spite of its relevance to the origin of complex networks, the interplay between form and function and its role during network formation remains largely unexplored. While recent studies introduce dynamics by considering rewiring processes of a pre-existent network, we study network growth and formation by proposing an evolutionary preferential attachment model, its main feature being that the capacity of a node to attract new links depends on a dynamical variable governed in turn by the node interactions. As a specific example, we focus on the problem of the emergence of cooperation by analyzing the formation of a social network with interactions given by the Prisoner's Dilemma. The resulting networks show many features of real systems, such as scale-free degree distributions, cooperative behavior and hierarchical clustering. Interestingly, results such as the cooperators being located mostly on nodes of intermediate degree are very different from the observations of cooperative behavior on static networks. The evolutionary preferential attachment mechanism points to an evolutionary origin of scale-free networks and may help understand similar feedback problems in the dynamics of complex networks by appropriately choosing the game describing the interaction of nodes.

  17. Whole-genome sequencing of uropathogenic Escherichia coli reveals long evolutionary history of diversity and virulence.

    Science.gov (United States)

    Lo, Yancy; Zhang, Lixin; Foxman, Betsy; Zöllner, Sebastian

    2015-08-01

    Uropathogenic Escherichia coli (UPEC) are phenotypically and genotypically very diverse. This diversity makes it challenging to understand the evolution of UPEC adaptations responsible for causing urinary tract infections (UTI). To gain insight into the relationship between evolutionary divergence and adaptive paths to uropathogenicity, we sequenced at deep coverage (190×) the genomes of 19 E. coli strains from urinary tract infection patients from the same geographic area. Our sample consisted of 14 UPEC isolates and 5 non-UTI-causing (commensal) rectal E. coli isolates. After identifying strain variants using de novo assembly-based methods, we clustered the strains based on pairwise sequence differences using a neighbor-joining algorithm. We examined evolutionary signals on the whole-genome phylogeny and contrasted these signals with those found on gene trees constructed based on specific uropathogenic virulence factors. The whole-genome phylogeny showed that the divergence between UPEC and commensal E. coli strains without known UPEC virulence factors happened over 32 million generations ago. Pairwise diversity between any two strains was also high, suggesting multiple genetic origins of uropathogenic strains in a small geographic region. Contrasting the whole-genome phylogeny with three gene trees constructed from common uropathogenic virulence factors, we detected no selective advantage of these virulence genes over other genomic regions. These results suggest that UPEC acquired uropathogenicity long time ago and used it opportunistically to cause extraintestinal infections.

  18. Molecular systematics and evolutionary history of the genus Carabus (Col. Carabidae).

    Science.gov (United States)

    Deuve, Thierry; Cruaud, Astrid; Genson, Gwenaëlle; Rasplus, Jean-Yves

    2012-10-01

    Despite the number of evolutionary, ecological and conservation studies that are conducted on Carabus, the global evolutionary history of the genus remains poorly understood. Here, we analysed 7.5 kilobases of DNA sequence data (six mitochondrial and four nuclear genes) from a worldwide sample of 45% of the known subgenera (99 species and 14 subspecies). We compared the nuclear and mitochondrial phylogenies obtained from Maximum likelihood and Bayesian analyses through topological tests of congruence and dating analyses. Our results mostly corroborate the monophyly of the morphological subgroups of Carabus. However, current morphological and molecular data appear unable to accurately infer the deep branchings within the genus. We show that Carabus originated ca. 16.7-25.1 Ma, approximately 25 Myr later than previously estimated. Major groups of Carabus are subdivided into clades that diverged from each other in a relatively short period of time around 10 Ma (6.6-14.8). This time frame suggests that the present-day distribution of Carabus subgroups may be explained by isolation resulting from Eurasian forest fragmentation brought on by Miocene climate changes and by mountain orogenesis. Finally, we highlight several conflicts between mitochondrial and nuclear topologies that may be explained by mitochondrial introgression.

  19. Deep Red (Profondo Rosso)

    CERN Document Server

    Cine Club

    2015-01-01

    Wednesday 29 April 2015 at 20:00 CERN Council Chamber    Deep Red (Profondo Rosso) Directed by Dario Argento (Italy, 1975) 126 minutes A psychic who can read minds picks up the thoughts of a murderer in the audience and soon becomes a victim. An English pianist gets involved in solving the murders, but finds many of his avenues of inquiry cut off by new murders, and he begins to wonder how the murderer can track his movements so closely. Original version Italian; English subtitles

  20. Results of a preliminary study of the potential of vasodilators for improving thermotherapy of deep-seated tumours [printed with original paging at end of 2(2); omitted from Int J Hyperthermia 1986 Jan-Mar;2(1)].

    Science.gov (United States)

    Nussbaum, G H; Babbs, C F; Mintun, M A

    1986-01-01

    Administration of the vasodilator hydralazine to a single mongrel dog with a transplanted, superficial transmissible venereal tumour in the abdomen permitted tumour-adjacent normal tissue temperature differences produced in local hyperthermia to be enhanced by nearly 2 degrees C. A preliminary study of tumour and normal tissue perfusion rate in the dog, employing the 15O-labelled water-positron emission tomography technique, suggested that administration of the vasodilator led to a significant reduction in the tumour perfusion rate, consistent with the observed tumour temperature enhancement. Computational studies with a multi-layer, one-dimensional cylindrical model of deep-tumour heating suggest that vasodilator-induced reductions of tumour perfusion rates could significantly increase deep tumour-superficial normal tissue temperature differences produced in deep-tumour thermotherapy.

  1. Deep homology in the age of next-generation sequencing.

    Science.gov (United States)

    Tschopp, Patrick; Tabin, Clifford J

    2017-02-05

    The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term 'deep homology' was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput next-generation sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. © 2016 The Author(s).

  2. Prevolutionary dynamics and the origin of evolution

    OpenAIRE

    Nowak, Martin A.; Ohtsuki, Hisashi

    2008-01-01

    Life is that which replicates and evolves. The origin of life is also the origin of evolution. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here, we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. Therefore, any theory for the origin of life must address the emergence of such a system. We describe prelife as an alphabet of active m...

  3. Investigation on Evolutionary Synthesis of Movement Commands

    Directory of Open Access Journals (Sweden)

    Zuzana Oplatková

    2009-01-01

    Full Text Available This paper deals with usage of an alternative tool for symbolic regression—analytic programming which is able to solve various problems from the symbolic domain, as well as genetic programming and grammatical evolution. This paper describes a setting of an optimal trajectory for a robot (originally designed as an artificial ant on Santa Fe trail solved by means of analytic programming. Firstly, main principles of analytic programming are described and explained. The second part shows how analytic programming was used for the application of finding a suitable trajectory step by step. Because analytic programming needs evolutionary algorithms for its run, three evolutionary algorithms were used—self-organizing migrating algorithm, differential evolution, and simulated annealing—to show that anyone can be used. The total number of simulations was 150 and results show that the first two used algorithms were more successful than not so robust simulated annealing.

  4. Teaching About Adaptation: Why Evolutionary History Matters

    Science.gov (United States)

    Kampourakis, Kostas

    2013-02-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to the survival and reproduction of its possessors. Finally, adaptation has been defined as a process, as well. Consequently, two questions arise: the first is a philosophical one and focuses on what adaptation actually is; the second is a pedagogical one and focuses on what science teachers and educators should teach about it. In this article, the various definitions of adaptation are discussed and their uses in some textbooks are presented. It is suggested that, given elementary students' intuitions about purpose and design in nature and secondary students' teleological explanations for the origin of adaptations, any definition of adaptation as a trait should include some information about its evolutionary history.

  5. Evolutionary stability in Lotka-Volterra systems.

    Science.gov (United States)

    Cressman, Ross; Garay, József

    2003-05-21

    The Lotka-Volterra model of population ecology, which assumes all individuals in each species behave identically, is combined with the behavioral evolution model of evolutionary game theory. In the resultant monomorphic situation, conditions for the stability of the resident Lotka-Volterra system, when perturbed by a mutant phenotype in each species, are analysed. We develop an evolutionary ecology stability concept, called a monomorphic evolutionarily stable ecological equilibrium, which contains as a special case the original definition by Maynard Smith of an evolutionarily stable strategy for a single species. Heuristically, the concept asserts that the resident ecological system must be stable as well as the phenotypic evolution on the "stationary density surface". The conditions are also shown to be central to analyse stability issues in the polymorphic model that allows arbitrarily many phenotypes in each species, especially when the number of species is small. The mathematical techniques are from the theory of dynamical systems, including linearization, centre manifolds and Molchanov's Theorem.

  6. Sculpting the endomembrane system in deep time: high resolution phylogenetics of Rab GTPases

    National Research Council Canada - National Science Library

    Elias, Marek; Brighouse, Andrew; Gabernet-Castello, Carme; Field, Mark C; Dacks, Joel B

    2012-01-01

    .... Resolving the evolutionary history of organelle-identity encoding proteins within the endomembrane system is a necessity for unravelling the origins and diversification of the endogenously derived organelles...

  7. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    This paper presents first results from an interdisciplinary project, in which the fields of architecture, philosophy and artificial life are combined to explore possible futures of architecture. Through an interactive evolutionary installation, called EvoCurtain, we investigate aspects of how...... to the development of designs tailored to the individual preferences of inhabitants, changing the roles of architects and designers entirely. Architecture-as-it-could-be is a philosophical approach conducted through artistic methods to anticipate the technological futures of human-centered development within...

  8. Constraints as evolutionary systems

    CERN Document Server

    Rácz, István

    2016-01-01

    The constraint equations for smooth $[n+1]$-dimensional (with $n\\geq 3$) Riemannian or Lorentzian spaces satisfying the Einstein field equations are considered. It is shown, regardless of the signature of the primary space, that the constraints can be put into the form of an evolutionary system comprised either by a first order symmetric hyperbolic system and a parabolic equation or, alternatively, by a strongly hyperbolic system and a subsidiary algebraic relation. In both cases the (local) existence and uniqueness of solutions are also discussed.

  9. An evolutionary approach

    Science.gov (United States)

    Healy, Thomas J.

    1993-04-01

    The paper describes an evolutionary approach to the development of aerospace systems, represented by the introduction of integrated product teams (IPTs), which are now used at Rockwell's Space Systems Division on all new programs and are introduced into existing projects after demonstrations of increases in quality and reductions in cost and schedule due to IPTs. Each IPT is unique and reflects its own program and lasts for the life of the program. An IPT includes customers, suppliers, subcontractors, and associate contractors, and have a charter, mission, scope of authority, budget, and schedule. Functional management is responsible for the staffing, training, method development, and generic technology development.

  10. Distributed Evolutionary Graph Partitioning

    CERN Document Server

    Sanders, Peter

    2011-01-01

    We present a novel distributed evolutionary algorithm, KaFFPaE, to solve the Graph Partitioning Problem, which makes use of KaFFPa (Karlsruhe Fast Flow Partitioner). The use of our multilevel graph partitioner KaFFPa provides new effective crossover and mutation operators. By combining these with a scalable communication protocol we obtain a system that is able to improve the best known partitioning results for many inputs in a very short amount of time. For example, in Walshaw's well known benchmark tables we are able to improve or recompute 76% of entries for the tables with 1%, 3% and 5% imbalance.

  11. An exceptional fossil skull from South America and the origins of the archosauriform radiation

    Science.gov (United States)

    Pinheiro, Felipe L.; França, Marco A. G.; Lacerda, Marcel B.; Butler, Richard J.; Schultz, Cesar L.

    2016-03-01

    Birds, dinosaurs, crocodilians, pterosaurs and their close relatives form the highly diverse clade Archosauriformes. Archosauriforms have a deep evolutionary history, originating in the late Permian, prior to the end-Permian mass extinction, and radiating in the Triassic to dominate Mesozoic ecosystems. However, the origins of this clade and its extraordinarily successful body plan remain obscure. Here, we describe an exceptionally preserved fossil skull from the Lower Triassic of Brazil, representing a new species, Teyujagua paradoxa, transitional in morphology between archosauriforms and more primitive reptiles. This skull reveals for the first time the mosaic assembly of key features of the archosauriform skull, including the antorbital and mandibular fenestrae, serrated teeth, and closed lower temporal bar. Phylogenetic analysis recovers Teyujagua as the sister taxon to Archosauriformes, and is congruent with a two-phase model of early archosauriform evolution, in response to two mass extinctions occurring at the end of the Guadalupian and the Permian.

  12. Deep blast

    Science.gov (United States)

    From southern New Mexico to the Great Slave Lake of Canada, scientists from the United States and Canada recently detonated 10 underground chemical explosions to generate a clearer picture of the Earth's crust and upper mantle. Called Project Deep Probe, the experiment is designed to see through the crust and into the upper mantle to a depth of 300 miles.In the United States, Earth scientists from Rice University, Purdue University, and the University of Oregon are participating in the project. “Researchers hope to get a picture of the upper mantle beneath the Rocky Mountains and the Colorado Plateau, to understand the role the mantle played in formation and uplift,” says Alan Levander of Rice. To enhance that “picture,” 750 portable seismographs were placed along a roughly north-south line extending from Crownpoint, New Mexico to Edmonton, Alberta. The seismic recordings will be used to enhance weak seismic waves that penetrated the upper mantle.

  13. Evolutionary ethics from Darwin to Moore.

    Science.gov (United States)

    Allhoff, Fritz

    2003-01-01

    Evolutionary ethics has a long history, dating all the way back to Charles Darwin. Almost immediately after the publication of the Origin, an immense interest arose in the moral implications of Darwinism and whether the truth of Darwinism would undermine traditional ethics. Though the biological thesis was certainly exciting, nobody suspected that the impact of the Origin would be confined to the scientific arena. As one historian wrote, 'whether or not ancient populations of armadillos were transformed into the species that currently inhabit the new world was certainly a topic about which zoologists could disagree. But it was in discussing the broader implications of the theory...that tempers flared and statements were made which could transform what otherwise would have been a quiet scholarly meeting into a social scandal' (Farber 1994, 22). Some resistance to the biological thesis of Darwinism sprung from the thought that it was incompatible with traditional morality and, since one of them had to go, many thought that Darwinism should be rejected. However, some people did realize that a secular ethics was possible so, even if Darwinism did undermine traditional religious beliefs, it need not have any effects on moral thought. Before I begin my discussion of evolutionary ethics from Darwin to Moore, I would like to make some more general remarks about its development. There are three key events during this history of evolutionary ethics. First, Charles Darwin published On the Origin of the Species (Darwin 1859). Since one did not have a fully developed theory of evolution until 1859, there exists little work on evolutionary ethics until then. Shortly thereafter, Herbert Spencer (1898) penned the first systematic theory of evolutionary ethics, which was promptly attacked by T.H. Huxley (Huxley 1894). Second, at about the turn of the century, moral philosophers entered the fray and attempted to demonstrate logical errors in Spencer's work; such errors were alluded

  14. The evolutionary language game.

    Science.gov (United States)

    Nowak, M A; Plotkin, J B; Krakauer, D C

    1999-09-21

    We explore how evolutionary game dynamics have to be modified to accomodate a mathematical framework for the evolution of language. In particular, we are interested in the evolution of vocabulary, that is associations between signals and objects. We assume that successful communication contributes to biological fitness: individuals who communicate well leave more offspring. Children inherit from their parents a strategy for language learning (a language acquisition device). We consider three mechanisms whereby language is passed from one generation to the next: (i) parental learning: children learn the language of their parents; (ii) role model learning: children learn the language of individuals with a high payoff; and (iii) random learning: children learn the language of randomly chosen individuals. We show that parental and role model learning outperform random learning. Then we introduce mistakes in language learning and study how this process changes language over time. Mistakes increase the overall efficacy of parental and role model learning: in a world with errors evolutionary adaptation is more efficient. Our model also provides a simple explanation why homonomy is common while synonymy is rare. Copyright 1999 Academic Press.

  15. The proper place of hopeful monsters in evolutionary biology.

    Science.gov (United States)

    Theissen, Günter

    2006-03-01

    Hopeful monsters are organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage. The Synthetic Theory of evolutionary biology has rejected the evolutionary relevance of hopeful monsters, but could not fully explain the mechanism and mode of macroevolution. On the other hand, several lines of evidence suggest that hopeful monsters played an important role during the origin of key innovations and novel body plans by saltational rather than gradual evolution. Homeotic mutants are identified as an especially promising class of hopeful monsters. Examples for animal and plant lineages that may have originated as hopeful monsters are given. Nevertheless, a brief review of the history of the concept of hopeful monsters reveals that it needs refinements and empirical tests if it is to be a useful addition to evolutionary biology. While evolutionary biology is traditionally zoocentric, hopeful monsters might be more relevant for plant than for animal evolution. Even though during recent years developmental genetics has provided detailed knowledge about how hopeful monsters can originate in the first place, we know almost nothing about their performance in natural populations and thus the ultimate difference between hopeful and hopeless. Studying the fitness of candidate hopeful monsters (suitable mutants with profound phenotype) in natural habitats thus remains a considerable challenge for the future.

  16. Prebiological evolution and the physics of the origin of life

    Science.gov (United States)

    Delaye, Luis; Lazcano, Antonio

    2005-03-01

    The basic tenet of the heterotrophic theory of the origin of life is that the maintenance and reproduction of the first living systems depended primarily on prebiotically synthesized organic molecules. It is unlikely that any single mechanism can account for the wide range of organic compounds that may have accumulated on the primitive Earth, suggesting that the prebiotic soup was formed by contributions from endogenous syntheses in reducing environments, metal sulphide-mediated synthesis in deep-sea vents, and exogenous sources such as comets, meteorites and interplanetary dust. The wide range of experimental conditions under which amino acids and nucleobases can be synthesized suggests that the abiotic syntheses of these monomers did not take place under a narrow range defined by highly selective reaction conditions, but rather under a wide variety of settings. The robustness of this type of chemistry is supported by the occurrence of most of these biochemical compounds in the Murchison meteorite. These results lend strong credence to the hypothesis that the emergence of life was the outcome of a long, but not necessarily slow, evolutionary processes. The origin of life may be best understood in terms of the dynamics and evolution of sets of chemical replicating entities. Whether such entities were enclosed within membranes is not yet clear, but given the prebiotic availability of amphiphilic compounds this may have well been the case. This scheme is not at odds with the theoretical models of self-organized emerging systems, but what is known of biology suggest that the essential traits of living systems could have not emerged in the absence of genetic material able to store, express and, upon replication, transmit to its progeny information capable of undergoing evolutionary change. How such genetic polymer first evolved is a central issue in origin-of-life studies.

  17. Deep subspace mapping in hyperspectral imaging

    Science.gov (United States)

    Wadströmer, Niclas; Gustafsson, David; Perersson, Henrik; Bergström, David

    2016-10-01

    We propose a novel Deep learning approach using autoencoders to map spectral bands to a space of lower dimensionality while preserving the information that makes it possible to discriminate different materials. Deep learning is a relatively new pattern recognition approach which has given promising result in many applications. In Deep learning a hierarchical representation of increasing level of abstraction of the features is learned. Autoencoder is an important unsupervised technique frequently used in Deep learning for extracting important properties of the data. The learned latent representation is a non-linear mapping of the original data which potentially preserve the discrimination capacity.

  18. THE CONCEPT OF USING EVOLUTIONARY ALGORITHMS AS TOOLS FOR OPTIMAL PLANNING OF MULTIMODAL COMPOSITION IN THE DIDACTIC TEXTS

    Directory of Open Access Journals (Sweden)

    Marek A. Jakubowski

    2014-11-01

    Full Text Available At the beginning we would like to provide a short description of the new theory of learning in the digital age called connectivism. It is the integration of principles explored by the following theories: chaos, network, complexity and self-organization. Next, we describe in short new visual solutions for the teaching of writing so called multimodal literacy 5–11. We define and describe the following notions: multimodal text and original theory so called NOS (non-optimum systems methodology as a basis for new methods of visual solutions at the classes and audiovisual texts applications. Especially, we would like to emphasize the tremendous usefulness of evolutionary algorithms VEGA and NSGA as tools for optimal planning of multimodal composition in teaching texts. Finally, we give some examples of didactic texts for classrooms, which provide a deep insight into learning skills and tasks needed in the Internet age.

  19. Evolutionary origins of hepatitis A virus in small mammals

    NARCIS (Netherlands)

    J.-F. Drexler (Jan-Felix); V.M. Corman (Victor); A.N. Lukashev (Alexander); J.M.A. van den Brand (Judith); A. Gmyl (Anatoly); S. Brunink (Sebastian); A. Rasche (Andrea); N. Seggewi (Nicole); H. Feng (Hui); L.M.E. Leijten (Lonneke); P. Vallo (Peter); T. Kuiken (Thijs); A. Dotzauer (Andreas); R.G. Ulrich (Rainer); S.M. Lemon (Stanley M.); C. Drosten (Christian)

    2015-01-01

    textabstractHepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian

  20. Evolutionary Origin of the Staphylococcal Cassette Chromosome mec (SCCmec)

    DEFF Research Database (Denmark)

    Rolo, Joana; Worning, Peder; Nielsen, Jesper Boye

    2017-01-01

    Several lines of evidence indicate that the most primitive staphylococcal species, those of the Staphylococcus sciuri group, were involved in the first stages of evolution of the staphylococcal cassette chromosome mec (SCCmec), the genetic element carrying the β-lactam resistance gene mecA. Howev...

  1. Quiescence: early evolutionary origins and universality do not imply uniformity.

    Science.gov (United States)

    O'Farrell, Patrick H

    2011-12-27

    Cell cycle investigations have focused on relentless exponential proliferation of cells, an unsustainable situation in nature. Proliferation of cells, whether microbial or metazoan, is interrupted by periods of quiescence. The vast majority of cells in an adult metazoan lie quiescent. As disruptions in this quiescence are at the foundation of cancer, it will be important for the field to turn its attention to the mechanisms regulating quiescence. While often presented as a single topic, there are multiple forms of quiescence each with complex inputs, some of which are tied to conceptually challenging aspects of metazoan regulation such as size control. In an effort to expose the enormity of the challenge, I describe the differing biological purposes of quiescence, and the coupling of quiescence in metazoans to growth and to the structuring of tissues during development. I emphasize studies in the organism rather than in tissue culture, because these expose the diversity of regulation. While quiescence is likely to be a primitive biological process, it appears that in adapting quiescence to its many distinct biological settings, evolution has diversified it. Consideration of quiescence in different models gives us an overview of this diversity.

  2. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis

    NARCIS (Netherlands)

    Tyler, B.M.; Tripathy, S.; Zhang, X.; Dehal, P.; Jiang, R.H.Y.; Aerts, A.; Arredondo, F.D.; Baxter, L.; Bensasson, D.; Beynon, J.L.; Chapman, J.; Damasceno, C.M.B.; Dorrance, A.E.; Dou, D.; Dickerman, A.W.; Dubchak, I.L.; Garbelotto, M.; Gijzen, M.; Gordon, S.G.; Govers, F.; Grunwald, N.J.; Huang, W.; Ivors, K.L.; Jones, R.W.; Kamoun, S.; Krampis, K.; Lamour, K.H.; Lee, M.K.; McDonald, W.H.; Medina, M.; Meijer, H.J.G.; Nordberg, E.K.; Maclean, D.J.; Ospina-Giraldo, M.D.; Morris, P.F.; Phuntumart, V.; Putnam, N.H.; Rash, S.; Rose, J.K.C.; Sakihama, Y.; Salamov, A.A.; Savidor, A.; Scheuring, C.F.; Smith, B.M.; Sobral, B.W.S.; Terry, A.; Torto-Alalibo, T.A.; Win, J.; Xu, Z.; Zhang, H.; Grigoriev, I.V.; Rokhsar, D.S.; Boore, J.L.

    2006-01-01

    Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora

  3. Evolutionary origins of hepatitis A virus in small mammals

    NARCIS (Netherlands)

    J.-F. Drexler (Jan-Felix); V.M. Corman (Victor); A.N. Lukashev (Alexander); J.M.A. van den Brand (Judith); A. Gmyl (Anatoly); S. Brunink (Sebastian); A. Rasche (Andrea); N. Seggewi (Nicole); H. Feng (Hui); L.M.E. Leijten (Lonneke); P. Vallo (Peter); T. Kuiken (Thijs); A. Dotzauer (Andreas); R.G. Ulrich (Rainer); S.M. Lemon (Stanley M.); C. Drosten (Christian)

    2015-01-01

    textabstractHepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian

  4. Evolutionary origins and ecological consequences of endophyte symbiosis with grasses.

    Science.gov (United States)

    Clay, Keith; Schardl, Christopher

    2002-10-01

    Over the past 20 yr much has been learned about a unique symbiotic interaction between fungal endophytes and grasses. The fungi (Clavicipitaceae, Ascomycota) grow intercellularly and systemically in aboveground plant parts. Vertically transmitted asexual endophytes forming asymptomatic infections of cool-season grasses have been repeatedly derived from sexual species that abort host inflorescences. The phylogenetic distribution of seed-transmitted endophytes is strongly suggestive of cocladogenesis with their hosts. Molecular evidence indicates that many seed-transmitted endophytes are interspecific hybrids. Superinfection may result in hyphal fusion and parasexual recombination. Most endophytes produce one or more alkaloid classes that likely play some role in defending the host plant against pests. Hybridization may have led to the proliferation of alkaloid-production genes among asexual endophytes, favoring hybrids. The ergot alkaloid ergovaline, lolitrems, and lolines are produced by only a single sexual species, Epichloë festucae, but they are common in seed-transmitted endophytes, suggesting that E. festucae contributed genes for their synthesis. Asexual hybrids may also be favored by the counteracting of the accumulation of deleterious mutations (Muller's rachet). Endophyte infection can provide other benefits, such as enhanced drought tolerance, photosynthetic rate, and growth. Estimates of infection frequency have revealed variable levels of infection with especially high prevalence in the subfamily Pooideae. Longitudinal studies suggest that the prevalence of seed-transmitted endophytes can increase rapidly over time. In field experiments, infected tall fescue suppressed other grasses and forbs relative to uninfected fescue and supported lower consumer populations. Unlike other widespread plant/microbial symbioses based on the acquisition of mineral resources, grass/endophyte associations are based primarily on protection of the host from biotic and abiotic stresses.

  5. Evolutionary origin and consequences of uniparental mitochondrial inheritance

    NARCIS (Netherlands)

    Hoekstra, R.F.

    2000-01-01

    In the great majority of sexual organisms, cytoplasmic genomes such as the mitochondrial genome are inherited (almost) exclusively through only one, usually the maternal, parent. This rule probably evolved to minimize the potential spread of selfish cytoplasmic genomic mutations through a species.

  6. When less is more: evolutionary origins of the affect heuristic.

    Directory of Open Access Journals (Sweden)

    Jerald D Kralik

    Full Text Available The human mind is built for approximations. When considering the value of a large aggregate of different items, for example, we typically do not summate the many individual values. Instead, we appear to form an immediate impression of the likeability of the option based on the average quality of the full collection, which is easier to evaluate and remember. While useful in many situations, this affect heuristic can lead to apparently irrational decision-making. For example, studies have shown that people are willing to pay more for a small set of high-quality goods than for the same set of high-quality goods with lower-quality items added [e.g. 1]. We explored whether this kind of choice behavior could be seen in other primates. In two experiments, one in the laboratory and one in the field, using two different sets of food items, we found that rhesus monkeys preferred a highly-valued food item alone to the identical item paired with a food of positive but lower value. This finding provides experimental evidence that, under certain conditions, macaque monkeys follow an affect heuristic that can cause them to prefer less food. Conservation of this affect heuristic could account for similar 'irrational' biases in humans, and may reflect a more general complexity reduction strategy in which averages, prototypes, or stereotypes represent a set or group.

  7. A common evolutionary origin for mitochondria and hydrogenosomes.

    OpenAIRE

    Bui, E T; Bradley, P J; Johnson, P J

    1996-01-01

    Trichomonads are among the earliest eukaryotes to diverge from the main line of eukaryotic descent. Keeping with their ancient nature, these facultative anaerobic protists lack two "hallmark" organelles found in most eukaryotes: mitochondria and peroxisomes. Trichomonads do, however, contain an unusual organelle involved in carbohydrate metabolism called the hydrogenosome. Like mitochondria, hydrogenosomes are double-membrane bounded organelles that produce ATP using pyruvate as the primary s...

  8. Evolutionary origin and consequences of uniparental mitochondrial inheritance

    NARCIS (Netherlands)

    Hoekstra, R.F.

    2000-01-01

    In the great majority of sexual organisms, cytoplasmic genomes such as the mitochondrial genome are inherited (almost) exclusively through only one, usually the maternal, parent. This rule probably evolved to minimize the potential spread of selfish cytoplasmic genomic mutations through a species. M

  9. Tracing the evolutionary origins of insect renal function.

    Science.gov (United States)

    Halberg, Kenneth A; Terhzaz, Selim; Cabrero, Pablo; Davies, Shireen A; Dow, Julian A T

    2015-04-21

    Knowledge on neuropeptide receptor systems is integral to understanding animal physiology. Yet, obtaining general insight into neuropeptide signalling in a clade as biodiverse as the insects is problematic. Here we apply fluorescent analogues of three key insect neuropeptides to map renal tissue architecture across systematically chosen representatives of the major insect Orders, to provide an unprecedented overview of insect renal function and control. In endopterygote insects, such as Drosophila, two distinct transporting cell types receive separate neuropeptide signals, whereas in the ancestral exopterygotes, a single, general cell type mediates all signals. Intriguingly, the largest insect Order Coleoptera (beetles) has evolved a unique approach, in which only a small fraction of cells are targets for neuropeptide action. In addition to demonstrating a universal utility of this technology, our results reveal not only a generality of signalling by the evolutionarily ancient neuropeptide families but also a clear functional separation of the types of cells that mediate the signal.

  10. The Evolutionary Origin and Genetic Makeup of Domestic Horses.

    Science.gov (United States)

    Librado, Pablo; Fages, Antoine; Gaunitz, Charleen; Leonardi, Michela; Wagner, Stefanie; Khan, Naveed; Hanghøj, Kristian; Alquraishi, Saleh A; Alfarhan, Ahmed H; Al-Rasheid, Khaled A; Der Sarkissian, Clio; Schubert, Mikkel; Orlando, Ludovic

    2016-10-01

    The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses. Copyright © 2016 by the Genetics Society of America.

  11. The evolutionary origin and genetic makeup of domestic horses

    DEFF Research Database (Denmark)

    Sanz, Pablo Librado; Fages, Antoine Alphonse; Gaunitz, Charleen

    2016-01-01

    The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude...... of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds...... of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped...

  12. Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

    Directory of Open Access Journals (Sweden)

    Purta Elzbieta

    2007-03-01

    Full Text Available Abstract Background SPOUT methyltransferases (MTases are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. In 2001, when no crystal structures were available for any of these proteins, Anantharaman, Koonin, and Aravind identified homology between SpoU and TrmD MTases and defined the SPOUT superfamily. Since then, multiple crystal structures of knotted MTases have been solved and numerous new homologous sequences appeared in the databases. However, no comprehensive comparative analysis of these proteins has been carried out to classify them based on structural and evolutionary criteria and to guide functional predictions. Results We carried out extensive searches of databases of protein structures and sequences to collect all members of previously identified SPOUT MTases, and to identify previously unknown homologs. Based on sequence clustering, characterization of domain architecture, structure predictions and sequence/structure comparisons, we re-defined families within the SPOUT superfamily and predicted putative active sites and biochemical functions for the so far uncharacterized members. We have also delineated the common core of SPOUT MTases and inferred a multiple sequence alignment for the conserved knot region, from which we calculated the phylogenetic tree of the superfamily. We have also studied phylogenetic distribution of different families, and used this information to infer the evolutionary history of the SPOUT superfamily. Conclusion We present the first phylogenetic tree of the SPOUT superfamily since it was defined, together with a new scheme for its classification, and discussion about conservation of sequence and structure in different families, and their functional implications. We identified four protein families as new members of the SPOUT superfamily. Three of these families are functionally uncharacterized (COG1772, COG1901, and COG4080

  13. Evolutionary and Political Economic Influences on Biological Diversity in African Americans.

    Science.gov (United States)

    Jackson, Fatimah Linda Collier

    1993-01-01

    Examines existing data on biological diversity among Americans of African descent within the contexts of their evolutionary backgrounds and political and economic realities. Explores the origins of the diversity, and provides an evolutionary and political economy synthesis for evaluating the biological distinctions apparent among African…

  14. Evolutionary neurobiology and aesthetics.

    Science.gov (United States)

    Smith, Christopher Upham

    2005-01-01

    If aesthetics is a human universal, it should have a neurobiological basis. Although use of all the senses is, as Aristotle noted, pleasurable, the distance senses are primarily involved in aesthetics. The aesthetic response emerges from the central processing of sensory input. This occurs very rapidly, beneath the level of consciousness, and only the feeling of pleasure emerges into the conscious mind. This is exemplified by landscape appreciation, where it is suggested that a computation built into the nervous system during Paleolithic hunter-gathering is at work. Another inbuilt computation leading to an aesthetic response is the part-whole relationship. This, it is argued, may be traced to the predator-prey "arms races" of evolutionary history. Mate selection also may be responsible for part of our response to landscape and visual art. Aesthetics lies at the core of human mentality, and its study is consequently of importance not only to philosophers and art critics but also to neurobiologists.

  15. Spore: Spawning Evolutionary Misconceptions?

    Science.gov (United States)

    Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

    2010-10-01

    The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

  16. Total Integrative Evolutionary Communication

    DEFF Research Database (Denmark)

    Nedergaard Thomsen, Ole; Brier, Søren

    2014-01-01

    ) instinctual-motivational-emotional sign plays (a level which is shared with other animals and is the domain of ethology), and (3) premeditated, intentional symbol-based language games (specifically human unitary thinking-speaking-gesturing, the domain of pragmatics-based functional linguistics......). In this inclusive hierarchy language games subsume the other stages, and thus human evolutionary communication is primarily a symbolic-conventional practice. It is intertwined with the practice of living, that is, with different life forms, including other forms of semiotic behavior. Together they form a coherent......In this paper we outline a cybersemiotic foundation for the trend of pragmatics-based functional linguistics, Functional Discourse Grammar. Cybersemiotics is a substantial inter- and transdisciplinary semiotic theory which integrates, on the one hand, second-order cybernetics and autopoiesis theory...

  17. Evolutionary Design of Boolean Functions

    Institute of Scientific and Technical Information of China (English)

    WANG Zhang-yi; ZHANG Huan-guo; QIN Zhong-ping; MENG Qing-shu

    2005-01-01

    We use evolutionary computing to synthesize Boolean functions randomly. By using specific crossover and mutation operator in evolving process and modifying search space and fitness function, we get some high non-linearity functions which have other good cryptography characteristics such as autocorrelation etc. Comparing to other heuristic search techniques, evolutionary computing approach is more effective because of global search strategy and implicit parallelism.

  18. Topics of Evolutionary Computation 2001

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem......This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem...

  19. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

    Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

    2016-01-01

    One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

  20. Evolutionary trends in directional hearing

    DEFF Research Database (Denmark)

    Carr, Catherine E; Christensen-Dalsgaard, Jakob

    2016-01-01

    Tympanic hearing is a true evolutionary novelty that arose in parallel within early tetrapods. We propose that in these tetrapods, selection for sound localization in air acted upon pre-existing directionally sensitive brainstem circuits, similar to those in fishes. Auditory circuits in birds...... interactions between coding strategies and evolutionary history....

  1. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

    Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

  2. Creative Generation of 3D Objects with Deep Learning and Innovation Engines

    DEFF Research Database (Denmark)

    Lehman, Joel Anthony; Risi, Sebastian; Clune, Jeff

    2016-01-01

    Advances in supervised learning with deep neural networks have enabled robust classification in many real world domains. An interesting question is if such advances can also be leveraged effectively for computational creativity. One insight is that because evolutionary algorithms are free from...... strict requirements of mathematical smoothness, they can exploit powerful deep learning representations through arbitrary computational pipelines. In this way, deep networks trained on typical supervised tasks can be used as an ingredient in an evolutionary algorithm driven towards creativity....... To highlight such potential, this paper creates novel 3D objects by leveraging feedback from a deep network trained only to recognize 2D images. This idea is tested by extending previous work with Innovation Engines, i.e. a principled combination of deep learning and evolutionary algorithms for computational...

  3. Creative Generation of 3D Objects with Deep Learning and Innovation Engines

    DEFF Research Database (Denmark)

    Lehman, Joel Anthony; Risi, Sebastian; Clune, Jeff

    2016-01-01

    Advances in supervised learning with deep neural networks have enabled robust classification in many real world domains. An interesting question is if such advances can also be leveraged effectively for computational creativity. One insight is that because evolutionary algorithms are free from...... strict requirements of mathematical smoothness, they can exploit powerful deep learning representations through arbitrary computational pipelines. In this way, deep networks trained on typical supervised tasks can be used as an ingredient in an evolutionary algorithm driven towards creativity....... To highlight such potential, this paper creates novel 3D objects by leveraging feedback from a deep network trained only to recognize 2D images. This idea is tested by extending previous work with Innovation Engines, i.e. a principled combination of deep learning and evolutionary algorithms for computational...

  4. DeepPy: Pythonic deep learning

    OpenAIRE

    Larsen, Anders Boesen Lindbo

    2016-01-01

    This technical report introduces DeepPy – a deep learning framework built on top of NumPy with GPU acceleration. DeepPy bridges the gap between highperformance neural networks and the ease of development from Python/NumPy. Users with a background in scientific computing in Python will quickly be able to understand and change the DeepPy codebase as it is mainly implemented using high-level NumPy primitives. Moreover, DeepPy supports complex network architectures by letting the user compose mat...

  5. DeepPy: Pythonic deep learning

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo

    This technical report introduces DeepPy – a deep learning framework built on top of NumPy with GPU acceleration. DeepPy bridges the gap between highperformance neural networks and the ease of development from Python/NumPy. Users with a background in scientific computing in Python will quickly...... be able to understand and change the DeepPy codebase as it is mainly implemented using high-level NumPy primitives. Moreover, DeepPy supports complex network architectures by letting the user compose mathematical expressions as directed graphs. The latest version is available at http...

  6. Organogenesis in deep time: A problem in genomics, development, and paleontology.

    Science.gov (United States)

    Pieretti, Joyce; Gehrke, Andrew R; Schneider, Igor; Adachi, Noritaka; Nakamura, Tetsuya; Shubin, Neil H

    2015-04-21

    The fossil record is a unique repository of information on major morphological transitions. Increasingly, developmental, embryological, and functional genomic approaches have also conspired to reveal evolutionary trajectory of phenotypic shifts. Here, we use the vertebrate appendage to demonstrate how these disciplines can mutually reinforce each other to facilitate the generation and testing of hypotheses of morphological evolution. We discuss classical theories on the origins of paired fins, recent data on regulatory modulations of fish fins and tetrapod limbs, and case studies exploring the mechanisms of digit loss in tetrapods. We envision an era of research in which the deep history of morphological evolution can be revealed by integrating fossils of transitional forms with direct experimentation in the laboratory via genome manipulation, thereby shedding light on the relationship between genes, developmental processes, and the evolving phenotype.

  7. Evolutionary biology of CD1.

    Science.gov (United States)

    Dascher, C C

    2007-01-01

    The recognition more than a decade ago that lipids presented by CD1 could function as T cell antigens revealed a startling and previously unappreciated complexity to the adaptive immune system. The initial novelty of lipid antigen presentation by CD1 has since given way to a broader perspective of the immune system's capacity to sense and respond to a diverse array of macromolecules. Some immune recognition systems such as Toll-like receptors can trace their origins back into the deep history of sea urchins and arthropods. Others such as the major histocompatibility complex (MHC) appear relatively recently and interestingly, only in animals that also possess a jaw. The natural history of CD1 is thus part of the wider story of immune system evolution and should be considered in this context. Most evidence indicates that CD1 probably evolved from a classical MHC class I (MHC I) gene at some point during vertebrate evolution. This chapter reviews the evidence for this phylogenetic relationship and attempts to connect CD1 to existing models of MHC evolution. This endeavor is facilitated today by the recent availability of whole genome sequence data from a variety of species. Investigators have used these data to trace the ultimate origin of the MHC to a series of whole genome duplications that occurred roughly 500 million years ago. Sequence data have also revealed homologs of the mammalian MHC I and MHC II gene families in virtually all jawed vertebrates including sharks, bony fishes, reptiles, and birds. In contrast, CD1 genes have thus far been found only in a subset of these animal groups. This pattern of CD1 occurrence in the genomes of living species suggests the emergence of CD 1 in an early terrestrial vertebrate.

  8. Symbiotic Origin of Aging.

    Science.gov (United States)

    Greenberg, Edward F; Vatolin, Sergei

    2017-09-25

    Normally aging cells are characterized by an unbalanced mitochondrial dynamic skewed toward punctate mitochondria. Genetic and pharmacological manipulation of mitochondrial fission/fusion cycles can contribute to both accelerated and decelerated cellular or organismal aging. In this work, we connect these experimental data with the symbiotic theory of mitochondrial origin to generate new insight into the evolutionary origin of aging. Mitochondria originated from autotrophic α-proteobacteria during an ancient endosymbiotic event early in eukaryote evolution. To expand beyond individual host cells, dividing α-proteobacteria initiated host cell lysis; apoptosis is a product of this original symbiont cell lytic exit program. Over the course of evolution, the host eukaryotic cell attenuated the harmful effect of symbiotic proto-mitochondria, and modern mitochondria are now functionally interdependent with eukaryotic cells; they retain their own circular genomes and independent replication timing. In nondividing differentiated or multipotent eukaryotic cells, intracellular mitochondria undergo repeated fission/fusion cycles, favoring fission as organisms age. The discordance between cellular quiescence and mitochondrial proliferation generates intracellular stress, eventually leading to a gradual decline in host cell performance and age-related pathology. Hence, aging evolved from a conflict between maintenance of a quiescent, nonproliferative state and the evolutionarily conserved propagation program driving the life cycle of former symbiotic organisms: mitochondria.

  9. Evolutionary financial market models

    Science.gov (United States)

    Ponzi, A.; Aizawa, Y.

    2000-12-01

    We study computer simulations of two financial market models, the second a simplified model of the first. The first is a model of the self-organized formation and breakup of crowds of traders, motivated by the dynamics of competitive evolving systems which shows interesting self-organized critical (SOC)-type behaviour without any fine tuning of control parameters. This SOC-type avalanching and stasis appear as realistic volatility clustering in the price returns time series. The market becomes highly ordered at ‘crashes’ but gradually loses this order through randomization during the intervening stasis periods. The second model is a model of stocks interacting through a competitive evolutionary dynamic in a common stock exchange. This model shows a self-organized ‘market-confidence’. When this is high the market is stable but when it gets low the market may become highly volatile. Volatile bursts rapidly increase the market confidence again. This model shows a phase transition as temperature parameter is varied. The price returns time series in the transition region is very realistic power-law truncated Levy distribution with clustered volatility and volatility superdiffusion. This model also shows generally positive stock cross-correlations as is observed in real markets. This model may shed some light on why such phenomena are observed.

  10. Evolutionary cytogenetics in salamanders.

    Science.gov (United States)

    Sessions, Stanley K

    2008-01-01

    Salamanders (Amphibia: Caudata/Urodela) have been the subject of numerous cytogenetic studies, and data on karyotypes and genome sizes are available for most groups. Salamanders show a more-or-less distinct dichotomy between families with large chromosome numbers and interspecific variation in chromosome number, relative size, and shape (i.e. position of the centromere), and those that exhibit very little variation in these karyological features. This dichotomy is the basis of a major model of karyotype evolution in salamanders involving a kind of 'karyotypic orthoselection'. Salamanders are also characterized by extremely large genomes (in terms of absolute mass of nuclear DNA) and extensive variation in genome size (and overall size of the chromosomes), which transcends variation in chromosome number and shape. The biological significance and evolution of chromosome number and shape within the karyotype is not yet understood, but genome size variation has been found to have strong phenotypic, biogeographic, and phylogenetic correlates that reveal information about the biological significance of this cytogenetic variable. Urodeles also present the advantage of only 10 families and less than 600 species, which facilitates the analysis of patterns within the entire order. The purpose of this review is to present a summary of what is currently known about overall patterns of variation in karyology and genome size in salamanders. These patterns are discussed within an evolutionary context.

  11. Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

    Science.gov (United States)

    Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

    2012-11-06

    All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

  12. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  13. Evolutionary pattern of fusulinacean foraminifer in Maokouan, middle Permian

    Institute of Scientific and Technical Information of China (English)

    杨湘宁; 周建平; 刘家润; 施贵军

    1999-01-01

    A composite standard section (CSS) has been established for the Maokouan (≈Guadalupian) in Guizhou Province, southwestern China, which includes stratigraphical ranges of 179 fusulinacean species from five sections of the Maokou Formation in this area. Based on statistical results of the first and last appearances of fusulinacean species in the CSS, three evolutionary radiations and four pulses of extinction, characterized by high rates of species origination and extinction significantly different from the rates of background evolution, are recognized in the Maokouan fusulinacean fauna. The evolutionary pattern of fusulinacean foraminifer suggests that the Maokouan mass extinction probably started at the middle Maokouan and dramatically intensified in the late Maokouan.

  14. Applied evolutionary theories for engineering of secondary metabolic pathways.

    Science.gov (United States)

    Bachmann, Brian O

    2016-12-01

    An expanded definition of 'secondary metabolism' is emerging. Once the exclusive provenance of naturally occurring organisms, evolved over geological time scales, secondary metabolism increasingly encompasses molecules generated via human engineered biocatalysts and biosynthetic pathways. Many of the tools and strategies for enzyme and pathway engineering can find origins in evolutionary theories. This perspective presents an overview of selected proposed evolutionary strategies in the context of engineering secondary metabolism. In addition to the wealth of biocatalysts provided via secondary metabolic pathways, improving the understanding of biosynthetic pathway evolution will provide rich resources for methods to adapt to applied laboratory evolution. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Original Misunderstanding

    Science.gov (United States)

    Holtzman, Alexander

    2009-01-01

    Humorist Josh Billings quipped, "About the most originality that any writer can hope to achieve honestly is to steal with good judgment." Billings was harsh in his view of originality, but his critique reveals a tension faced by students every time they write a history paper. Research is the essence of any history paper. Especially in high school,…

  16. Evolutionary computation for reinforcement learning

    NARCIS (Netherlands)

    S. Whiteson

    2012-01-01

    Algorithms for evolutionary computation, which simulate the process of natural selection to solve optimization problems, are an effective tool for discovering high-performing reinforcement-learning policies. Because they can automatically find good representations, handle continuous action spaces, a

  17. Evolutionary disarmament in interspecific competition.

    Science.gov (United States)

    Kisdi, E; Geritz, S A

    2001-12-22

    Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

  18. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  19. Evolutionary constraints or opportunities?

    Science.gov (United States)

    Sharov, Alexei A.

    2014-01-01

    Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term “constraint” has negative connotations, I use the term “regulated variation” to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch “on” or “off” preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). PMID:24769155

  20. Endosymbiotic theories for eukaryote origin

    Science.gov (United States)

    Martin, William F.; Garg, Sriram; Zimorski, Verena

    2015-01-01

    For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe. PMID:26323761

  1. Optimal Control of Evolutionary Dynamics

    CERN Document Server

    Chakrabarti, Raj; McLendon, George

    2008-01-01

    Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

  2. Greedy Deep Dictionary Learning

    OpenAIRE

    Tariyal, Snigdha; Majumdar, Angshul; Singh, Richa; Vatsa, Mayank

    2016-01-01

    In this work we propose a new deep learning tool called deep dictionary learning. Multi-level dictionaries are learnt in a greedy fashion, one layer at a time. This requires solving a simple (shallow) dictionary learning problem, the solution to this is well known. We apply the proposed technique on some benchmark deep learning datasets. We compare our results with other deep learning tools like stacked autoencoder and deep belief network; and state of the art supervised dictionary learning t...

  3. Greedy Deep Dictionary Learning

    OpenAIRE

    Tariyal, Snigdha; Majumdar, Angshul; Singh, Richa; Vatsa, Mayank

    2016-01-01

    In this work we propose a new deep learning tool called deep dictionary learning. Multi-level dictionaries are learnt in a greedy fashion, one layer at a time. This requires solving a simple (shallow) dictionary learning problem, the solution to this is well known. We apply the proposed technique on some benchmark deep learning datasets. We compare our results with other deep learning tools like stacked autoencoder and deep belief network; and state of the art supervised dictionary learning t...

  4. Schizophrenia-an evolutionary enigma?

    Science.gov (United States)

    Brüne, Martin

    2004-03-01

    The term 'schizophrenia' refers to a group of disorders that have been described in every human culture. Two apparently well established findings have corroborated the need for an evolutionary explanation of these disorders: (1) cross-culturally stable incidence rates and (2) decreased fecundity of the affected individuals. The rationale behind this relates to the evolutionary paradox that susceptibility genes for schizophrenia are obviously preserved in the human genepool, despite fundamental reproductive disadvantages associated with the disorders. Some researchers have therefore proposed that a compensatory advantage must exist in people who are carriers of these genes or in their first-degree relatives. Such advantages were hypothesised to be outside the brain (e.g. greater resistance against toxins or infectious diseases), or within the social domain (e.g. schizotypal shamans, creativity). More specifically, T.J. Crow has suggested an evolutionary theory of schizophrenia that relates the disorders to an extreme of variation of hemispheric specialisation and the evolution of language due to a single gene mutation located on homologous regions of the sex chromosomes. None of the evolutionary scenarios does, however, fully account for the diversity of the symptomatology, nor does any one hypothesis acknowledge the objection that the mere prevalence of a disorder must not be confused with adaptation. In the present article, I therefore discuss the evolutionary hypotheses of schizophrenia, arguing that a symptom-based approach to psychotic disorders in evolutionary perspective may improve upon the existing models of schizophrenia.

  5. An integrative approach to understanding bird origins.

    Science.gov (United States)

    Xu, Xing; Zhou, Zhonghe; Dudley, Robert; Mackem, Susan; Chuong, Cheng-Ming; Erickson, Gregory M; Varricchio, David J

    2014-12-12

    Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs, and furthermore, demonstrate that distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and a novel pulmonary system originated among Mesozoic terrestrial dinosaurs. The transition from ground-living to flight-capable theropod dinosaurs now probably represents one of the best-documented major evolutionary transitions in life history. Recent studies in developmental biology and other disciplines provide additional insights into how bird characteristics originated and evolved. The iconic features of extant birds for the most part evolved in a gradual and stepwise fashion throughout archosaur evolution. However, new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex, mosaic evolutionary distribution of major bird characteristics on the theropod tree. Research into bird origins provides a premier example of how paleontological and neontological data can interact to reveal the complexity of major innovations, to answer key evolutionary questions, and to lead to new research directions. A better understanding of bird origins requires multifaceted and integrative approaches, yet fossils necessarily provide the final test of any evolutionary model.

  6. Women in evolution - highlighting the changing face of evolutionary biology.

    Science.gov (United States)

    Wellenreuther, Maren; Otto, Sarah

    2016-01-01

    The face of science has changed. Women now feature alongside men at the forefront of many fields, and this is particularly true in evolutionary biology. This special issue celebrates the outstanding achievements and contributions of women in evolutionary biology, by highlighting a sample of their research and accomplishments. In addition to original research contributions, this collection of articles contains personal reflections to provide perspective and advice on succeeding as a woman in science. By showcasing the diversity and research excellence of women and drawing on their experiences, we wish to enhance the visibility of female scientists and provide inspiration as well as role models. These are exciting times for evolutionary biology, and the field is richer and stronger for the diversity of voices contributing to the field.

  7. Evolutionary Evaluation: implications for evaluators, researchers, practitioners, funders and the evidence-based program mandate.

    Science.gov (United States)

    Urban, Jennifer Brown; Hargraves, Monica; Trochim, William M

    2014-08-01

    Evolutionary theory, developmental systems theory, and evolutionary epistemology provide deep theoretical foundations for understanding programs, their development over time, and the role of evaluation. This paper relates core concepts from these powerful bodies of theory to program evaluation. Evolutionary Evaluation is operationalized in terms of program and evaluation evolutionary phases, which are in turn aligned with multiple types of validity. The model of Evolutionary Evaluation incorporates Chen's conceptualization of bottom-up versus top-down program development. The resulting framework has important implications for many program management and evaluation issues. The paper illustrates how an Evolutionary Evaluation perspective can illuminate important controversies in evaluation using the example of the appropriate role of randomized controlled trials that encourages a rethinking of "evidence-based programs". From an Evolutionary Evaluation perspective, prevailing interpretations of rigor and mandates for evidence-based programs pose significant challenges to program evolution. This perspective also illuminates the consequences of misalignment between program and evaluation phases; the importance of supporting both researcher-derived and practitioner-derived programs; and the need for variation and evolutionary phase diversity within portfolios of programs.

  8. Origins of adaptive immunity.

    Science.gov (United States)

    Liongue, Clifford; John, Liza B; Ward, Alister

    2011-01-01

    Adaptive immunity, involving distinctive antibody- and cell-mediated responses to specific antigens based on "memory" of previous exposure, is a hallmark of higher vertebrates. It has been argued that adaptive immunity arose rapidly, as articulated in the "big bang theory" surrounding its origins, which stresses the importance of coincident whole-genome duplications. Through a close examination of the key molecules and molecular processes underpinning adaptive immunity, this review suggests a less-extreme model, in which adaptive immunity emerged as part of longer evolutionary journey. Clearly, whole-genome duplications provided additional raw genetic materials that were vital to the emergence of adaptive immunity, but a variety of other genetic events were also required to generate some of the key molecules, whereas others were preexisting and simply co-opted into adaptive immunity.

  9. Clinical analyses of patients with intractable epistaxis originated from deep-seated nasal cavity%鼻腔深部难治性鼻出血临床分析

    Institute of Scientific and Technical Information of China (English)

    许彤; 李娜; 姜彦; 于海玲; 于龙刚; 姜叶

    2015-01-01

    Objective To investigate the clinical features and management of intractable deep-seated epistaxis.Methods Clinical data were analyzed retrospectively in 195 patients with intractable deep-seated epistaxis treated in Affiliated Hospital of Qingdao College between June 2008 and June 2014.The analyses included common risk factors,bleeding sites,treatments and therapeutic effects.SPSS 17.0 software was used to analyze the data.Results There were 162 males and 33 females,aged from 15 to 88 years old (mean 52 16 years).One hundred and eighty-seven cases (95.9%) were unilateral and 8 cases (4.1%) were bilateral.One hundred and twenty-six eases (64.6%) had the history of hypertension or blood pressure higher than normal on admission.Eight patients were cured by nasal packing and appropriate drugs,and 187 patients were treated by endoscopy and electrocoagulation.The numbers of treatment needed to stop bleeding were 1 time in 184 cases(98.4%),2 times in 3 cases(1.6%).Thirteen cases did not have certain bleeding point,while the other 174 had certain one or more bleeding sites.The rewarded bleeding sites were 222,which were found in the following different sites:posterior inferior nasal meatus (33.3%,74/222),olfactory cleft of nasal septum (26.6%,59/222),the root of the middle turbinate (14.0%,31/222),and so on.Hypertension and diabetes were risk factors(OR value was 3.411,7.142,both P < 0.05).Conclusions Intractable deep-seated epistaxis are mainly found in males and are almost unilatera1.Hypertension and diabetes are the common risk factor.The most effective and safe treatment for intractable deep-seated epistaxis is electrocoagulation under nasal endoscopy.%目的 探讨鼻腔深部难治性鼻出血的临床特点、治疗方法及疗效.方法 回顾性分析青岛大学医学院附属医院耳鼻咽喉头颈外科2008年6月至2014年6月因鼻腔深部难治性鼻出血入院治疗的195例患者的临床资料,分析常见危险冈素、出血部位

  10. ORIGINAL ARTICLES

    African Journals Online (AJOL)

    the standard enzyme-linked immunoassay (ELISA) test. Design. Prospective ... African origin,' since most of the available commercial tests are not manufactured in ... specimens (plasma or whole blood), and it has a long shelf life. Study sites.

  11. ORIGINAL ARTICLES

    African Journals Online (AJOL)

    Mogensen CE. Combined high blood pressure and glucose in type 2 diabetes: double .... relevant exercise-induced tachycardia originating in the right yentricular ..... of pain, and considers the physical, pharmacological and psychological in-.

  12. ORIGINAL ARTICLES

    African Journals Online (AJOL)

    abundant component of the human leucocyte population and although essential for host .... ORIGINAL ARTICLES kinase,'6 an important enzyme in the signal transduction ... neutrophils from two different subjects. FMLP (!-)and PAF (¥).

  13. ORIGINAL ARTICLES

    African Journals Online (AJOL)

    ORIGINAL ARTICLES. Cannabis and other drug use among trauma patients in three ... Department of Psychology, Stellenbosch University, W Cape. Charles D H ..... of cannabis and methaqualone on cognitive or psychomotor skills, including.

  14. Evolutionary divergence of chloroplast FAD synthetase proteins

    Directory of Open Access Journals (Sweden)

    Arilla-Luna Sonia

    2010-10-01

    Full Text Available Abstract Background Flavin adenine dinucleotide synthetases (FADSs - a group of bifunctional enzymes that carry out the dual functions of riboflavin phosphorylation to produce flavin mononucleotide (FMN and its subsequent adenylation to generate FAD in most prokaryotes - were studied in plants in terms of sequence, structure and evolutionary history. Results Using a variety of bioinformatics methods we have found that FADS enzymes localized to the chloroplasts, which we term as plant-like FADS proteins, are distributed across a variety of green plant lineages and constitute a divergent protein family clearly of cyanobacterial origin. The C-terminal module of these enzymes does not contain the typical riboflavin kinase active site sequence, while the N-terminal module is broadly conserved. These results agree with a previous work reported by Sandoval et al. in 2008. Furthermore, our observations and preliminary experimental results indicate that the C-terminus of plant-like FADS proteins may contain a catalytic activity, but different to that of their prokaryotic counterparts. In fact, homology models predict that plant-specific conserved residues constitute a distinct active site in the C-terminus. Conclusions A structure-based sequence alignment and an in-depth evolutionary survey of FADS proteins, thought to be crucial in plant metabolism, are reported, which will be essential for the correct annotation of plant genomes and further structural and functional studies. This work is a contribution to our understanding of the evolutionary history of plant-like FADS enzymes, which constitute a new family of FADS proteins whose C-terminal module might be involved in a distinct catalytic activity.

  15. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower.

    Science.gov (United States)

    Chanderbali, André S; Yoo, Mi-Jeong; Zahn, Laura M; Brockington, Samuel F; Wall, P Kerr; Gitzendanner, Matthew A; Albert, Victor A; Leebens-Mack, James; Altman, Naomi S; Ma, Hong; dePamphilis, Claude W; Soltis, Douglas E; Soltis, Pamela S

    2010-12-28

    The origin and rapid diversification of the angiosperms (Darwin's "Abominable Mystery") has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants.

  16. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower

    Science.gov (United States)

    Chanderbali, André S.; Yoo, Mi-Jeong; Zahn, Laura M.; Brockington, Samuel F.; Wall, P. Kerr; Gitzendanner, Matthew A.; Albert, Victor A.; Leebens-Mack, James; Altman, Naomi S.; Ma, Hong; dePamphilis, Claude W.; Soltis, Douglas E.; Soltis, Pamela S.

    2010-01-01

    The origin and rapid diversification of the angiosperms (Darwin's “Abominable Mystery”) has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants. PMID:21149731

  17. Adaptive radiation of chemosymbiotic deep-sea mussels.

    Science.gov (United States)

    Lorion, Julien; Kiel, Steffen; Faure, Baptiste; Kawato, Masaru; Ho, Simon Y W; Marshall, Bruce; Tsuchida, Shinji; Miyazaki, Jun-Ichi; Fujiwara, Yoshihiro

    2013-11-07

    Adaptive radiations present fascinating opportunities for studying the evolutionary process. Most cases come from isolated lakes or islands, where unoccupied ecological space is filled through novel adaptations. Here, we describe an unusual example of an adaptive radiation: symbiotic mussels that colonized island-like chemosynthetic environments such as hydrothermal vents, cold seeps and sunken organic substrates on the vast deep-sea floor. Our time-calibrated molecular phylogeny suggests that the group originated and acquired sulfur-oxidizing symbionts in the Late Cretaceous, possibly while inhabiting organic substrates and long before its major radiation in the Middle Eocene to Early Oligocene. The first appearance of intracellular and methanotrophic symbionts was detected only after this major radiation. Thus, contrary to expectations, the major radiation may have not been triggered by the evolution of novel types of symbioses. We hypothesize that environmental factors, such as increased habitat availability and/or increased dispersal capabilities, sparked the radiation. Intracellular and methanotrophic symbionts were acquired in several independent lineages and marked the onset of a second wave of diversification at vents and seeps. Changes in habitat type resulted in adaptive trends in shell lengths (related to the availability of space and energy, and physiological trade-offs) and in the successive colonization of greater water depths.

  18. Evolutionary relationships between miRNA genes and their activity.

    Science.gov (United States)

    Zhu, Yan; Skogerbø, Geir; Ning, Qianqian; Wang, Zhen; Li, Biqing; Yang, Shuang; Sun, Hong; Li, Yixue

    2012-12-22

    The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained. In order to systematically understand the evolutionary relationship between miRNAs gene and their function, we classified human known miRNAs into eight groups based on their evolutionary ages estimated by maximum parsimony method. New miRNA genes with new functional sequences accumulated more dynamically in vertebrates than that observed in Drosophila. Different levels of evolutionary selection were observed over miRNA gene sequences with different time of origin. Most genic miRNAs differ from their host genes in time of origin, there is no particular relationship between the age of a miRNA and the age of its host genes, genic miRNAs are mostly younger than the corresponding host genes. MicroRNAs originated over different time-scales are often predicted/verified to target the same or overlapping sets of genes, opening the possibility of substantial functional redundancy among miRNAs of different ages. Higher degree of tissue specificity and lower expression level was found in young miRNAs. Our data showed that compared with protein coding genes, miRNA genes are more dynamic in terms of emergence and decay. Evolution patterns are quite different between miRNAs of different ages. MicroRNAs activity is under tight control with well-regulated expression increased and targeting decreased over time. Our work calls attention to the study of miRNA activity with a consideration of their origin time.

  19. Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae.

    Science.gov (United States)

    Prasad, V; Strömberg, C A E; Leaché, A D; Samant, B; Patnaik, R; Tang, L; Mohabey, D M; Ge, S; Sahni, A

    2011-09-20

    Rice and its relatives are a focal point in agricultural and evolutionary science, but a paucity of fossils has obscured their deep-time history. Previously described cuticles with silica bodies (phytoliths) from the Late Cretaceous period (67-65 Ma) of India indicate that, by the latest Cretaceous, the grass family (Poaceae) consisted of members of the modern subclades PACMAD (Panicoideae-Aristidoideae-Chloridoideae-Micrairoideae-Arundinoideae-Danthonioideae) and BEP (Bambusoideae-Ehrhartoideae-Pooideae), including a taxon with proposed affinities to Ehrhartoideae. Here we describe additional fossils and show that, based on phylogenetic analyses that combine molecular genetic data and epidermal and phytolith features across Poaceae, these can be assigned to the rice tribe, Oryzeae, of grass subfamily Ehrhartoideae. The new Oryzeae fossils suggest substantial diversification within Ehrhartoideae by the Late Cretaceous, pushing back the time of origin of Poaceae as a whole. These results, therefore, necessitate a re-evaluation of current models for grass evolution and palaeobiogeography.

  20. Origin of marine planktonic cyanobacteria.

    Science.gov (United States)

    Sánchez-Baracaldo, Patricia

    2015-12-01

    Marine planktonic cyanobacteria contributed to the widespread oxygenation of the oceans towards the end of the Pre-Cambrian and their evolutionary origin represents a key transition in the geochemical evolution of the Earth surface. Little is known, however, about the evolutionary events that led to the appearance of marine planktonic cyanobacteria. I present here phylogenomic (135 proteins and two ribosomal RNAs), Bayesian relaxed molecular clock (18 proteins, SSU and LSU) and Bayesian stochastic character mapping analyses from 131 cyanobacteria genomes with the aim to unravel key evolutionary steps involved in the origin of marine planktonic cyanobacteria. While filamentous cell types evolved early on at around 2,600-2,300 Mya and likely dominated microbial mats in benthic environments for most of the Proterozoic (2,500-542 Mya), marine planktonic cyanobacteria evolved towards the end of the Proterozoic and early Phanerozoic. Crown groups of modern terrestrial and/or benthic coastal cyanobacteria appeared during the late Paleoproterozoic to early Mesoproterozoic. Decrease in cell diameter and loss of filamentous forms contributed to the evolution of unicellular planktonic lineages during the middle of the Mesoproterozoic (1,600-1,000 Mya) in freshwater environments. This study shows that marine planktonic cyanobacteria evolved from benthic marine and some diverged from freshwater ancestors during the Neoproterozoic (1,000-542 Mya).

  1. Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes.

    Science.gov (United States)

    Kohli, Gurjeet S; John, Uwe; Van Dolah, Frances M; Murray, Shauna A

    2016-08-01

    Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success.

  2. The extended evolutionary synthesis: its structure, assumptions and predictions

    Science.gov (United States)

    Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

    2015-01-01

    Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

  3. Applying evolutionary genetics to developmental toxicology and risk assessment.

    Science.gov (United States)

    Leung, Maxwell C K; Procter, Andrew C; Goldstone, Jared V; Foox, Jonathan; DeSalle, Robert; Mattingly, Carolyn J; Siddall, Mark E; Timme-Laragy, Alicia R

    2017-03-04

    Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models. We review five molecular systems of stress response and update 18 consensual cell-cell signaling pathways that are the hallmark for early development, organogenesis, and differentiation; and revisit the principles of teratology in light of recent advances in high-throughput screening, big data techniques, and systems toxicology. Multiscale systems modeling plays an integral role in the evolutionary approach to cross-species extrapolation. Phylogenetic analysis and comparative bioinformatics are both valuable tools in identifying and validating the molecular initiating events that account for adverse developmental outcomes in humans. The discordance of susceptibility between test species and humans (ontogeny) reflects their differences in evolutionary history (phylogeny). This synthesis not only can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease.

  4. The Evolutionary Potential of Phenotypic Mutations.

    Science.gov (United States)

    Yanagida, Hayato; Gispan, Ariel; Kadouri, Noam; Rozen, Shelly; Sharon, Michal; Barkai, Naama; Tawfik, Dan S

    2015-08-01

    Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3'-UTR. Exploring putative cryptic signals in all 3'-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3'-UTR sequences, but also boost the potential for future genetic adaptations.

  5. Structural symmetry in evolutionary games.

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-10-06

    In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be 'evolutionarily equivalent' in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term 'homogeneous' should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry.

  6. Cooperation and conflict in cancer: An evolutionary perspective

    Directory of Open Access Journals (Sweden)

    Jonathan Featherston

    2012-09-01

    Full Text Available Evolutionary approaches to carcinogenesis have gained prominence in the literature and enhanced our understanding of cancer. However, an appreciation of neoplasia in the context of evolutionary transitions, particularly the transition from independent genes to a fullyintegrated genome, is largely absent. In the gene–genome evolutionary transition, mobile genetic elements (MGEs can be studied as the extant exemplars of selfish autonomous lowerlevel units that cooperated to form a higher-level, functionally integrated genome. Here,we discuss levels of selection in cancer cells. In particular, we examine the tension between gene and genome units of selection by examining the expression profiles of MGE domains in an array of human cancers. Overall, across diverse cancers, there is an aberrant expression of several families of mobile elements, including the most common MGE in the human genome, retrotransposon LINE 1. These results indicate an alternative life-history strategy for MGEs in the cancers studied. Whether the aberrant expression is the cause or effect oftumourigenesis is unknown, although some evidence suggests that dysregulation of MGEs can play a role in cancer origin and progression. These data are interpreted in combination with phylostratigraphic reports correlating the origin of cancer genes with multicellularity and other potential increases in complexity in cancer cell populations. Cooperation and conflict between individuals at the gene, genome and cell level provide an evolutionary medicineperspective of cancer that enhances our understanding of disease pathogenesis and treatment.

  7. Evolutionary trade-offs in kidney injury and repair.

    Science.gov (United States)

    Lei, Yutian; Anders, Hans-Joachim

    2017-11-01

    Evolutionary medicine has proven helpful to understand the origin of human disease, e.g. in identifying causal roles of recent environmental changes impacting on human physiology (environment-phenotype mismatch). In contrast, diseases affecting only a limited number of members of a species often originate from evolutionary trade-offs for usually physiologic adaptations assuring reproductive success in the context of extrinsic threats. For example, the G1 and G2 variants of the APOL1 gene supporting control of Trypanosoma infection come with the trade-off that they promote the progression of kidney disease. In this review we extend the concept of evolutionary nephrology by discussing how the physiologic adaptations (danger responses) to tissue injury create evolutionary trade-offs that drive histopathological changes underlying acute and chronic kidney diseases. The evolution of multicellular organisms positively selected a number of danger response programs for their overwhelming benefits in assuring survival such as clotting, inflammation, epithelial healing and mesenchymal healing, i.e. fibrosis and sclerosis. Upon kidney injury these danger programs often present as pathomechanisms driving persistent nephron loss and renal failure. We explore how classic kidney disease entities involve insufficient or overshooting activation of these danger response programs for which the underlying genetic basis remains largely to be defined. Dissecting the causative and hierarchical relationships between danger programs should help to identify molecular targets to control kidney injury and to improve disease outcomes.

  8. Living at the Limits: Evidence for Microbial Eukaryotes Thriving under Pressure in Deep Anoxic, Hypersaline Habitats

    Directory of Open Access Journals (Sweden)

    Thorsten Stoeck

    2014-01-01

    Full Text Available The advent of molecular tools in microbial ecology paved the way to exploit the diversity of microbes in extreme environments. Here, we review these tools as applied in one of the most polyextreme habitats known on our planet, namely, deep hypersaline anoxic basins (DHABs, located at ca. 3000–3500 m depth in the Eastern Mediterranean Sea. Molecular gene signatures amplified from environmental DHAB samples identified a high degree of genetic novelty, as well as distinct communities in the DHABs. Canonical correspondence analyses provided strong evidence that salinity, ion composition, and anoxia were the strongest selection factors shaping protistan community structures, largely preventing cross-colonization among the individual basins. Thus, each investigated basin represents a unique habitat (“isolated islands of evolution”, making DHABs ideal model sites to test evolutionary hypotheses. Fluorescence in situ hybridization assays using specifically designed probes revealed that the obtained genetic signatures indeed originated from indigenous polyextremophiles. Electron microscopy imaging revealed unknown ciliates densely covered with prokaryote ectosymbionts, which may enable adaptations of eukaryotes to DHAB conditions. The research reviewed here significantly advanced our knowledge on polyextremophile eukaryotes, which are excellent models for a number of biological research areas, including ecology, diversity, biotechnology, evolutionary research, physiology, and astrobiology.

  9. Original pedagogues

    DEFF Research Database (Denmark)

    Schmidt, Christina Haandbæk

    and professional autonomy in exercising judgment concerning pedagogical situations. To understand how pedagogues can struggle the distention between being competent and being original the project draws on both Michel Foucault and Charles Taylor as two incompatible theories on modern identity. The study......Original pedagogues Distention between competences and originality By Christina Haandbæk Schmidt, ph. d. student Aarhus University, Denmark This presentation concerns a Ph.D. project (Sept. 2012 –Sept. 2015) about pedagogues in day care facilities and their struggles to develop and retain...... of pedagogues and in everyday life in daycare facilities. The competence term includes at least two discourses of interest; a pedagogical competence discourse and a political jurisdiction discourse which forms a distention between authenticity and competence. In order that pedagogues may regain their autonomy I...

  10. Genomics and the origin of species

    NARCIS (Netherlands)

    Seehausen, Ole; Butlin, Roger K.; Keller, Irene; Wagner, Catherine E.; Boughman, Janette W.; Hohenlohe, Paul A.; Peichel, Catherine L.; Saetre, Glenn-Peter; Bank, Claudia; Brännström, Åke; Brelsford, Alan; Clarkson, Chris S.; Eroukhmanoff, Fabrice; Feder, Jeffrey L.; Fischer, Martin C.; Foote, Andrew D.; Franchini, Paolo; Jiggins, Chris D.; Jones, Felicity C.; Lindholm, Anna K.; Lucek, Kay; Maan, Martine E.; Marques, David A.; Martin, Simon H.; Matthews, Blake; Meier, Joana I.; Möst, Markus; Nachman, Michael W.; Nonaka, Etsuko; Rennison, Diana J.; Schwarzer, Julia; Watson, Eric T.; Westram, Anja M.; Widmer, Alex

    Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive

  11. Genomics and the origin of species

    NARCIS (Netherlands)

    Seehausen, Ole; Butlin, Roger K.; Keller, Irene; Wagner, Catherine E.; Boughman, Janette W.; Hohenlohe, Paul A.; Peichel, Catherine L.; Saetre, Glenn-Peter; Bank, Claudia; Brännström, Åke; Brelsford, Alan; Clarkson, Chris S.; Eroukhmanoff, Fabrice; Feder, Jeffrey L.; Fischer, Martin C.; Foote, Andrew D.; Franchini, Paolo; Jiggins, Chris D.; Jones, Felicity C.; Lindholm, Anna K.; Lucek, Kay; Maan, Martine E.; Marques, David A.; Martin, Simon H.; Matthews, Blake; Meier, Joana I.; Möst, Markus; Nachman, Michael W.; Nonaka, Etsuko; Rennison, Diana J.; Schwarzer, Julia; Watson, Eric T.; Westram, Anja M.; Widmer, Alex

    2014-01-01

    Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isola

  12. Genomics and the origin of species

    NARCIS (Netherlands)

    Seehausen, Ole; Butlin, Roger K.; Keller, Irene; Wagner, Catherine E.; Boughman, Janette W.; Hohenlohe, Paul A.; Peichel, Catherine L.; Saetre, Glenn-Peter; Bank, Claudia; Brännström, Åke; Brelsford, Alan; Clarkson, Chris S.; Eroukhmanoff, Fabrice; Feder, Jeffrey L.; Fischer, Martin C.; Foote, Andrew D.; Franchini, Paolo; Jiggins, Chris D.; Jones, Felicity C.; Lindholm, Anna K.; Lucek, Kay; Maan, Martine E.; Marques, David A.; Martin, Simon H.; Matthews, Blake; Meier, Joana I.; Möst, Markus; Nachman, Michael W.; Nonaka, Etsuko; Rennison, Diana J.; Schwarzer, Julia; Watson, Eric T.; Westram, Anja M.; Widmer, Alex

    2014-01-01

    Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isola

  13. Neuronal boost to evolutionary dynamics.

    Science.gov (United States)

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-06

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

  14. Neuronal boost to evolutionary dynamics

    Science.gov (United States)

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

  15. Multivariate Evolutionary Analyses in Astrophysics

    CERN Document Server

    Fraix-Burnet, Didier

    2011-01-01

    The large amount of data on galaxies, up to higher and higher redshifts, asks for sophisticated statistical approaches to build adequate classifications. Multivariate cluster analyses, that compare objects for their global similarities, are still confidential in astrophysics, probably because their results are somewhat difficult to interpret. We believe that the missing key is the unavoidable characteristics in our Universe: evolution. Our approach, known as Astrocladistics, is based on the evolutionary nature of both galaxies and their properties. It gathers objects according to their "histories" and establishes an evolutionary scenario among groups of objects. In this presentation, I show two recent results on globular clusters and earlytype galaxies to illustrate how the evolutionary concepts of Astrocladistics can also be useful for multivariate analyses such as K-means Cluster Analysis.

  16. Evolutionary engineering for industrial microbiology.

    Science.gov (United States)

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  17. Origin and Indicators of Deep-seated Fluids in Sedimentary Basins%盆地深部流体主要来源及判识标志研究

    Institute of Scientific and Technical Information of China (English)

    胡文蠧

    2016-01-01

    Based on the recent research data related to deep-seated fluids in sedimentary basins,three kinds of fluids can be classified:Crustal-derived hydrothermal fluids,hydrocarbon source rock-related fluids and mantle-derived fluids.In this study,the crustal-derived hydrothermal fluid activities related reservoir beds of the Tarim Basin are discussed,and their identification features are summarized.Combined with data from the Wilcox Basin in the Gulf of Mexico,the Norway and Junggar Basins,isotopic characteristics of the hydrocarbon source rock-related fluids and their implication in reservoir beds are addressed.Rift basins in eastern China and the Huangqiao CO2 reservoir are used to constrain the features of man-tle-derived fluids.The role of mantle-derived CO2-rich fluids in the alteration of sandstone of the Huangqiao reservoir bed is discussed as well.%结合近年来的研究资料,将盆地深部流体划分为壳源热流体、烃源热流体和幔源热流体3种类型。结合塔里木盆地的实例,总结讨论了壳源热流体的作用特征和判识标志;结合墨西哥湾 Wilcox 盆地、北海挪威盆地和准噶尔盆地的资料,讨论了“烃源热流体”的同位素特征及其对储集层形成的意义;结合中国东部裂谷盆地资料和江苏黄桥 CO2气田实例,总结了幔源流体基本特点和判识标志,解剖了幔源 CO2流体对黄桥气藏砂岩储集层的改造作用特征。

  18. DeepFlavour in CMS

    CERN Document Server

    CERN. Geneva

    2017-01-01

    Flavour-tagging of jets is an important task in collider based high energy physics and a field where machine learning tools are applied by all major experiments. A new tagger (DeepFlavour) was developed and commissioned in CMS that is based on an advanced machine learning procedure. A deep neural network is used to do multi-classification of jets that origin from a b-quark, two b-quarks, a c-quark, two c-quarks or light colored particles (u, d, s-quark or gluon). The performance was measured in both, data and simulation. The talk will also include the measured performance of all taggers in CMS. The different taggers and results will be discussed and compared with some focus on details of the newest tagger.

  19. Evolutionary optimization of optical antennas

    CERN Document Server

    Feichtner, Thorsten; Kiunke, Markus; Hecht, Bert

    2012-01-01

    The design of nano-antennas is so far mainly inspired by radio-frequency technology. However, material properties and experimental settings need to be reconsidered at optical frequencies, which entails the need for alternative optimal antenna designs. Here a checkerboard-type, initially random array of gold cubes is subjected to evolutionary optimization. To illustrate the power of the approach we demonstrate that by optimizing the near-field intensity enhancement the evolutionary algorithm finds a new antenna geometry, essentially a split-ring/two-wire antenna hybrid which surpasses by far the performance of a conventional gap antenna by shifting the n=1 split-ring resonance into the optical regime.

  20. Evolutionary Aesthetics and Print Advertising

    Directory of Open Access Journals (Sweden)

    Kamil Luczaj

    2015-06-01

    Full Text Available The article analyzes the extent to which predictions based on the theory of evolutionary aesthetics are utilized by the advertising industry. The purpose of a comprehensive content analysis of print advertising is to determine whether the items indicated by evolutionists such as animals, flowers, certain types of landscapes, beautiful humans, and some colors are part of real advertising strategies. This article has shown that many evolutionary hypotheses (although not all of them are supported by empirical data. Along with these hypotheses, some inferences from Bourdieu’s cultural capital theory were tested. It turned out that advertising uses both biological schemata and cultural patterns to make an image more likable.