Lukashov, Vladimir V.; Goudsmit, Jaap
To study the evolutionary relationships among astroviruses, all available sequences for members of the family Astroviridae were collected. Phylogenetic analysis distinguished two deep-rooted groups: one comprising mammalian astroviruses, with ovine astrovirus being an outlier, and the other
Matsuda, Y.; Tobari, I.; Utsugi, T.
In this study, dose-response relationships were examined for chromosome aberrations observed at diakinesis-metaphase I of spermatocytes with X-irradiation at various stages of meiosis (diplotene, mid-pachytene, zygotene and leptotene). The frequencies of cells with X-ray-induced chromosome aberrations increased with dose at all stages in the applied range of 0.5-3.0 Gy and tended to increase as the irradiated stages descended after leptotene stage. In three stages, the frequencies increased exponentially with dose, but the rates of induction of chromosome breaks were markedly different depending on the stages at which spermatocytes were irradiated with X-rays. The rate of induction was the highest at diplotene and the lowest at leptotene, suggesting that diplotene spermatocytes had the highest radiosensitivity to the induction of chromosome breaks, followed by pachytene, zygotene and leptotene spermatocytes in that order. The dose-response relationships fitted well to linear equations for deletion-type aberrations at each stage, and to linear-quadratic equations for exchange-type aberrations at all stages except for leptotene. At leptotene, the chromatid exchanges were hardly observed, the aberrations being mainly consisted of iso-chromatid fragments. On the contrary, chromatid exchanges and iso-chromatide deletions were mainly observed at later stages (zygotene-diplotene).
To determine the genetic diversity and evolutionary relationships among red radishes, 37 accessions ... determined that plant height, fresh leaf weight, and root ... Flower-shaped. Red .... according to Levan's karyotype classification standards.
To determine the genetic diversity and evolutionary relationships among red radishes, 37 accessions with different flesh colors were analyzed in terms of the red pigment content, karyotypes, and simple sequence repeat markers. Red pigment content of red radish was 3.4 to 28.8% with an average of 15.62%. The karyotype ...
Zhu, Yan; Skogerbø, Geir; Ning, Qianqian; Wang, Zhen; Li, Biqing; Yang, Shuang; Sun, Hong; Li, Yixue
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.
Sutcliffe, Alistair; Dunbar, Robin; Binder, Jens; Arrow, Holly
Psychological studies of relationships tend to focus on specific types of close personal relationships (romantic, parent-offspring, friendship) and examine characteristics of both the individuals and the dyad. This paper looks more broadly at the wider range of relationships that constitute an individual's personal social world. Recent work on the composition of personal social networks suggests that they consist of a series of layers that differ in the quality and quantity of relationships involved. Each layer increases relationship numbers by an approximate multiple of 3 (5-15-50-150) but decreasing levels of intimacy (strong, medium, and weak ties) and frequency of interaction. To account for these regularities, we draw on both social and evolutionary psychology to argue that relationships at different layers serve different functions and have different cost-benefit profiles. At each layer, the benefits are asymptotic but the costs of maintaining a relationship at that level (most obviously, the time that has to be invested in servicing it) are roughly linear with the number of relationships. The trade-off between costs and benefits at a given level, and across the different types of demands and resources typical of different levels, gives rise to a distribution of social effort that generates and maintains a hierarchy of layered sets of relationships within social networks. We suggest that, psychologically, these trade-offs are related to the level of trust in a relationship, and that this is itself a function of the time invested in the relationship. ©2011 The British Psychological Society.
Sevastyanova Antonina A
Full Text Available Abstract Published results were reassessed and original data are provided regarding the origin and relatedness of four postulated chicken breed lineages, egg-type, game, meat-type and Bantam, to each other and to the basic ancestral species of jungle fowls, Gallus gallus. A system approach was employed concerning the planning of the experiments. One element of the system approach is the choice of the breeds to be compared with G. gallus. These breeds were supposed to represent major evolutionary branches of chickens. Four experiments on genetic relationships were conducted using different estimation criteria including morphological discrete characters, body measurements, biochemical markers, and the activity of serum esterase-1. The greatest similarity was found between G. gallus and the egg-type breeds of Mediterranean roots and/or true Bantams. This fact might testify that the indicated chicken groups occupied earlier stages in the evolution from the wild progenitor to the present biodiversity of chickens in the world.
White, Roderick E.; Thornhill, Stewart; Hampson, Elizabeth
Biological evolutionary processes select for heritable behaviors providing a survival and reproductive advantage. Accordingly, how we behave is, at least in part, affected by the evolutionary history of our species. This research uses evolutionary psychology as the theoretical perspective for exploring the relationship between a heritable…
Takahashi, Hideki; Buchner, Peter; Yoshimoto, Naoko; Hawkesford, Malcolm J; Shiu, Shin-Han
Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR, and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal SUL and animal anion exchangers (SLC26). The lineage of plant SULTR family is expanded into four subfamilies (SULTR1-SULTR4) in land plant species. By contrast, the putative SULTR homologs from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4), and the other diverged before the appearance of lineages for SUL, SULTR, and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13) and plant tonoplast-localized dicarboxylate transporters (TDT). The putative sulfur-sensing protein (SAC1) and SAC1-like transporters (SLT) of Chlorophyte green algae, bryophyte, and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.
Full Text Available Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal sulfate transporters (SUL and animal anion exchangers (SLC26. The lineage of plant SULTR family is expanded into four subfamilies (SULTR1 to SULTR4 in land plant species. By contrast, the putative SULTR homologues from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4, and the other diverged before the appearance of lineages for SUL, SULTR and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13 and plant tonoplast-localized dicarboxylate transporters (TDT. The putative sulfur-sensing protein (SAC1 and SAC1-like transporters (SLT of Chlorophyte green algae, bryophyte and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is completely absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.
Full Text Available Vertebrates are the only animals that produce bone, but the molecular genetic basis for this evolutionary novelty remains obscure. Here, we synthesize information from traditional evolutionary and modern molecular genetic studies in order to generate a working hypothesis on the evolution of the gene regulatory network (GRN underlying bone formation. To make this argument, we focus on three skeletal tissues that comprise the majority of the vertebrate skeleton: immature cartilage, mature cartilage, and bone. Immature cartilage is produced during early stages of cartilage differentiation and can persist into adulthood, whereas mature cartilage undergoes additional stages of differentiation, including hypertrophy and mineralization. Functionally, histologically, and embryologically, these three skeletal tissues are very similar, yet unique, suggesting that one might have evolved from another. Traditional studies of the fossil record, comparative anatomy and embryology demonstrate clearly that immature cartilage evolved before mature cartilage or bone. Modern molecular approaches show that the GRNs regulating differentiation of these three skeletal cell fates are similar, yet unique, just like the functional and histological features of the tissues themselves. Intriguingly, the Sox9 GRN driving cartilage formation appears to be dominant to the Runx2 GRN of bone. Emphasizing an embryological and evolutionary transcriptomic view, we hypothesize that the Runx2 GRN underlying bone formation was co-opted from mature cartilage. We discuss how modern molecular genetic experiments, such as comparative transcriptomics, can test this hypothesis directly, meanwhile permitting levels of constraint and adaptation to be evaluated quantitatively. Therefore, comparative transcriptomics may revolutionize understanding of not only the clade-specific evolution of skeletal cells, but also the generation of evolutionary novelties, providing a modern paradigm for the
Zheng, Wei Hao; Västermark, Åke; Shlykov, Maksim A; Reddy, Vamsee; Sun, Eric I; Saier, Milton H
The ATP-Binding Cassette (ABC) functional superfamily includes integral transmembrane exporters that have evolved three times independently, forming three families termed ABC1, ABC2 and ABC3, upon which monophyletic ATPases have been superimposed for energy-coupling purposes [e.g., J Membr Biol 231(1):1-10, 2009]. The goal of the work reported in this communication was to understand how the integral membrane constituents of ABC uptake transporters with different numbers of predicted or established transmembrane segments (TMSs) evolved. In a few cases, high resolution 3-dimensional structures were available, and in these cases, their structures plus primary sequence analyses allowed us to predict evolutionary pathways of origin. All of the 35 currently recognized families of ABC uptake proteins except for one (family 21) were shown to be homologous using quantitative statistical methods. These methods involved using established programs that compare native protein sequences with each other, after having compared each sequence with thousands of its own shuffled sequences, to gain evidence for homology. Topological analyses suggested that these porters contain numbers of TMSs ranging from four or five to twenty. Intragenic duplication events occurred multiple times during the evolution of these porters. They originated from a simple primordial protein containing 3 TMSs which duplicated to 6 TMSs, and then produced porters of the various topologies via insertions, deletions and further duplications. Except for family 21 which proved to be related to ABC1 exporters, they are all related to members of the previously identified ABC2 exporter family. Duplications that occurred in addition to the primordial 3 → 6 duplication included 5 → 10, 6 → 12 and 10 → 20 TMSs. In one case, protein topologies were uncertain as different programs gave discrepant predictions. It could not be concluded with certainty whether a 4 TMS ancestral protein or a 5 TMS ancestral protein
Pánek, Matěj; Fér, Tomáš; Mráček, Jaroslav; Tomšovský, Michal
The Phytophthora cactorum species complex in Europe is composed of P. cactorum, Phytophthora hedraiandra, and a hybrid species Phytophthora × serendipita. Evolutionary analyses using the amplified fragment length polymorphism (AFLP) method were carried out on 133 isolates from 19 countries. The AFLP data were complemented by sequence analysis of three genes (ITS region of ribosomal RNA gene, phenolic acid decarboxylase - Pheca I, and Cytochrome oxidase - Cox I), morphometric analysis and cardinal temperature data. The high proportion of clonal genotypes, low gene flow among groups, which was defined by the structure analysis, and low Nei's gene diversity confirms the homothallic life cycle of the groups. On the other hand, the ITS, Cox I and Pheca I sequence data support occasional hybridization between species. The structure K = 5 grouping revealed two groups of hybrid origin (C2 and F). While the C2 group resembles P. × serendipita, the F group includes Finnish isolates characterized by high oogonial abortion rates and slow growth. The morphological characters routinely used in identification of Phytophthora species are not useful for delimitation of species from the P. cactorum complex. Therefore, we discuss the status of P. hedraiandra as a separate species. The epitypification of P. cactorum is proposed. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.
Smoliga, James M.; Zavorsky, Gerald S.
In recent years, various studies have attempted to understand human evolution by examining relationships between athletic performance or physical fitness and facial attractiveness. Over a wide range of five homogeneous groups (n = 327), there is an approximate 3% shared variance between facial attractiveness and athletic performance or physical fitness (95% CI = 0.5–8%, p = 0.002). Further, studies relating human performance and attractiveness often have major methodological limitations that ...
Smoliga, James M; Zavorsky, Gerald S
In recent years, various studies have attempted to understand human evolution by examining relationships between athletic performance or physical fitness and facial attractiveness. Over a wide range of five homogeneous groups (n = 327), there is an approximate 3% shared variance between facial attractiveness and athletic performance or physical fitness (95% CI = 0.5-8%, p = 0.002). Further, studies relating human performance and attractiveness often have major methodological limitations that limit their generalizability. Thus, despite statistical significance, the association between facial attractiveness and human performance has questionable biological importance. Here, we present a critique of these studies and provide recommendations to improve the quality of future research in this realm. © 2015 The Author(s).
Kvičerová, Jana; Hypša, Václav; Dvořáková, Nela; Mikulíček, Peter; Jandzik, David; Gardner, Michael George; Javanbakht, Hossein; Tiar, Ghoulem; Siroký, Pavel
The generic name Hemolivia has been used for haemogregarines characterized by morphological and biological features. The few molecular studies, focused on other haemogregarine genera but involving Hemolivia samples, indicated its close relationship to the genus Hepatozoon. Here we analyze molecular data for Hemolivia from a broad geographic area and host spectrum and provide detailed morphological documentation of the included samples. Based on molecular analyses in context of other haemogregarines, we demonstrate that several sequences deposited in GenBank from isolates described as Hepatozoon belong to the Hemolivia cluster. This illustrates the overall difficulty with recognizing Hemolivia and Hepatozoon without sufficient morphological and molecular information. The close proximity of both genera is also reflected in uncertainty about their precise phylogeny when using 18S rDNA. They cluster with almost identical likelihood either as two sister taxa or as monophyletic Hemolivia within paraphyletic Hepatozoon. However, regardless of these difficulties, the results presented here provide a reliable background for the unequivocal placement of new samples into the Hemolivia/ Hepatozoon complex. Copyright © 2014 Elsevier GmbH. All rights reserved.
Full Text Available Collodaria are the only group of Radiolaria that has a colonial lifestyle. This group is potentially the most important plankton in the oligotrophic ocean because of its large biomass and the high primary productivity associated with the numerous symbionts inside a cell or colony. The evolution of Collodaria could thus be related to the changes in paleo-productivity that have affected organic carbon fixation in the oligotrophic ocean. However, the fossil record of Collodaria is insufficient to trace their abundance through geological time, because most collodarians do not have silicified shells. Recently, molecular phylogeny based on nuclear small sub-unit ribosomal DNA (SSU rDNA confirmed Collodaria to be one of five orders of Radiolaria, though the relationship among collodarians is still unresolved because of inadequate taxonomic sampling. Our phylogenetic analysis has revealed four novel collodarian sequences, on the basis of which collodarians can be divided into four clades that correspond to taxonomic grouping at the family level: Thalassicollidae, Collozoidae, Collosphaeridae, and Collophidae. Comparison of the results of our phylogenetic analyses with the morphological characteristics of each collodarian family suggests that the first ancestral collodarians had a solitary lifestyle and left no silica deposits. The timing of events estimated from molecular divergence calculations indicates that naked collodarian lineages first appeared around 45.6 million years (Ma ago, coincident with the diversification of diatoms in the pelagic oceans. Colonial collodarians appeared after the formation of the present ocean circulation system and the development of oligotrophic conditions in the equatorial Pacific (ca. 33.4 Ma ago. The divergence of colonial collodarians probably caused a shift in the efficiency of primary production during this period.
Ishitani, Yoshiyuki; Ujiié, Yurika; de Vargas, Colomban; Not, Fabrice; Takahashi, Kozo
Collodaria are the only group of Radiolaria that has a colonial lifestyle. This group is potentially the most important plankton in the oligotrophic ocean because of its large biomass and the high primary productivity associated with the numerous symbionts inside a cell or colony. The evolution of Collodaria could thus be related to the changes in paleo-productivity that have affected organic carbon fixation in the oligotrophic ocean. However, the fossil record of Collodaria is insufficient to trace their abundance through geological time, because most collodarians do not have silicified shells. Recently, molecular phylogeny based on nuclear small sub-unit ribosomal DNA (SSU rDNA) confirmed Collodaria to be one of five orders of Radiolaria, though the relationship among collodarians is still unresolved because of inadequate taxonomic sampling. Our phylogenetic analysis has revealed four novel collodarian sequences, on the basis of which collodarians can be divided into four clades that correspond to taxonomic grouping at the family level: Thalassicollidae, Collozoidae, Collosphaeridae, and Collophidae. Comparison of the results of our phylogenetic analyses with the morphological characteristics of each collodarian family suggests that the first ancestral collodarians had a solitary lifestyle and left no silica deposits. The timing of events estimated from molecular divergence calculations indicates that naked collodarian lineages first appeared around 45.6 million years (Ma) ago, coincident with the diversification of diatoms in the pelagic oceans. Colonial collodarians appeared after the formation of the present ocean circulation system and the development of oligotrophic conditions in the equatorial Pacific (ca. 33.4 Ma ago). The divergence of colonial collodarians probably caused a shift in the efficiency of primary production during this period. PMID:22567112
Victoria Cabrera García
Full Text Available The explanation of marital satisfaction and stability in trajectories of couple relationships has been the central interest in different studies (Karney, Bradbury. & Johnson, 1999; Sabatelli & Ripoll, 2004; Schoebi, Karney & Bradbury, 2012. However, there are still several questions and unknown aspects surrounding the topic. Within this context, the present reflection seeks to analyze whether the principles of Evolutionary Theory suffice to explain three marital trajectories in terms of satisfaction and stability. With this in mind, we have included other explanations proposed by the Psychosocial Theory that Evolutionary Theory does not refer to in order to better understand mating behavior. Moreover, other factors that could account for satisfied and stable relationships were analyzed. Suggestions for future investigations include the analysis of other marital trajectories that may or may not end in separation or divorce but are not included in this article.
Full Text Available EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.
Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu
EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.
Stone Eric A
Full Text Available Abstract Background Protein sequences are subject to a mosaic of constraint. Changes to functional domains and buried residues, for example, are more apt to disrupt protein structure and function than are changes to residues participating in loops or exposed to solvent. Regions of constraint on the tertiary structure of a protein often result in loose segmentation of its primary structure into stretches of slowly- and rapidly-evolving amino acids. This clustering can be exploited, and existing methods have done so by relying on local sequence conservation as a signature of selection to help identify functionally important regions within proteins. We invert this paradigm by leveraging the regional nature of protein structure and function to both illuminate and make use of genome-wide patterns of local sequence conservation. Results Our hypothesis is that the regional nature of structural and functional constraints will assert a positive autocorrelation on the evolutionary rates of neighboring sites, which, in a pairwise comparison of orthologous proteins, will manifest itself as the clustering of non-synonymous changes across the amino acid sequence. We introduce a dispersion ratio statistic to test this and related hypotheses. Using genome-wide interspecific comparisons of orthologous protein pairs, we reveal a strong log-linear relationship between the degree of clustering and the intensity of constraint. We further demonstrate how this relationship varies with the evolutionary distance between the species being compared. We provide some evidence that proteins with a history of positive selection deviate from genome-wide trends. Conclusions We find a significant association between the evolutionary rate of a protein and the degree to which non-synonymous changes cluster along its primary sequence. We show that clustering is a non-redundant predictor of evolutionary rate, and we speculate that conflicting signals of clustering and constraint may
Brucker, Robert M; Bordenstein, Seth R
The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species' microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ-proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.
Moctezuma, Victor; Sánchez-Huerta, José Luis; Halffter, Gonzalo
Two new species of the genus Ateuchus Weber are described from the region of Los Chimalapas, Oaxaca, Mexico: A. benitojuarezi sp. n. and A. colossus sp. n. A diagnosis for distinguishing these new species from the other species of this genus in North America is included. This paper is illustrated with pictures of the dorsal habitus and the male genitalia of the new species. The evolutionary relationships of the species are discussed, as well as their distribution and ecology. It is considered that the species of the genus Ateuchus present in North and Central America correspond to the Typical Neotropical and Mountain Mesoamerican distribution patterns.
Inagaki, Y; Dacks, J B; Doolittle, W F; Watanabe, K I; Ohama, T
The marine dinoflagellates Peridinium balticum and Peridinium foliaceum are known for bearing diatom endosymbionts instead of peridinin-containing plastids. While evidence clearly indicates that their endosymbionts are closely related, the relationship between the host dinoflagellate cells is not settled. To examine the relationship of the two dinoflagellates, the DNA sequences of nuclear small-subunit rRNA genes (SSU rDNA) from Peridinium balticum, Peridinium foliaceum and one other peridinin-containing species, Peridinium bipes, were amplified, cloned and sequenced. While phylogenetic analyses under simple models of nucleotide substitution weakly support the monophyly of Peridinium balticum and Peridinium foliaceum, analyses under more sophisticated models significantly increased the statistical support for this relationship. Combining these results with the similarity between the two endosymbionts, it is concluded that (i) the two hosts have the closest sister relationship among dinoflagellates tested, (ii) the hypothesis that the diatom endosymbiosis occurred prior to the separation of the host cells is most likely to explain their evolutionary histories, and (iii) phylogenetic inferences under complex nucleotide evolution models seem to be able to compensate significant rate variation in the two SSU rDNA.
Dan F. DeBlasio
Full Text Available We present the phylogeny analysis software SICLE (Sister Clade Extractor, an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.
DeBlasio, Dan F; Wisecaver, Jennifer H
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.
Liu, Tong; Sun, Keping; Park, Yung Chul; Feng, Jiang
The greater horseshoe bat, Rhinolophus ferrumequinum , is an important model organism for studies on chiropteran phylogeographic patterns. Previous studies revealed the population history of R. ferrumequinum from Europe and most Asian regions, yet there continue to be arguments about their evolutionary process in Northeast Asia. In this study, we obtained mitochondrial DNA cyt b and D-loop data of R. ferrumequinum from Northeast China, South Korea and Japan to clarify their phylogenetic relationships and evolutionary process. Our results indicate a highly supported monophyletic group of Northeast Asian greater horseshoe bats, in which Japanese populations formed a single clade and clustered into the mixed branches of Northeast Chinese and South Korean populations. We infer that R. ferrumequinum in Northeast Asia originated in Northeast China and South Korea during a cold glacial period, while some ancestors likely arrived in Japan by flying or land bridge and subsequently adapted to the local environment. Consequently, during the warm Eemian interglaciation, the Korea Strait, between Japan and South Korea, became a geographical barrier to Japanese and inland populations, while the Changbai Mountains, between China and North Korea, did not play a significant role as a barrier between Northeast China and South Korea populations.
Timothy J Page
Full Text Available BACKGROUND: We investigated the large and small scale evolutionary relationships of the endemic Western Australian subterranean shrimp genus Stygiocaris (Atyidae using nuclear and mitochondrial genes. Stygiocaris is part of the unique cave biota of the coastal, anchialine, limestones of the Cape Range and Barrow Island, most of whose nearest evolutionary relations are found in coastal caves of the distant North Atlantic. The dominance of atyids in tropical waters and their food resources suggest they are pivotal in understanding these groundwater ecosystems. METHODOLOGY/PRINCIPLE FINDINGS: Our nuclear and mitochondrial analyses all recovered the Mexican cave genus Typhlatya as the sister taxon of Stygiocaris, rather than any of the numerous surface and cave atyids from Australia or the Indo-Pacific region. The two described Stygiocaris species were recovered as monophyletic, and a third, cryptic, species was discovered at a single site, which has very different physiochemical properties from the sites hosting the two described species. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that Stygiocaris and Typhlatya may descend from a common ancestor that lived in the coastal marine habitat of the ancient Tethys Sea, and were subsequently separated by plate tectonic movements. This vicariant process is commonly thought to explain the many disjunct anchialine faunas, but has rarely been demonstrated using phylogenetic techniques. The Cape Range's geological dynamism, which is probably responsible for the speciation of the various Stygiocaris species, has also led to geographic population structure within species. In particular, Stygiocaris lancifera is split into northern and southern groups, which correspond to population splits within other sympatric subterranean taxa.
Lehmiller, Justin J.; Agnew, Christopher R.
Little research has addressed age-gap romantic relationships (romantic involvements characterized by substantial age differences between partners). Drawing on evolutionary and socio-cultural perspectives, the present study examined normative beliefs and commitment processes among heterosexual women involved in age-gap and age-concordant…
Novick, Laura R.; Catley, Kefyn M.
Science is an important domain for investigating students' responses to information that contradicts their prior knowledge. In previous studies of this topic, this information was communicated verbally. The present research used diagrams, specifically trees (cladograms) depicting evolutionary relationships among taxa. Effects of college…
Horizontal gene transfer has, over the past 25 years, become a part of evolutionary thinking. In the present paper I discuss horizontal gene transfer (HGT) in relation to contingency, natural selection, evolutionary change speed and the Tree-of-Life endeavour, with the aim of contributing to the understanding of the role of HGT in evolutionary processes. In addition, the challenges that HGT imposes on the current view of evolution are emphasized.
Zhang, W Q; Zhang, M H
Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.
Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B
Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.
Sandra L Talbot
Full Text Available Subspecies relationships within the peregrine falcon (Falco peregrinus have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons-F. p. tundrius, anatum, and pealei-for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings-a coastal grouping
Talbot, Sandra L.; Sage, Kevin; Sonsthagen, Sarah A.; Gravley, Meg C.; Swem, Ted; Williams, Jeffrey C.; Longmire, Jonathan L.; Ambrose, Skip; Flamme, Melanie J; Lewis, Stephen B.; Phillips, Laura M.; Anderson, Clifford; White, Clayton M
Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–F. p. tundrius, anatum, and pealei–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping
Sinclair, Anne; And Others
Researchers administered surveys to college zoology students prior to, and immediately following a study of evolutionary theory, to assess their understanding and acceptance of evidence supporting the theory. Results showed students had many misconceptions about the theory. Their beliefs interfered with their ability to objectively view scientific…
Townsend, Ted M.; Larson, Allan; Louis, Edward; Macey, J. Robert
Squamate reptiles serve as model systems for evolutionary studies of a variety of morphological and behavioral traits, and phylogeny is crucial to many generalizations derived from such studies. Specifically, the traditional dichotomy between Iguania and Scleroglossa has been correlated with major evolutionary shifts within Squamata. We present a molecular phylogenetic study of squamates using DNA sequence data from the nuclear genes RAG-1 and c-mos and the mitochondrial ND2 region, sampling all major clades and most major subclades. Monophyly of Iguania, Anguimorpha, and almost all currently recognized squamate families is strongly supported. However, monophyly is rejected for Scleroglossa, Varanoidea, and several other higher taxa, and Iguania is highly nested within Squamata. Limblessness evolved independently in snakes, dibamids, and amphisbaenians, suggesting widespread morphological convergence or parallelism in limbless, burrowing forms. Amphisbaenians are the sister group of lacertids, and snakes are grouped with iguanians and anguimorphs. Dibamids diverged early in squamate evolutionary history. Xantusiidae is the sister taxon of Cordylidae. Studies of functional tongue morphology and feeding mode have found significant differences between Scleroglossa and Iguania, and our finding of a nonmonophyletic Scleroglossa and a highly nested Iguania suggest that similar states evolved separately in Sphenodon and Iguania, and that jaw prehension is the ancestral feeding mode in squamates.
Phillips, R D; Brown, G R; Dixon, K W; Hayes, C; Linde, C C; Peakall, R
The mechanism of pollinator attraction is predicted to strongly influence both plant diversification and the extent of pollinator sharing between species. Sexually deceptive orchids rely on mimicry of species-specific sex pheromones to attract their insect pollinators. Given that sex pheromones tend to be conserved among related species, we predicted that in sexually deceptive orchids, (i) pollinator sharing is rare, (ii) closely related orchids use closely related pollinators and (iii) there is strong bias in the wasp lineages exploited by orchids. We focused on species that are pollinated by sexual deception of thynnine wasps in the distantly related genera Caladenia and Drakaea, including new field observations for 45 species of Caladenia. Specialization was extreme with most orchids using a single pollinator species. Unexpectedly, seven cases of pollinator sharing were found, including two between Caladenia and Drakaea, which exhibit strikingly different floral morphology. Phylogenetic analysis of pollinators using four nuclear sequence loci demonstrated that although orchids within major clades primarily use closely related pollinator species, up to 17% of orchids within these clades are pollinated by a member of a phylogenetically distant wasp genus. Further, compared to the total diversity of thynnine wasps within the study region, orchids show a strong bias towards exploiting certain genera. Although these patterns may arise through conservatism in the chemical classes used in sex pheromones, apparent switches between wasp clades suggest unexpected flexibility in floral semiochemical production. Alternatively, wasp sex pheromones within lineages may exhibit greater chemical diversity than currently appreciated. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.
Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu
EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that...
Wei, Fangping; Chen, Bowen
To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.
Full Text Available Filarial nematodes currently infect up to 54 million people worldwide, with millions more at risk for infection, representing the leading cause of disability in the developing world. Brugia malayi is one of the causative agents of lymphatic filariasis and remains the only human filarial parasite that can be maintained in small laboratory animals. Many filarial nematode species, including B. malayi, carry an obligate endosymbiont, the alpha-proteobacteria Wolbachia, which can be eliminated through antibiotic treatment. Elimination of the endosymbiont interferes with development, reproduction, and survival of the worms within the mamalian host, a clear indicator that the Wolbachia are crucial for survival of the parasite. Little is understood about the mechanism underlying this symbiosis.To better understand the molecular interplay between these two organisms we profiled the transcriptomes of B. malayi and Wolbachia by dual RNA-seq across the life cycle of the parasite. This helped identify functional pathways involved in this essential symbiotic relationship provided by the co-expression of nematode and bacterial genes. We have identified significant stage-specific and gender-specific differential expression in Wolbachia during the nematode's development. For example, during female worm development we find that Wolbachia upregulate genes involved in ATP production and purine biosynthesis, as well as genes involved in the oxidative stress response.This global transcriptional analysis has highlighted specific pathways to which both Wolbachia and B. malayi contribute concurrently over the life cycle of the parasite, paving the way for the development of novel intervention strategies.
de Bruyn, Mark; Rüber, Lukas; Nylinder, Stephan; Stelbrink, Björn; Lovejoy, Nathan R; Lavoué, Sébastien; Tan, Heok Hui; Nugroho, Estu; Wowor, Daisy; Ng, Peter K L; Siti Azizah, M N; Von Rintelen, Thomas; Hall, Robert; Carvalho, Gary R
Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earth's land surface, more than half the world's plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southeast (SE) Asia displays extraordinary species richness, encompassing four biodiversity hotspots, though disentangling multiple potential drivers of species richness is confounded by the region's dynamic geological and climatic history. Here, we use multilocus molecular genetic data from dense multispecies sampling of freshwater fishes across three biodiversity hotspots, to test the effect of Quaternary climate change and resulting drainage rearrangements on aquatic faunal diversification. While Cenozoic geological processes have clearly shaped evolutionary history in SE Asian halfbeak fishes, we show that paleo-drainage re-arrangements resulting from Quaternary climate change played a significant role in the spatiotemporal evolution of lowland aquatic taxa, and provide priorities for conservation efforts.
Guise, Kevin; Kelly, Karen; Romanowski, Jennifer; Vogeley, Kai; Platek, Steven M; Murray, Elizabeth; Keenan, Julian Paul
Although theories that examine direct links between behavior and brain remain incomplete, it is known that brain expansion significantly correlates with caloric and oxygen demands. Therefore, one of the principles governing evolutionary cognitive neuroscience is that cognitive abilities that require significant brain function (and/or structural support) must be accompanied by significant fitness benefit to offset the increased metabolic demands. One such capacity is self-awareness (SA), which (1) is found only in the greater apes and (2) remains unclear in terms of both cortical underpinning and possible fitness benefit. In the current experiment, transcranial magnetic stimulation (TMS) was applied to the prefrontal cortex during a spatial perspective-taking task involving self and other viewpoints. It was found that delivery of TMS to the right prefrontal region disrupted self-, but not other-, perspective. These data suggest that self-awareness may have evolved in concert with other right hemisphere cognitive abilities.
Carmen J Figueredo-Urbina
Full Text Available Agave inaequidens and A. cupreata are wild species with some populations under incipient management, while A. hookeri is exclusively cultivated, used for producing the fermented beverage pulque. These species are closely related and sympatric members of the Crenatae group, but taxonomists have previously hypothesized that A. inaequidens is the most probable ancestor of A. hookeri. Our study aims at evaluating patterns of morphological and genetic divergence among populations of the three species, in order to analyze their ecological and possible evolutionary relationships. We studied 24 agave populations, 16 of them of Agave inaequidens, four of A. cupreata and four of A. hookeri. Population morphometric and genetics studies were performed using 39 morphological characters and 10 nuclear microsatellites, respectively. We estimated levels of morphological and genetic diversity and dissimilarity, as well as genetic structure and gene flow among populations and species. The three species were clearly differentiated by general plant size, lateral teeth, terminal spines, flowers and fruit size. The largest plants were those of A. hookeri followed by A. inaequidens and the smallest were A. cupreata. Multivariate analyses indicated greater morphological similarity between A. hookeri and cultivated A. inaequidens, while A. cupreata consistently appeared as a separate group. We identified similar levels of morphological diversity index (MDI in the three species, but higher genetic diversity in A. inaequidens (MDI = 0.401-0.435; HE = 0.704-0.733, than in A. cupreata (MDI = 0.455-0.523; HE = 0.480-0.510 and the predominantly vegetative propagated crop A. hookeri (MDI = 0.335-0.688; HE = 0.450-0.567, a pattern consistent with our expectations. The morphological and genetic similarities between cultivated A. inaequidens and A. hookeri support the hypothetical evolutionary relationships among these species, but studies with cpDNA and SNPs, and including other
Figueredo-Urbina, Carmen J; Casas, Alejandro; Torres-García, Ignacio
Agave inaequidens and A. cupreata are wild species with some populations under incipient management, while A. hookeri is exclusively cultivated, used for producing the fermented beverage pulque. These species are closely related and sympatric members of the Crenatae group, but taxonomists have previously hypothesized that A. inaequidens is the most probable ancestor of A. hookeri. Our study aims at evaluating patterns of morphological and genetic divergence among populations of the three species, in order to analyze their ecological and possible evolutionary relationships. We studied 24 agave populations, 16 of them of Agave inaequidens, four of A. cupreata and four of A. hookeri. Population morphometric and genetics studies were performed using 39 morphological characters and 10 nuclear microsatellites, respectively. We estimated levels of morphological and genetic diversity and dissimilarity, as well as genetic structure and gene flow among populations and species. The three species were clearly differentiated by general plant size, lateral teeth, terminal spines, flowers and fruit size. The largest plants were those of A. hookeri followed by A. inaequidens and the smallest were A. cupreata. Multivariate analyses indicated greater morphological similarity between A. hookeri and cultivated A. inaequidens, while A. cupreata consistently appeared as a separate group. We identified similar levels of morphological diversity index (MDI) in the three species, but higher genetic diversity in A. inaequidens (MDI = 0.401-0.435; HE = 0.704-0.733), than in A. cupreata (MDI = 0.455-0.523; HE = 0.480-0.510) and the predominantly vegetative propagated crop A. hookeri (MDI = 0.335-0.688; HE = 0.450-0.567), a pattern consistent with our expectations. The morphological and genetic similarities between cultivated A. inaequidens and A. hookeri support the hypothetical evolutionary relationships among these species, but studies with cpDNA and SNPs, and including other member of the
Lawrence, David J.; Beauchamp, David A.; Olden, Julian D.
-history stage that likely sets the distributional limits of all other life-history stages. We anticipate the framework developed here could be employed to identify how similar stage-specific environmental sensitivity determines distribution in many other ectothermic species.
Lyons, Minna T
In the present study, shame and guilt proneness were investigated in relation to primary and secondary psychopathy, looking at parental care as a possible mediator. A sample of 388 volunteers participated in an on-line study, completing several self-report measurements. Primary psychopathy, robust to parental care and sex of the participant, was associated with lower guilt proneness after a private transgression and lower negative self-evaluations after a public transgression. Secondary psychopathy was not associated with guilt or shame proneness. Paternal care played a mediating role between primary psychopathy and guilt, but only in male participants. High paternal care was associated with lower guilt repair in high psychopathy males, suggesting that a positive father-son relationship might be essential for development of exploitive strategies in primary psychopathy. The results highlight the fundamental differences between primary and secondary psychopathy, and provide support for the idea that primary psychopathy is an evolutionary cheater-strategy.
Patrick Denis R
Full Text Available Abstract Background As key regulators of mitotic chromosome segregation, the Aurora family of serine/threonine kinases play an important role in cell division. Abnormalities in Aurora kinases have been strongly linked with cancer, which has lead to the recent development of new classes of anti-cancer drugs that specifically target the ATP-binding domain of these kinases. From an evolutionary perspective, the species distribution of the Aurora kinase family is complex. Mammals uniquely have three Aurora kinases, Aurora-A, Aurora-B, and Aurora-C, while for other metazoans, including the frog, fruitfly and nematode, only Aurora-A and Aurora-B kinases are known. The fungi have a single Aurora-like homolog. Based on the tacit assumption of orthology to human counterparts, model organism studies have been central to the functional characterization of Aurora kinases. However, the ortholog and paralog relationships of these kinases across various species have not been rigorously examined. Here, we present comprehensive evolutionary analyses of the Aurora kinase family. Results Phylogenetic trees suggest that all three vertebrate Auroras evolved from a single urochordate ancestor. Specifically, Aurora-A is an orthologous lineage in cold-blooded vertebrates and mammals, while structurally similar Aurora-B and Aurora-C evolved more recently in mammals from a duplication of an ancestral Aurora-B/C gene found in cold-blooded vertebrates. All so-called Aurora-A and Aurora-B kinases of non-chordates are ancestral to the clade of chordate Auroras and, therefore, are not strictly orthologous to vertebrate counterparts. Comparisons of human Aurora-B and Aurora-C sequences to the resolved 3D structure of human Aurora-A lends further support to the evolutionary scenario that vertebrate Aurora-B and Aurora-C are closely related paralogs. Of the 26 residues lining the ATP-binding active site, only three were variant and all were specific to Aurora-A. Conclusions In
Soliveres, Santiago; Torices, Rubén; Maestre, Fernando T.
Positive and negative plant-plant interactions are major processes shaping plant communities. They are affected by environmental conditions and evolutionary relationships among the interacting plants. However, the generality of these factors as drivers of pairwise plant interactions and their combined effects remain virtually unknown. We conducted an observational study to assess how environmental conditions (altitude, temperature, irradiance and rainfall), the dispersal mechanism of beneficiary species and evolutionary relationships affected the co-occurrence of pairwise interactions in 11 Stipa tenacissima steppes located along an environmental gradient in Spain. We studied 197 pairwise plant-plant interactions involving the two major nurse plants (the resprouting shrub Quercus coccifera and the tussock grass S. tenacissima) found in these communities. The relative importance of the studied factors varied with the nurse species considered. None of the factors studied were good predictors of the co-ocurrence between S. tenacissima and its neighbours. However, both the dispersal mechanism of the beneficiary species and the phylogenetic distance between interacting species were crucial factors affecting the co-occurrence between Q. coccifera and its neighbours, while climatic conditions (irradiance) played a secondary role. Values of phylogenetic distance between 207-272.8 Myr led to competition, while values outside this range or fleshy-fruitness in the beneficiary species led to positive interactions. The low importance of environmental conditions as a general driver of pairwise interactions was caused by the species-specific response to changes in either rainfall or radiation. This result suggests that factors other than climatic conditions must be included in theoretical models aimed to generally predict the outcome of plant-plant interactions. Our study helps to improve current theory on plant-plant interactions and to understand how these interactions can
Chute, H.; Dombard, A. J.; Byrne, P. K.
Lithospheric flexure associated with Arsia, Pavonis, and Ascraeus Montes has been previously studied to constrain the timeline and breadth of endogenic surface features surrounding these volcanoes. Here, we simulate the radial extent of two specific load-related features: annular graben and flank terraces. Detailed mapping of Ascraeus Mons (the youngest of the three volcanoes) showed a phase of compression of the edifice, forming the terraces and an annulus of graben immediately off the flanks, followed by a period of extension that formed additional graben superposed on the terraces on the lower flanks of the edifice. This transition from compression to extension on the lower flanks has been difficult to reconcile in mechanical models. We explore, with finite-element simulations, the effects of a thermal anomaly associated with an intrusive crustal underplate, which results in locally thinning the lithosphere (in contrast to past efforts that assumed a constant-thickness lithosphere). We find that it is primarily the horizontal extent of this thermal anomaly that governs how the lithosphere flexes under a volcano, as well as the transition from flank compression to a tight annulus of extensional stresses. Specifically, we propose that the structures on Ascraeus may be consistent with an early stage of volcanic growth accompanied by an underplate about the same width as the edifice that narrowed as volcanism waned, resulting in an inward migration of the extensional horizontal stresses from the surrounding plains onto the lower flanks. By linking the surface strains on the volcano with the volcano-tectonic evolution predicted by our flexure model, we can further constrain a more accurate timeline for the tectonic history of Ascraeus Mons. More broadly, because these tectonic structures are commonly observed, our results provide a general evolutionary model for large shield volcanoes on Mars.
Li, X C; Barringer, B C; Barbash, D A
Sterility is a commonly observed phenotype in interspecific hybrids. Sterility may result from chromosomal or genic incompatibilities, and much progress has been made toward understanding the genetic basis of hybrid sterility in various taxa. The underlying mechanisms causing hybrid sterility, however, are less well known. The pachytene checkpoint is a meiotic surveillance system that many organisms use to detect aberrant meiotic products, in order to prevent the production of defective gametes. We suggest that activation of the pachytene checkpoint may be an important mechanism contributing to two types of hybrid sterility. First, the pachytene checkpoint may form the mechanistic basis of some gene-based hybrid sterility phenotypes. Second, the pachytene checkpoint may be an important mechanism that mediates chromosomal-based hybrid sterility phenotypes involving gametes with non-haploid (either non-reduced or aneuploid) chromosome sets. Studies in several species suggest that the strength of the pachytene checkpoint is sexually dimorphic, observations that warrant future investigation into whether such variation may contribute to differences in patterns of sterility between male and female interspecific hybrids. In addition, plants seem to lack the pachytene checkpoint, which correlates with increased production of unreduced gametes and a higher incidence of polyploid species in plants versus animals. Although the pachytene checkpoint occurs in many animals and in fungi, at least some of the genes that execute the pachytene checkpoint are different among organisms. This finding suggests that the penetrance of the pachytene checkpoint, and even its presence or absence can evolve rapidly. The surprising degree of evolutionary flexibility in this meiotic surveillance system may contribute to the observed variation in patterns of hybrid sterility and in rates of polyploidization.
Reichard, Martin; Liu, H.; Smith, C.
Roč. 9, č. 2 (2007), s. 239-259 ISSN 1522-0613 Grant - others:NSFC(CN) 30470237 Institutional research plan: CEZ:AV0Z60930519 Keywords : brood parasitism * co-evolution * egg ejection * host-parasite relationship * mutualism * oviposition Subject RIV: EG - Zoology Impact factor: 1.409, year: 2007
Hof, van den K.; Berg, van den R.G.; Gravendeel, B.
Phylogenetic relationships among and within the subsections of the genus Viola are still far from resolved. We present the first organismal phylogeny of predominantly western European species of subsection Rostratae based on the plastid trnS¿trnG intron and intergenic spacer and the nuclear low-copy
Geiser, D.M.; Frisvad, Jens Christian; Taylor, J.W.
are heterothallic. Phylogenetic relationships were inferred among members of Aspergillus section Fumigati based on partial DNA sequences from the benA beta-tubulin and rodA hydrophobin genes. Aspergillus clavatus was chosen as an outgroup. The two gene regions provided nearly equal numbers of phylogenetically...... informative nucleotide characters. The rodA region possessed a considerably higher level of inferred amino acid variation than did the benA region. The results of a partition homogeneity test showed that the benA and rodA data sets were not in significant conflict, and the topologies of the most parsimonious...
Evolutionary relationships between Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici isolates inferred from mating type, elongation factor-1a exopolygalacturonase sequences
Lievens, B.; Baarlen, van P.; Verreth, C.; Kerckhove, van S.; Rep, M.; Thomma, B.P.H.J.
Fusarium oxysporum is a ubiquitous species complex of soilborne plant pathogens that comprises many different formae speciales, each characterized by a high degree of host specificity. In this study, the evolutionary relationships between different isolates of the F. oxysporum species complex have
Caira, J N; Jensen, K
There is general consensus that the living elasmobranchs comprise a monophyletic taxon. There is evidence that, among tetraphyllidean tapeworms, the approximately 201 hooked species (Onchobothriidae) may also comprise a monophyletic group. Determinations of host specificity are contingent upon correct specific identifications. Since 1960, over 200 new elasmobranch species and over 100 new onchobothriid species have been described. Some confidence can be placed in host and parasite identifications of recent studies, but specific identifications provided in older literature in many cases are suspect. There is some consensus among published works on the phylogenetic relationships among elasmobranchs. Phylogenetic relationships among onchobothriids remain largely unresolved. Elasmobranchs have been poorly sampled for onchobothriids; records exist for approximately 20% of the 911 species and approximately 44% of the 170 elasmobranch genera. Onchobothriids are remarkably host specific, exhibiting essentially oioxenous specificity for their definitive hosts. Multiple onchobothriid species commonly parasitise the same host species; in some cases these are congeners, in other cases these are members of two different onchobothriid genera. There is substantial incongruence between available host and parasite phylogenies. For example, Acanthobothrium is by far the most ubiquitous onchobothriid genus, parasitising almost all orders of elasmobranchs known to host onchobothriids, yet, there is no evidence of major clades of Acanthobothrium corresponding to postulated major subgroupings of elasmobranchs (e.g. Galea and Squalea or sharks and rays). Potamotrygonocestus appears to be among the most basal onchobothriid groups, yet it parasitises one of the most derived elasmobranch groups (the freshwater stingray genus Potamotrygon). It appears that congeners parasitising the same host species are not necessarily each other's closest relatives. At this point the preliminary and
Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca
Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect
Gudowska, Agnieszka; Schramm, Bartosz W; Czarnoleski, Marcin; Kozłowski, Jan; Bauchinger, Ulf
The tight association between ambient temperature (T) and metabolic rate (MR) is a common occurrence in ectotherms, but the determinants of this association are not fully understood. This study examined whether the relationship between MR and T is the same among individuals, as predicted by the Universal Temperature Dependence hypothesis, or whether this relationship differs between them. We used flow-through respirometry to measure standard MR and to determine gas exchange patterns for 111 individuals of three Carabidae species which differ in size (Abax ovalis, Carabus linnei and C. coriaceus), exposed to four different temperatures (ten individuals of each species measured at 6, 11, 16 and 21°C). We found a significant interaction between ln body mass and the inverse of temperature, indicating that in a given species, the effect of temperature on MR was weaker in larger individuals than in smaller individuals. Overall, this finding shows that the thermal dependence of MR is not body mass invariant. We observed three types of gas exchange patterns among beetles: discontinuous, cyclic and continuous. Additionally, the appearance of these patterns was associated with MR and T. Evolution in diverse terrestrial environments could affect diverse ventilation patterns, which accommodate changes in metabolism in response to temperature variation. In conclusion, explaining the variance in metabolism only through fundamental physical laws of thermodynamics, as predicted by the Universal Temperature Dependence hypothesis, appears to oversimplify the complexity of nature, ignoring evolutionary trade-offs that should be taken into account in the temperature - metabolism relationship. Copyright © 2016 Elsevier Ltd. All rights reserved.
Westneat, Mark W; Alfaro, Michael E
The family Labridae (including scarines and odacines) contains 82 genera and about 600 species of fishes that inhabit coastal and continental shelf waters in tropical and temperate oceans throughout the world. The Labridae (the wrasses) is the fifth largest fish family and second largest marine fish family, and is one of the most morphologically and ecologically diversified families of fishes in size, shape, and color. Labrid phylogeny is a long-standing problem in ichthyology that is part of the larger question of relationships within the suborder Labroidei. A phylogenetic analysis of labrids was conducted to investigate relationships among the six classical tribes of wrasses, the affinities of the wrasses to the parrotfishes (scarines), and the broad phylogenetic structure among labrid genera. Four gene fragments were sequenced from 98 fish species, including 84 labrid fishes and 14 outgroup taxa. Taxa were chosen from all major labrid clades and most major global ocean regions where labrid fishes exist, as well as cichlid, pomacentrid, and embiotocid outgroups. From the mitochondrial genome we sequenced portions of 12S rRNA (1000 bp) and 16S rRNA (585 bp), which were aligned by using a secondary structure model. From the nuclear genome, we sequenced part of the protein-coding genes RAG2 (846 bp) and Tmo4C4 (541 bp). Maximum likelihood, maximum parsimony, and Bayesian analyses on the resulting 2972 bp of DNA sequence produced similar topologies that confirm the monophyly of a family Labridae that includes the parrotfishes and butterfishes and strong support for many previously identified taxonomic subgroups. The tribe Hypsigenyini (hogfishes, tuskfishes) is the sister group to the remaining labrids and includes odacines and the chisel-tooth wrasse Pseudodax moluccanus, a species previously considered close to scarines. Cheilines and scarines are sister-groups, closely related to the temperate Labrini, and pseudocheilines and cheilines are split in all phylogenies
Hehman, Jessica A.; Bugental, Daphne Blunt
In a test of life stage-specific responses to age-based stigma, older (n = 54, ages 62-92) and younger (n = 81, ages 17-22) adults were told that a task (Weschler Adult Intelligence Scale-III block design) required either (a) speed/contemporary knowledge (YA; "youth advantage") or (b) life experience/wisdom (OA; "age…
Hendrix, Roger W.; Dedrick, Rebekah; Mitchell, Kaitlin; Ko, Ching-Chung; Russell, Daniel; Bell, Emma; Gregory, Matthew; Bibb, Maureen J.; Pethick, Florence; Jacobs-Sera, Deborah; Herron, Paul; Buttner, Mark J.; Hatfull, Graham F.
The genome sequences of eight Streptomyces phages are presented, four of which were isolated for this study. Phages R4, TG1, ϕHau3, and SV1 were isolated previously and have been exploited as tools for understanding and genetically manipulating Streptomyces spp. We also extracted five apparently intact prophages from recent Streptomyces spp. genome projects and, together with six phage genomes in the database, we analyzed all 19 Streptomyces phage genomes with a view to understanding their relationships to each other and to other actinophages, particularly the mycobacteriophages. Fifteen of the Streptomyces phages group into four clusters of related genomes. Although the R4-like phages do not share nucleotide sequence similarity with other phages, they clearly have common ancestry with cluster A mycobacteriophages, sharing many protein homologues, common gene syntenies, and similar repressor-stoperator regulatory systems. The R4-like phage ϕHau3 and the prophage StrepC.1 (from Streptomyces sp. strain C) appear to have hijacked a unique adaptation of the streptomycetes, i.e., use of the rare UUA codon, to control translation of the essential phage protein, the terminase. The Streptomyces venezuelae generalized transducing phage SV1 was used to predict the presence of other generalized transducing phages for different Streptomyces species. PMID:23995638
Kevin M King
Full Text Available The fungal genus Rhynchosporium (causative agent of leaf blotch contains several host-specialised species, including R. commune (colonising barley and brome-grass, R. agropyri (couch-grass, R. secalis (rye and triticale and the more distantly related R. orthosporum (cocksfoot. This study used molecular fingerprinting, multilocus DNA sequence data, conidial morphology, host range tests and scanning electron microscopy to investigate the relationship between Rhynchosporium species on ryegrasses, both economically important forage grasses and common wild grasses in many cereal growing areas, and other plant species. Two different types of Rhynchosporium were found on ryegrasses in the UK. Firstly, there were isolates of R. commune that were pathogenic to both barley and Italian ryegrass. Secondly, there were isolates of a new species, here named R. lolii, that were pathogenic only to ryegrass species. R. lolii was most closely related to R. orthosporum, but exhibited clear molecular, morphological and host range differences. The species was estimated to have diverged from R. orthosporum ca. 5735 years before the present. The colonisation strategy of all of the different Rhynchosporium species involved extensive hyphal growth in the sub-cuticular regions of the leaves. Finally, new species-specific PCR diagnostic tests were developed that could distinguish between these five closely related Rhynchosporium species.
Sánchez-Navarro, J A; Pallás, V
The complete nucleotide sequence of an isolate of prunus necrotic ringspot virus (PNRSV) RNA 3 has been determined. Elucidation of the amino acid sequence of the proteins encoded by the two large open reading frames (ORFs) allowed us to carry out comparative and phylogenetic studies on the movement (MP) and coat (CP) proteins in the ilarvirus group. Amino acid sequence comparison of the MP revealed a highly conserved basic sequence motif with an amphipathic alpha-helical structure preceding the conserved motif of the '30K superfamily' proposed by Mushegian and Koonin  for MP's. Within this '30K' motif a strictly conserved transmembrane domain is present in all ilarviruses sequenced so far. At the amino-terminal end, prune dwarf virus (PDV) has an extension not present in other ilarviruses but which is observed in all bromo- and cucumoviruses, suggesting a common ancestor or a recombinational event in the Bromoviridae family. Examination of the N-terminus of the CP's of all ilarviruses revealed a highly basic region, part of which resembles the Arg-rich motif that has been characterized in the RNA-binding protein family. This motif has also been found in the other members of the Bromoviridae family, suggesting its involvement in a structural function. Furthermore this region is required for infectivity in ilarviruses. The similarities found in this Arg-rich motif are discussed in terms of this process known as genome activation. Finally, phylogenetic analysis of both the MP and CP proteins revealed a higher relationship of A1MV to PNRSV, apple mosaic virus (ApMV) and PDV than any other member of the ilarvirus group. In that sense, A1MV should be considered as a true ilarvirus instead of forming a distinct group of viruses.
Full Text Available In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59% and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 kbp to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C and environmental (E, all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins were present in all human pathogenic strains (both biotype 3 and non-biotype 3 and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and
García-Pereira, María Jesús; Caballero, Armando; Quesada, Humberto
Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony
Full Text Available Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE, and multilocus sequence typing (MLST, permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678, but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen.
Radhey S. Gupta
Full Text Available The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia and Chlamydiae, along with the Lentisphaerae, Poribacteria and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, 6 conserved signature indels (CSIs in the proteins Cyt c oxidase, UvrD helicase, urease and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms.
Full Text Available During the blood meal of a Plasmodium-infected mosquito, 10 to 100 parasites are inoculated into the skin and a proportion of these migrate via the bloodstream to the liver where they infect hepatocytes. The Plasmodium liver stage, despite its clinical silence, represents a highly promising target for antimalarial drug and vaccine approaches. Successfully invaded parasites undergo a massive proliferation in hepatocytes, producing thousands of merozoites that are transported into a blood vessel to infect red blood cells. To successfully develop from the liver stage into infective merozoites, a tight regulation of gene expression is needed. Although this is a very interesting aspect in the biology of Plasmodium, little is known about gene regulation in Plasmodium parasites in general and in the liver stage in particular. We have functionally analyzed a novel promoter region of the rodent parasite Plasmodium berghei that is exclusively active during the liver stage of the parasite. To prove stage-specific activity of the promoter, GFP and luciferase reporter assays have been successfully established, allowing both qualitative and accurate quantitative analysis. To further characterize the promoter region, the transcription start site was mapped by rapid amplification of cDNA ends (5'-RACE. Using promoter truncation experiments and site-directed mutagenesis within potential transcription factor binding sites, we suggest that the minimal promoter contains more than one binding site for the recently identified parasite-specific ApiAP2 transcription factors. The identification of a liver stage-specific promoter in P. berghei confirms that the parasite is able to tightly regulate gene expression during its life cycle. The identified promoter region might now be used to study the biology of the Plasmodium liver stage, which has thus far proven problematic on a molecular level. Stage-specific expression of dominant-negative mutant proteins and
Full Text Available Flagellar attachment is a visibly striking morphological feature of African trypanosomes but little is known about the requirements for attachment at a molecular level. This study characterizes a previously undescribed membrane protein, FLA3, which plays an essential role in flagellar attachment in Trypanosoma brucei. FLA3 is heavily N-glycosylated, locates to the flagellar attachment zone and appears to be a bloodstream stage specific protein. Ablation of the FLA3 mRNA rapidly led to flagellar detachment and a concomitant failure of cytokinesis in the long slender bloodstream form but had no effect on the procyclic form. Flagellar detachment was obvious shortly after induction of the dsRNA and the newly synthesized flagellum was often completely detached after it emerged from the flagellar pocket. Within 12 h most cells possessed detached flagella alongside the existing attached flagellum. These results suggest that proteins involved in attachment are not shared between the new and old attachment zones. In other respects the detached flagella appear normal, they beat rapidly although directional motion was lost, and they possess an apparently normal axoneme and paraflagellar rod structure. The flagellar attachment zone appeared to be disrupted when FLA3 was depleted. Thus, while flagellar attachment is a constitutive feature of the life cycle of trypanosomes, attachment requires stage specific elements at the protein level.
Wieland, Kai; Hinrichsen, H.H.; Grønkjær, P.
A study on cod egg mortality was carried out in the Bornholm Basin (southern central Baltic Sea) toward the end of July 1996. An initial egg aggregation marked by a satellite-tracked drifter buoy was sampled repeatedly over an Ii-day period; profiles of temperature, salinity and dissolved oxygen...... were concurrently recorded. Three replicate estimates of mortality were obtained for each pair of subsequent developmental stages from newly spawned eggs to early larvae. A consistent pattern of stage-specific mortality coincided well with previous experimental observations. Average daily mortality...... rates were 7.2% (eggs IA/IB), 38.7% (eggs (IB/II), 25.6% (eggs II/III), 40.0% (eggs III/IV), and 42.3% (eggs IV/early larvae). The cumulative mortality until hatch amounted to 99.9%. Results from hydrodynamic modelling, however, indicated that the drifter's trajectory was influenced by wind stress...
Twine, Natalie; Chen, Li; Wilkins, Marc
to age-matched control (n=4). Using RNA-seq and cluster analysis, we identified a set of stage-specific molecular markers that define the progression of OB phenotype during ex vivo culture of hMSC, predict in vivo bone formation capacity of hMSC and can be employed to study the mechanisms of impaired......The phenotype of osteoblastic (OB) cells in culture is currently defined using a limited number of markers of low sensitivity and specificity which belong mostly to extracellular matrix proteins. Also, for clinical use of human skeletal (mesenchymal) stem cells (hMSC) in bone regeneration......, there is a need to identify predictive markers for in vivo bone forming capacity. Thus, we employed Illumina RNA sequencing (RNASeq) to examine changes in gene expression across 8 time points between 0-12 days of ex vivo OB differentiation of hMSC. We identified a subset of expressed genes as potentially...
Chen, Si; Zhenjiang, Zhou; Andersen, Mathias Neumann
To investigate the sensitivity of tomato yield and water use efficiency (WUE) to soil water content at different growth stages, the central composite rotatable design (CCRD) was employed in a five-factor-five-level pot experiment under regulated deficit irrigation. Two regression models concerning...... the effects of stage-specific soil water content on tomato yield and WUE were established. The results showed that the lowest available soil water (ASW) content (around 28%) during vegetative growth stage (here denoted θ1) resulted in high yield and WUE. Moderate (around 69% ASW) during blooming and fruit...... effects of ASW in two growth stages were between θ2 and θ5, θ3. In both cases a moderate θ2 was a precondition for maximum yield response to increasing θ5 and θ3. Sensitivity analysis revealed that yield was most sensitive to soil water content at fruit maturity (θ5). Numerical inspection...
Full Text Available Abstract Background Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to be invoked and analyzed. The unclear evolutionary relationship between classical mammalian lipases and the recently discovered human adipose triglyceride lipase (ATGL; a patatin family member is an exemplary case for such a problem. Results We describe an unsupervised, sensitive sequence segment collection heuristic suitable for assembling very large protein families. It is based on fan-like expanding, iterative database searches. To prevent inclusion of unrelated hits, additional criteria are introduced: minimal alignment length and overlap with starting sequence segments, finding starting sequences in reciprocal searches, automated filtering for compositional bias and repetitive patterns. This heuristic was implemented as FAMILYSEARCHER in the ANNIE sequence analysis environment and applied to search for protein links between the classical lipase family and the patatin-like group. Conclusion The FAMILYSEARCHER is an efficient tool for tracing distant evolutionary relationships involving large protein families. Although classical lipases and ATGL have no obvious sequence similarity and differ with regard to fold and catalytic mechanism, homology links detected with FAMILYSEARCHER show that they are evolutionarily related. The conserved sequence parts can be narrowed down to an ancestral core module consisting of three β-strands, one α-helix and a turn containing the typical nucleophilic serine. Moreover, this ancestral module also appears in numerous enzymes with various substrate specificities, but that critically rely on nucleophilic attack mechanisms.
Ono, Hajime; Rewitz, Kim; Shinoda, Tetsu
is eliminated in larvae carrying mutations in molting defective (mld), a gene encoding a nuclear zinc finger protein that is required for production of ecdysone during Drosophila larval development. Intriguingly, mld is not present in the Bombyx mori genome, and we have identified only one spook homolog in both...... Bombyx and Manduca that is expressed in both embryos and larva. These studies suggest an evolutionary split between Diptera and Lepidoptera in how the ecdysone biosynthetic pathway is regulated during development....
Chevalier, Robert L
Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.
Ottaviani, E; Valensin, S; Franceschi, C
The evolutionary perspective indicates that an immune-neuroendocrine effector system integrating innate immunity, stress and inflammation is present in invertebrates. This defense network, centered on the macrophage and exerting primitive and highly promiscuous recognition units, is very effective, ancestral and appears to have been conserved throughout evolution from invertebrates to higher vertebrates. It would seem that there was a "big bang" in the recognition system of lower vertebrates, and T and B cell repertoires, MHC and antibodies suddenly appeared. We argue that this phenomenon is the counterpart of the increasing complexity of the internal circuitry and recognition units in the effector system. The immediate consequences were a progressive enlargement of the pathogen repertoire and new problems regarding self/not-self discrimination. Probably not by chance, a new organ appeared, capable of purging cells able of excessive self recognition. This organ, the thymus, appears to be the result of a well known evolutionary strategy of re-using pre-existing material (neuroendocrine cells and mediators constituting the thymic microenvironment). This bricolage at an organ level is similar to the effect we have already described at the level of molecules and functions of the defense network, and has a general counterpart at genetic level. Thus, in vertebrates, the conserved immune-neuroendocrine effector system remains of fundamental importance in defense against pathogens, while its efficiency has increased through synergy with the new, clonotipical recognition repertoire.
Full Text Available Abstract Background Despite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances to antimalarials are widely spread. Hence, new antimalarial drugs are urgently needed. Results Here, we present a computational analysis of the metabolism of Plasmodium falciparum, the deadliest malaria pathogen. We assembled a compartmentalized metabolic model and predicted life cycle stage specific metabolism with the help of a flux balance approach that integrates gene expression data. Predicted metabolite exchanges between parasite and host were found to be in good accordance with experimental findings when the parasite's metabolic network was embedded into that of its host (erythrocyte. Knock-out simulations identified 307 indispensable metabolic reactions within the parasite. 35 out of 57 experimentally demonstrated essential enzymes were recovered and another 16 enzymes, if additionally the assumption was made that nutrient uptake from the host cell is limited and all reactions catalyzed by the inhibited enzyme are blocked. This predicted set of putative drug targets, shown to be enriched with true targets by a factor of at least 2.75, was further analyzed with respect to homology to human enzymes, functional similarity to therapeutic targets in other organisms and their predicted potency for prophylaxis and disease treatment. Conclusions The results suggest that the set of essential enzymes predicted by our flux balance approach represents a promising starting point for further drug development.
Govindaraghavan, Meera; Lad, Alisha A.
The G2-M transition in Aspergillus nidulans requires the NIMA kinase, the founding member of the Nek kinase family. Inactivation of NIMA results in a late G2 arrest, while overexpression of NIMA is sufficient to promote mitotic events independently of cell cycle phase. Endogenously tagged NIMA-GFP has dynamic mitotic localizations appearing first at the spindle pole body and then at nuclear pore complexes before transitioning to within nuclei and the mitotic spindle and back at the spindle pole bodies at mitotic exit, suggesting that it functions sequentially at these locations. Since NIMA is indispensable for mitotic entry, it has been difficult to determine the requirement of NIMA for subaspects of mitosis. We show here that when NIMA is partially inactivated, although mitosis can be initiated, a proportion of cells fail to successfully generate two daughter nuclei. We further define the mitotic defects to show that normal NIMA function is required for the formation of a bipolar spindle, nuclear pore complex disassembly, completion of chromatin segregation, and the normal structural rearrangements of the nuclear envelope required to generate two nuclei from one. In the remaining population of cells that enter mitosis with inadequate NIMA, two daughter nuclei are generated in a manner dependent on the spindle assembly checkpoint, indicating highly penetrant defects in mitotic progression without sufficient NIMA activity. This study shows that NIMA is required not only for mitotic entry but also sequentially for successful completion of stage-specific mitotic events. PMID:24186954
Sagomonyants, Karen; Mina, Mina
Dentinogenesis is a complex and multistep process, which is regulated by various growth factors, including members of the Fibroblast Growth Factor (FGF) family. Both positive and negative effects of FGFs on dentinogenesis have been reported but the underlying mechanisms of these conflicting results are still unclear. To gain better insight into the role of FGF2 in dentinogenesis, we used dental pulp cells from various transgenic mice, in which fluorescent protein expression identifies cells at different stages of odontoblast differentiation. Our results showed that continuous exposure of pulp cells to FGF2 inhibited mineralization and revealed both stimulatory and inhibitory effects of FGF2 on expression of markers of dentinogenesis and various transgenes. During the proliferation phase of in vitro growth FGF2 increased expression of markers of dentinogenesis and the percentages of DMP1-GFP+ functional odontoblasts and DSPP-Cerulean+ odontoblasts. Additional exposure to FGF2 during the differentiation/mineralization phase of in vitro growth decreased the extent of mineralization, expression of markers of dentinogenesis, and expression of DMP1-GFP and DSPP-Cerulean transgenes. Recovery experiments showed that the inhibitory effects of FGF2 on dentinogenesis were related to the blocking of differentiation of cells into mature odontoblasts. These observations together showed stage-specific effects of FGF2 on dentinogenesis by dental pulp cells and provide critical information for the development of improved treatments for vital pulp therapy and dentin regeneration. PMID:25823776
Full Text Available BACKGROUND: Most filarial parasite species contain Wolbachia, obligatory bacterial endosymbionts that are crucial for filarial development and reproduction. They are targets for alternative chemotherapy, but their role in the biology of filarial nematodes is not well understood. Light microscopy provides important information on morphology, localization and potential function of these bacteria. Surprisingly, immunohistology and in situ hybridization techniques have not been widely used to monitor Wolbachia distribution during the filarial life cycle. METHODS/PRINCIPAL FINDINGS: A monoclonal antibody directed against Wolbachia surface protein and in situ hybridization targeting Wolbachia 16S rRNA were used to monitor Wolbachia during the life cycle of B. malayi. In microfilariae and vector stage larvae only a few cells contain Wolbachia. In contrast, large numbers of Wolbachia were detected in the lateral chords of L4 larvae, but no endobacteria were detected in the genital primordium. In young adult worms (5 weeks p.i., a massive expansion of Wolbachia was observed in the lateral chords adjacent to ovaries or testis, but no endobacteria were detected in the growth zone of the ovaries, uterus, the growth zone of the testis or the vas deferens. Confocal laser scanning and transmission electron microscopy showed that numerous Wolbachia are aligned towards the developing ovaries and single endobacteria were detected in the germline. In inseminated females (8 weeks p.i. Wolbachia were observed in the ovaries, embryos and in decreasing numbers in the lateral chords. In young males Wolbachia were found in distinct zones of the testis and in large numbers in the lateral chords in the vicinity of testicular tissue but never in mature spermatids or spermatozoa. CONCLUSIONS: Immunohistology and in situ hybridization show distinct tissue and stage specific distribution patterns for Wolbachia in B. malayi. Extensive multiplication of Wolbachia occurs in the
Lorenz, Viola; Ramsey, Haley; Liu, Zhi-Jian; Italiano, Joseph; Hoffmeister, Karin; Bihorel, Sihem; Mager, Donald; Hu, Zhongbo; Slayton, William B; Kile, Benjamin T; Sola-Visner, Martha; Ferrer-Marin, Francisca
Congenital amegakaryocytic thrombocytopaenia (CAMT) is a disorder caused by c-MPL mutations that impair thrombopoietin (TPO) signalling, resulting in a near absence of megakaryocytes (MKs). While this phenotype is consistent in adults, neonates with CAMT can present with severe thrombocytopaenia despite normal MK numbers. To investigate this, we characterized MKs and platelets in newborn c-MPL –/– mice. Liver MKs in c-MPL –/– neonates were reduced in number and size compared with wild-type (WT) age-matched MKs, and exhibited ultrastructural abnormalities not found in adult c-MPL –/– MKs. Platelet counts were lower in c-MPL –/– compared with WT mice at birth and did not increase over the first 2 weeks of life. In vivo biotinylation revealed a significant reduction in the platelet half-life of c-MPL –/– newborn mice (P2) compared with age-matched WT pups, which was not associated with ultrastructural abnormalities. Genetic deletion of the pro-apoptotic Bak did not rescue the severely reduced platelet half-life of c-MPL –/– newborn mice, suggesting that it was due to factors other than platelets entering apoptosis early. Indeed, adult GFP+ (green fluorescent protein transgenic) platelets transfused into thrombocytopenic c-MPL –/– P2 pups also had a shortened lifespan, indicating the importance of cell-extrinsic factors. In addition, neonatal platelets from WT and c-MPL –/– mice exhibited reduced P-selectin surface expression following stimulation compared with adult platelets of either genotype, and platelets from c-MPL –/– neonates exhibited reduced glycoprotein IIb/IIIa (GPIIb/IIIa) activation in response to thrombin compared with age-matched WT platelets. Taken together, our findings indicate that c-MPL deficiency is associated with abnormal maturation of neonatal MKs and developmental stage-specific defects in platelet function.
Ostberg, C.O.; Pavlov, S.D.; Hauser, L.
We investigated the evolutionary relationships among five sympatric morphs of Dolly Varden Salvelinus malma (white, Schmidti, longhead, river, and dwarf) inhabiting landlocked Kronotsky Lake on the Kamchatka Peninsula, Russia, and an anadromous population below the barrier waterfall on the outflowing Kronotsky River. Morphological analyses indicated phenotypic differentiation corresponding to preferred habitat, the longhead (a limnetic piscivorous morph) having a fusiform body, long jaw, and short fins and the Schmidti (a benthic morph) having a robust body, small jaw, and long fins. Analysis of molecular variance among the Kronotsky Lake morphs indicated that contemporary gene flow is restricted both among morphs within locations and among locations within morphs. Gene flow from Kronotsky Lake into the anadromous population also appears to be restricted. Our findings indicate that there are two divergent evolutionary lineages, one consisting of the white, Schmidti, river, and dwarf morphs and the other of the longhead morph and the anadromous population, which suggests that Kronotsky Lake was subject to separate waves of immigration. The Kronotsky Lake Dolly Varden morphs may represent an example of ecological speciation in progress, and we present a working hypothesis for the diversification of morphs within Kronotsky Lake.
Full Text Available In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing.In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.
Robert L. Chevalier
Full Text Available Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as “maladaptive.” In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or from evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ∼40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons, evolutionary selection for APOL1 mutations (which provide resistance to trypanosome infection, a tradeoff, and modern life experience (Western diet mismatch leading to diabetes and hypertension. Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout the life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo, developmental programming, and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.
Warburton, P.E.; Gosden, J.; Lawson, D. [Western General Hospital, Edinburgh (United Kingdom)] [and others
Alpha satellite DNA is a tandemly repeated DNA family found at the centromeres of all primate chromosomes examined. The fundamental repeat units of alpha satellite DNA are diverged 169- to 172-bp monomers, often found to be organized in chromosome-specific higher-order repeat units. The chromosomes of human (Homo sapiens (HSA)), chimpanzee (Pan troglodytes (PTR) and Pan paniscus), and gorilla (Gorilla gorilla) share a remarkable similarity and synteny. It is of interest to ask if alpha satellite arrays at centromeres of homologous chromosomes between these species are closely related (evolving in an orthologous manner) or if the evolutionary processes that homogenize and spread these arrays within and between chromosomes result in nonorthologous evolution of arrays. By using PCR primers specific for human chromosome 17-specific alpha satellite DNA, we have amplified, cloned, and characterized a chromosome-specific subset from the PTR chimpanzee genome. Hybridization both on Southern blots and in situ as well as sequence analysis show that this subset is most closely related, as expected, to sequences on HSA 17. However, in situ hybridization reveals that this subset is not found on the homologous chromosome in chimpanzee (PTR 19), but instead on PTR 12, which is homologous to HSA 2p. 40 refs., 3 figs.
Maggie CY Lau
Full Text Available Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1 screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S and N; (2 to characterize the biodiversity represented by the common functional genes; (3 to investigate the subsurface biogeography as revealed by this subset of genes; and (4 to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAP reductase, NifH, NifD, NifK, NifE and NifN genes. Although these 8 common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with either geographical, environmental or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.
Henrique L Lenzi
Full Text Available Schistosomes, ancestors and recent species, have pervaded many hosts and several phylogenetic levels of immunity, causing an evolutionary pressure to eosinophil lineage expression and response. Schistosoma mansoni adult worms have capitalized on the apparent adversity of living within the mesenteric veins, using the dispersion of eggs and antigens to other tissues besides intestines to set a systemic activation of several haematopoietic lineages, specially eosinophils and monocytes/macrophages. This activation occurs in bone marrow, spleen, liver, lymph nodes, omental and mesenteric milky spots (activation of the old or primordial and recent or new lymphomyeloid tissue, increasing and making easy the migration of eosinophils, monocytes and other cells to the intestinal periovular granulomas. The exudative perigranulomatous stage of the periovular reaction, which present hystolitic characteristics, is then exploited by the parasites, to release the eggs into the intestinal lumen. The authors hypothesize here that eosinophils, which have a long phylogenic story, could participate in the parasite - host co-evolution, specially with S. mansoni, operating together with monocytes/ macrophages, upon parasite transmission.
An Evolutionary Perspective of the Relationship Between Corporate Strategy and Performance, Through the Use of Artificial Neural Networks and Genetic AlgorithmsHttp://Dx.Doi.Org/10.5585/Riae.V9i3.1689
Alexandre Teixeira Dias
Full Text Available This study aims to contribute to the understanding of the relationship between Corporate Strategy and Performance, from the perspective of the Evolutionary Theory. As methods of data processing, obtained in secondary databases, we used artificial neural networks and genetic algorithms. The results of processing neural networks and genetic algorithms demonstrate the importance of corporate strategies in determining performance. The evolutionary perspective emphasizes the importance of investing in operations as a factor influencing the adequacy of the organization, in order to achieve an improved performance, in addition to establishing relationships with other organizations, through members of the board.
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. PMID:26478766
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......Demography is the quantitative study of population processes, while evolution is a population process that influences all aspects of biological organisms, including their demography. Demographic traits common to all human populations are the products of biological evolution or the interaction...
Full Text Available Abstract Background Fluorescent proteins are powerful molecular biology tools that have been used to study the subcellular dynamics of proteins within live cells for well over a decade. Two fluorescent proteins commonly used to enable dual protein labelling are GFP (green and mCherry (red. Sporulation in the Gram positive bacterium Bacillus subtilis has been studied for many years as a paradigm for understanding the molecular basis for differential gene expression. As sporulation initiates, cells undergo an asymmetric division leading to differential gene expression in the small prespore and large mother cell compartments. Use of two fluorescent protein reporters permits time resolved examination of differential gene expression either in the same compartments or between compartments. Due to the spectral properties of GFP and mCherry, they are considered an ideal combination for co-localisation and co-expression experiments. They can also be used in combination with fluorescent DNA stains such as DAPI to correlate protein localisation patterns with the developmental stage of sporulation which can be linked to well characterised changes in DNA staining patterns. Findings While observing the recruitment of the transcription machinery into the forespore of sporulating Bacillus subtilis, we noticed the occurrence of stage-specific fluorescence intensity differences between GFP and mCherry. During vegetative growth and the initial stages of sporulation, fluorescence from both GFP and mCherry fusions behaved similarly. During stage II-III of sporulation we found that mCherry fluorescence was considerably diminished, whilst GFP signals remained clearly visible. This fluorescence pattern reversed during the final stage of sporulation with strong mCherry and low GFP fluorescence. These trends were observed in reciprocal tagging experiments indicating a direct effect of sporulation on fluorescent protein fluorophores. Conclusions Great care should be taken
/frequency of independent forearm/hand muscles, and particularly the independent extensors, is likely to be a major factor in sesamoid reversion in hominoids. The argument is based on the link between the metatarsal break induced by the digitigrade locomotion observed in quadrupedal mammals and tetrapods and the amount of extra-extension of the metacarpo-phalangeal joints conferred by the individualization of some forearm extensors. The same rationale yielded similar conclusions when applied to both the hand and foot. The manipulative function of the hand and the plantigrade locomotion of the foot required such extra-extension in specific digits and consequently, a higher frequency of digital sesamoids was associated with these two different functions. The new evolutionary analysis suggests evolutionary pathways for both, the sesamoids of the hands and feet, and speculates that muscle individualization would have induced a very slow re-acquisition of digital sesamoids when compared to their rapid decline after brachiation. It is the first hypothesis offering a plausible explication on the recent evolution of digital sesamoids; specifically, the progression of sesamoid frequency in African apes and its resurgence, prevalence and distribution in humans. Anat Rec, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Horowitz, Brent B; Ospina-Giraldo, Manuel D
Phytophthora sojae is an oomycete pathogen that causes the disease known as root and stem rot in soybean plants, frequently leading to massive economic damage. Additionally, P. sojae is increasingly being utilized as a model for phytopathogenic oomycete research. Despite the economic and scientific importance of P. sojae, the mechanism by which it penetrates the host roots is not yet fully understood. It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall. Pectin methylesterases have been suggested to be important for Phytophthora pathogenicity, but no data exist on their role in the P. sojae infection process. We have scanned the newly revised version of the annotated P. sojae genome for the presence of putative pectin methylesterases genes and conducted a sequence analysis of all gene models found. We also searched for potential regulatory motifs in the promoter region of the proposed P. sojae models, and investigated the gene expression levels throughout the early course of infection on soybean plants. We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism. Phylogenetic analyses confirmed the evolutionary relatedness of the pectin methylesterase-coding genes within and across Phytophthora spp. In addition, the gene duplication events that led to the emergence of this gene family appear to have occurred prior to many speciation events in the genus Phytophthora. Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time. Our study provides evidence that pectin methylesterases may be important for the early action of the P. sojae infection process.
Brent B Horowitz
Full Text Available Phytophthora sojae is an oomycete pathogen that causes the disease known as root and stem rot in soybean plants, frequently leading to massive economic damage. Additionally, P. sojae is increasingly being utilized as a model for phytopathogenic oomycete research. Despite the economic and scientific importance of P. sojae, the mechanism by which it penetrates the host roots is not yet fully understood. It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall. Pectin methylesterases have been suggested to be important for Phytophthora pathogenicity, but no data exist on their role in the P. sojae infection process. We have scanned the newly revised version of the annotated P. sojae genome for the presence of putative pectin methylesterases genes and conducted a sequence analysis of all gene models found. We also searched for potential regulatory motifs in the promoter region of the proposed P. sojae models, and investigated the gene expression levels throughout the early course of infection on soybean plants. We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism. Phylogenetic analyses confirmed the evolutionary relatedness of the pectin methylesterase-coding genes within and across Phytophthora spp. In addition, the gene duplication events that led to the emergence of this gene family appear to have occurred prior to many speciation events in the genus Phytophthora. Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time. Our study provides evidence that pectin methylesterases may be important for the early action of the P. sojae infection process.
Nash, Ulrik William
, 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...... 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......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...
Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.
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.
Van den Eynde, H.; De Baere, R.; Shah, H. N.; Gharbia, S. E.; Fox, G. E.; Michalik, J.; Van de Peer, Y.; De Wachter, R.
The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.
Brunnhuber, Stefan; Michalsen, Andreas
The text outlines the relation between psychosomatic medicine as an established medical discipline and the emerging concept of mind-body medicine from a historical, clinical and epistemological perspective. Limitations and contributions of both disciplines are discussed and the opportunities within the concept of Integrative Medicine are outlined. Whereas psychosomatic medicine is perceived as a form of transformation through a primarily verbal discoursive relationship, mind-body medicine claims healing through increased traditional techniques of the relaxation response, increased awareness, mindfulness, increasing des-identification and health-promoting lifestyle modification. It becomes clear that mind-body medicine seems to be epistemologically the broader theoretical framework, whereas in a clinical context the combination of both disciplines appears to be complementary and synergistic. The connection between psychosomatic medicine and mind-body medicine can make an important and exemplary contribution to the concept of Integrative Medicine. Copyright © 2012 S. Karger AG, Basel.
In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various investigators to ...
Full Text Available In a previous study we described the prevalence and distribution in Thailand of the retroposon p- SINE1-r2, in the intron 10 of the waxy gene in cultivated and wild rice with the AA genome. In this study, additional varieties of rice were collected and sequencing was used to further characterize p-SINE1-r2. It was found that the length of the p-SINE1-r2 nucleotide sequences was about 125 bp, flanked by identical direct repeats of a 14 bp sequence. These sequences were compared and found to be similar to the sequences of p- SINE1-r2 found in Nipponbare, a rice strain discussed in a separate study. However, when compared the 48 DNA sequences identified in this study, much dissimilarity was found within the nucleotide sequences of p- SINE1-r2, in the form of base substitution mutations. Phylogenetic relationships inferred from the nucleotide sequences of these elements in cultivated rice (O. sativa and wild rice (O. nivara. It was found that rice accessions collected from the same geographical distribution have been placed in the same clade. The phylogenetic tree supports the origin and distribution of these rice strains.
Bevans, Carville G; Krettler, Christoph; Reinhart, Christoph; Watzka, Matthias; Oldenburg, Johannes
In humans and other vertebrate animals, vitamin K 2,3-epoxide reductase (VKOR) family enzymes are the gatekeepers between nutritionally acquired K vitamins and the vitamin K cycle responsible for posttranslational modifications that confer biological activity upon vitamin K-dependent proteins with crucial roles in hemostasis, bone development and homeostasis, hormonal carbohydrate regulation and fertility. We report a phylogenetic analysis of the VKOR family that identifies five major clades. Combined phylogenetic and site-specific conservation analyses point to clade-specific similarities and differences in structure and function. We discovered a single-site determinant uniquely identifying VKOR homologs belonging to human pathogenic, obligate intracellular prokaryotes and protists. Building on previous work by Sevier et al. (Protein Science 14:1630), we analyzed structural data from both VKOR and prokaryotic disulfide bond formation protein B (DsbB) families and hypothesize an ancient evolutionary relationship between the two families where one family arose from the other through a gene duplication/deletion event. This has resulted in circular permutation of primary sequence threading through the four-helical bundle protein folds of both families. This is the first report of circular permutation relating distant a-helical membrane protein sequences and folds. In conclusion, we suggest a chronology for the evolution of the five extant VKOR clades.
Dumack, Kenneth; Mylnikov, Alexander P; Bonkowski, Michael
The genus Kraken represents a distinct lineage of filose amoebae within the Cercozoa. Currently a single species, Kraken carinae, has been described. SSU rDNA phylogeny showed an affiliation to the Cercomonadida, branching with weak support at its base, close to Paracercomonas, Metabolomonas, and Brevimastigomonas. Light microscopical analyses showed several unique features of the genus Kraken, but ultrastructure data were lacking. In this study, K. carinae has been studied by electron microscopy, these data conjoined with a two-gene phylogeny were used to give more insight into the evolutionary relationship of the genus Kraken within Cercozoa. The data confirmed the absence of flagella, but also showed novel characteristics, such as the presence of extrusomes, osmiophilic bodies, and mitochondria with flat cristae. Surprising was the presence of single-tier scales which are carried by cell outgrowths, much of what is expected of the last common ancestor of the class Imbricatea. The phylogenetic analyses however confirmed previous results, indicating Kraken as a sister group to Paracercomonas in Sarcomonadea with an increased but still low support of 0.98 PP/63 BP. Based on the unique features of Kraken we establish the Krakenidae fam. nov. that we, due to contradictory results in morphology and phylogeny, assign incertae sedis, Monadofilosa. Copyright © 2017 Elsevier GmbH. All rights reserved.
Full Text Available Abstract Background Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS markers for the rice (Oryza sativa L. genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences. Results We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS. Primers were designed for 17,966 (92% GNMS repeats, including 4,288 (94% hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3% followed by markers in the promoter region (53.3% and least in the CDS (26.6%. The robust polymerase chain reaction (PCR amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya compared to short
Fürstenberg, Dr Kai
Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.
Lippke, Sonia; Plotnikoff, Ronald C
Two different theories of health behaviour have been chosen with the aim of theory integration: a continuous theory (protection motivation theory, PMT) and a stage model (transtheoretical model, TTM). This is the first study to test whether the stages of the TTM moderate the interrelation of PMT-variables and the mediation of motivation, as well as PMT-variables' interactions in predicting stage transitions. Hypotheses were tested regarding (1) mean patterns, stage pair-comparisons and nonlinear trends using ANOVAs; (2) prediction-patterns for the different stage groups employing multi-group structural equation modelling (MSEM) and nested model analyses; and (3) stage transitions using binary logistic regression analyses. Adults (N=1,602) were assessed over a 6 month period on their physical activity stages, PMT-variables and subsequent behaviour. (1) Particular mean differences and nonlinear trends in all test variables were found. (2) The PMT adequately fitted the five stage groups. The MSEM revealed that covariances within threat appraisal and coping appraisal were invariant and all other constrains were stage-specific, i.e. stage was a moderator. Except for self-efficacy, motivation fully mediated the relationship between the social-cognitive variables and behaviour. (3) Predicting stage transitions with the PMT-variables underscored the importance of self-efficacy. Only when threat appraisal and coping appraisal were high, stage movement was more likely in the preparation stage. Results emphasize stage-specific differences of the PMT mechanisms, and hence, support the stage construct. The findings may guide further theory building and research integrating different theoretical approaches.
Douglas H Kerlin
Full Text Available The emergence of highly chloroquine (CQ resistant P. vivax in Southeast Asia has created an urgent need for an improved understanding of the mechanisms of drug resistance in these parasites, the development of robust tools for defining the spread of resistance, and the discovery of new antimalarial agents. The ex vivo Schizont Maturation Test (SMT, originally developed for the study of P. falciparum, has been modified for P. vivax. We retrospectively analysed the results from 760 parasite isolates assessed by the modified SMT to investigate the relationship between parasite growth dynamics and parasite susceptibility to antimalarial drugs. Previous observations of the stage-specific activity of CQ against P. vivax were confirmed, and shown to have profound consequences for interpretation of the assay. Using a nonlinear model we show increased duration of the assay and a higher proportion of ring stages in the initial blood sample were associated with decreased effective concentration (EC(50 values of CQ, and identify a threshold where these associations no longer hold. Thus, starting composition of parasites in the SMT and duration of the assay can have a profound effect on the calculated EC(50 for CQ. Our findings indicate that EC(50 values from assays with a duration less than 34 hours do not truly reflect the sensitivity of the parasite to CQ, nor an assay where the proportion of ring stage parasites at the start of the assay does not exceed 66%. Application of this threshold modelling approach suggests that similar issues may occur for susceptibility testing of amodiaquine and mefloquine. The statistical methodology which has been developed also provides a novel means of detecting stage-specific drug activity for new antimalarials.
Fuchs, Sebastian; Herzog, Dominik; Sumara, Grzegorz
-renewal and proliferation of later stage, but not early migratory NCSCs. This stage-specific requirement for small Rho GTPases is due to changes in NCSCs that, during development, acquire responsiveness to mitogenic EGF acting upstream of both Cdc42 and Rac1. Thus, our data reveal distinct mechanisms for growth control......The neural crest (NC) generates a variety of neural and non-neural tissues during vertebrate development. Both migratory NC cells and their target structures contain cells with stem cell features. Here we show that these populations of neural crest-derived stem cells (NCSCs) are differentially...
Kotini, Andriana G; Chang, Chan-Jung; Chow, Arthur; Yuan, Han; Ho, Tzu-Chieh; Wang, Tiansu; Vora, Shailee; Solovyov, Alexander; Husser, Chrystel; Olszewska, Malgorzata; Teruya-Feldstein, Julie; Perumal, Deepak; Klimek, Virginia M; Spyridonidis, Alexandros; Rampal, Raajit K; Silverman, Lewis; Reddy, E Premkumar; Papaemmanuil, Elli; Parekh, Samir; Greenbaum, Benjamin D; Leslie, Christina S; Kharas, Michael G; Papapetrou, Eirini P
Myeloid malignancy is increasingly viewed as a disease spectrum, comprising hematopoietic disorders that extend across a phenotypic continuum ranging from clonal hematopoiesis to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). In this study, we derived a collection of induced pluripotent stem cell (iPSC) lines capturing a range of disease stages encompassing preleukemia, low-risk MDS, high-risk MDS, and secondary AML. Upon their differentiation, we found hematopoietic phenotypes of graded severity and/or stage specificity that together delineate a phenotypic roadmap of disease progression culminating in serially transplantable leukemia. We also show that disease stage transitions, both reversal and progression, can be modeled in this system using genetic correction or introduction of mutations via CRISPR/Cas9 and that this iPSC-based approach can be used to uncover disease-stage-specific responses to drugs. Our study therefore provides insight into the cellular events demarcating the initiation and progression of myeloid transformation and a new platform for testing genetic and pharmacological interventions. Copyright © 2017 Elsevier Inc. All rights reserved.
Nascarella, Marc A.; Stoffolano, John G.; Stanek, Edward J.; Kostecki, Paul T.; Calabrese, Edward J
This is the first report of a heavy metal displaying a hormetic-like biphasic response for early developmental success, while at the same time displaying stage-specific toxicity at a later developmental stage. - Hormesis is an adaptive response, commonly characterized by a biphasic dose-response that can be either directly induced, or the result of compensatory biological processes following an initial disruption in homeostasis [Calabrese and Baldwin, Hum. Exp. Toxicol., 21 (2002), 91]. Low and environmentally relevant levels of dietary cadmium significantly enhanced the pupation rate of blowfly larvae, while higher doses inhibited pupation success. However, dietary cadmium at all exposure levels adversely affected the emergence of the adult fly from the pupal case. Such findings represent the first report of a heavy metal displaying a hormetic-like biphasic response for pupation success, while at the same time displaying stage-specific toxicity at a later developmental period. These conclusions are based on substantial experimentation of over 1750 blowflies, in seven replicate experiments, involving 10 concentrations per experiment. These findings indicate the need to assess the impact of environmental stressors over a broad range of potential exposures as well as throughout the entire life cycle.
Nascarella, Marc A.; Stoffolano, John G.; Stanek, Edward J.; Kostecki, Paul T.; Calabrese, Edward J.
This is the first report of a heavy metal displaying a hormetic-like biphasic response for early developmental success, while at the same time displaying stage-specific toxicity at a later developmental stage. - Hormesis is an adaptive response, commonly characterized by a biphasic dose-response that can be either directly induced, or the result of compensatory biological processes following an initial disruption in homeostasis [Calabrese and Baldwin, Hum. Exp. Toxicol., 21 (2002), 91]. Low and environmentally relevant levels of dietary cadmium significantly enhanced the pupation rate of blowfly larvae, while higher doses inhibited pupation success. However, dietary cadmium at all exposure levels adversely affected the emergence of the adult fly from the pupal case. Such findings represent the first report of a heavy metal displaying a hormetic-like biphasic response for pupation success, while at the same time displaying stage-specific toxicity at a later developmental period. These conclusions are based on substantial experimentation of over 1750 blowflies, in seven replicate experiments, involving 10 concentrations per experiment. These findings indicate the need to assess the impact of environmental stressors over a broad range of potential exposures as well as throughout the entire life cycle
Background During the last part of the 1990s the chance of surviving breast cancer increased. Changes in survival functions reflect a mixture of effects. Both, the introduction of adjuvant treatments and early screening with mammography played a role in the decline in mortality. Evaluating the contribution of these interventions using mathematical models requires survival functions before and after their introduction. Furthermore, required survival functions may be different by age groups and are related to disease stage at diagnosis. Sometimes detailed information is not available, as was the case for the region of Catalonia (Spain). Then one may derive the functions using information from other geographical areas. This work presents the methodology used to estimate age- and stage-specific Catalan breast cancer survival functions from scarce Catalan survival data by adapting the age- and stage-specific US functions. Methods Cubic splines were used to smooth data and obtain continuous hazard rate functions. After, we fitted a Poisson model to derive hazard ratios. The model included time as a covariate. Then the hazard ratios were applied to US survival functions detailed by age and stage to obtain Catalan estimations. Results We started estimating the hazard ratios for Catalonia versus the USA before and after the introduction of screening. The hazard ratios were then multiplied by the age- and stage-specific breast cancer hazard rates from the USA to obtain the Catalan hazard rates. We also compared breast cancer survival in Catalonia and the USA in two time periods, before cancer control interventions (USA 1975–79, Catalonia 1980–89) and after (USA and Catalonia 1990–2001). Survival in Catalonia in the 1980–89 period was worse than in the USA during 1975–79, but the differences disappeared in 1990–2001. Conclusion Our results suggest that access to better treatments and quality of care contributed to large improvements in survival in Catalonia. On
Vadodaria, Krishna C; Brakebusch, Cord; Suter, Ueli
The molecular mechanisms underlying the generation, maturation, and integration of new granule cells generated throughout life in the mammalian hippocampus remain poorly understood. Small Rho GTPases, such as Cdc42 and Rac1, have been implicated previously in neural stem/progenitor cell (NSPC......) proliferation and neuronal maturation during embryonic development. Here we used conditional genetic deletion and virus-based loss-of-function approaches to identify temporally distinct functions for Cdc42 and Rac1 in adult hippocampal neurogenesis. We found that Cdc42 is involved in mouse NSPC proliferation......, initial dendritic development, and dendritic spine maturation. In contrast, Rac1 is dispensable for early steps of neuronal development but is important for late steps of dendritic growth and spine maturation. These results establish cell-autonomous and stage-specific functions for the small Rho GTPases...
Homma-Takeda, S.; Nishimura, Y.; Watanabe, Y.; Imaseki, H.; Yukawa, M.
Stage-specific and age-dependent profiles of zinc, copper, manganese, and selenium in testis were examined in Wistar rats by both inductively coupled argon plasma-mass spectrometry (ICP-MS) with a microdissection technique and in situ elemental imaging of micro-PIXE analysis. The young adult animals (10 weeks old) contained higher levels of zinc and manganese in the seminiferous tubules at stages VII-VIII than stages XI through VI and IX-X and the levels were higher than those of the immature and old animals. Copper and selenium levels at stages VII-VIII of the young adult animals were also higher than those of the immature and old animals. In stages VII and VIII, zinc was higher in the central area of the seminiferous epithelium, where spermatozoa were localized, demonstrating a cell-specific property. (author)
Fang, Xin; Reifman, Jaques; Wallqvist, Anders
The human malaria parasite Plasmodium falciparum goes through a complex life cycle, including a roughly 48-hour-long intraerythrocytic developmental cycle (IDC) in human red blood cells. A better understanding of the metabolic processes required during the asexual blood-stage reproduction will enhance our basic knowledge of P. falciparum and help identify critical metabolic reactions and pathways associated with blood-stage malaria. We developed a metabolic network model that mechanistically links time-dependent gene expression, metabolism, and stage-specific growth, allowing us to predict the metabolic fluxes, the biomass production rates, and the timing of production of the different biomass components during the IDC. We predicted time- and stage-specific production of precursors and macromolecules for P. falciparum (strain HB3), allowing us to link specific metabolites to specific physiological functions. For example, we hypothesized that coenzyme A might be involved in late-IDC DNA replication and cell division. Moreover, the predicted ATP metabolism indicated that energy was mainly produced from glycolysis and utilized for non-metabolic processes. Finally, we used the model to classify the entire tricarboxylic acid cycle into segments, each with a distinct function, such as superoxide detoxification, glutamate/glutamine processing, and metabolism of fumarate as a byproduct of purine biosynthesis. By capturing the normal metabolic and growth progression in P. falciparum during the IDC, our model provides a starting point for further elucidation of strain-specific metabolic activity, host-parasite interactions, stress-induced metabolic responses, and metabolic responses to antimalarial drugs and drug candidates.
Li, Jun; Siegel, David A; King, Jessica B
Current literature shows different findings on the contemporary trends of distant-stage prostate cancer incidence, in part, due to low study population coverage and wide age groupings. This study aimed to examine the stage-specific incidence rates and trends of prostate cancer by age (5-year grouping), race, and ethnicity using nationwide cancer registry data. Data on prostate cancer cases came from the 2004-2014 United States Cancer Statistics data set. We calculated stage-specific incidence and 95% confidence intervals by age (5-year age grouping), race, and ethnicity. To measure the changes in rates over time, we calculated annual percentage change (APC). We identified 2,137,054 incident prostate cancers diagnosed during 2004-2014, with an age-adjusted incidence rate of 453.8 per 100,000. Distant-stage prostate cancer incidence significantly decreased during 2004-2010 (APC = -1.2) and increased during 2010-2014 (APC = 3.3). Significant increases in distant prostate cancer incidence also occurred in men aged older than or equal to 50 years except men aged 65-74 and older than or equal to 85 years, in men with white race (APC = 3.9), and non-Hispanic ethnicity (APC = 3.5). Using data representing over 99% of U.S. population, we found that incidence rates of distant-stage prostate cancer significantly increased during 2010-2014 among men in certain ages, in white, and with non-Hispanic ethnicity. Published by Elsevier Inc.
Li, Yang; Wang, Guanghui; Xu, Jin-Rong; Jiang, Cong
The hemibiotrophic pathogen Magnaporthe oryzae causes one of the most destructive diseases in cultivated rice. Complex infection-related morphogenesis and production of various effectors are known to be important for successful colonization and disease development. In this study, we characterized the activation of the MoGTI1 transcription factor and its role in infection-related morphogenesis and effector gene expression. The Mogti1 mutant was nonpathogenic, although it was normal in appressorium formation and turgor generation. Close examination showed that Mogti1 was defective in penetration and growth of normal invasive hyphae. Deletion of MoGTI1 affected the expression of the majority of effector genes. The expression of MoGti1 appeared to be controlled by the Mps1 but not Pmk1 mitogen-activated protein kinase (MAPK), and the mps1 and Mogti1 mutants had similar phenotypes in plant infection and cell wall integrity defects. However, lack of MAPK phosphorylation sites and dispensability of the putative MAPK docking site suggested that MoGti1 is not a direct target of Mps1. Site-specific mutagenesis analyses showed that the putative protein kinase A phosphorylation site was not essential for localization of MoGti1 to the nucleus but important for its normal function. Although the cyclin-dependent kinase (CDK) phosphorylation site of MoGti1 is dispensable during vegetative growth and appressorium formation, the S77A mutation affected penetration and invasive growth. Localization of MoGti1(S77A)-green fluorescent protein to the nucleus in late stages of appressorium formation and during invasive growth was not observed, suggesting a stage-specific CDK phosphorylation of MoGti1. Overall, our data indicate that Mps1 may indirectly regulate the expression of MoGti1 in maintaining cell wall integrity, conidiation, and plant infection. MoGti1 is likely a stage-specific target of CDK and plays a crucial role in effector gene expression and morphogenesis related to the
Karlestrand, Sølvi Dørum
Women who use hormonal contraceptives have been shown to report more intense affective responses to partner infidelity than women with a natural cycle. Also, previous research suggests that female jealousy is sensitive to hormonal changes when naturally cycling, with a peak around ovulation, while women using hormonal contraceptives are less sensitive. This research is aimed at exploring women`s perception of couple conflicts in line with predictions derived from evolutionary theory. A fa...
Chaitanya, Bharatula Sri Krishna; Kumar, Sumit; Kaki, Shiva Shanker; Balakrishna, Marrapu; Karuna, Mallampalli Sri Lakshmi; Prasad, Rachapudi Badari Narayana; Sastry, Pidaparty Seshadri; Reddy, Attipalli Ramachandra
The present study describes the changes in lipid profile as well as fatty acid fluxes during seed development in Jatropha curcas L. Endosperm from 34, 37, and 40 days after anthesis (DAA), incubated with [(14)C]acetate, showed significant synthesis of phosphatidylcholine (PC) at seed maturation. The fatty acid methyl ester profile showed PC from 34 DAA was rich in palmitic acid (16:0), whereas PC from 37 and 40 DAA was rich in oleic acid (18:1n-9). Molecular species analysis of diacylglycerol (DAG) indicated DAG (16:0/18:2n-6) was in abundance at 34 DAA, whereas DAG (18:1n-9/18:2n-6) was significantly high at 40 DAA. Triacylglycerol (TAG) analysis revealed TAG (16:0/18:2n-6/16:0) was abundant at 34 DAA, whereas TAG (18:1n-9/18:2n-6/18:1n-9) formed the majority at 40 DAA. Expression of two types of diacylglycerol acyltransferases varied with seed maturation. These data demonstrate stage-specific distinct pools of PC and DAG synthesis during storage TAG accumulation in Jatropha seed.
Srivastava, Anubhav; Philip, Nisha; Hughes, Katie R; Georgiou, Konstantina; MacRae, James I; Barrett, Michael P; Creek, Darren J; McConville, Malcolm J; Waters, Andrew P
Malaria parasites (Plasmodium spp.) encounter markedly different (nutritional) environments during their complex life cycles in the mosquito and human hosts. Adaptation to these different host niches is associated with a dramatic rewiring of metabolism, from a highly glycolytic metabolism in the asexual blood stages to increased dependence on tricarboxylic acid (TCA) metabolism in mosquito stages. Here we have used stable isotope labelling, targeted metabolomics and reverse genetics to map stage-specific changes in Plasmodium berghei carbon metabolism and determine the functional significance of these changes on parasite survival in the blood and mosquito stages. We show that glutamine serves as the predominant input into TCA metabolism in both asexual and sexual blood stages and is important for complete male gametogenesis. Glutamine catabolism, as well as key reactions in intermediary metabolism and CoA synthesis are also essential for ookinete to oocyst transition in the mosquito. These data extend our knowledge of Plasmodium metabolism and point towards possible targets for transmission-blocking intervention strategies. Furthermore, they highlight significant metabolic differences between Plasmodium species which are not easily anticipated based on genomics or transcriptomics studies and underline the importance of integration of metabolomics data with other platforms in order to better inform drug discovery and design.
Wang, Yi-Wen; Yuan, Jin-Qiang; Gao, Xin; Yang, Xian-Yu
There are six micronuclear divisions during conjugation of Paramecium caudatum: three prezygotic and three postzygotic divisions. Four haploid nuclei are formed during the first two meiotic prezygotic divisions. Usually only one meiotic product is located in the paroral cone (PC) region at the completion of meiosis, which survives and divides mitotically to complete the third prezygotic division to yield a stationary and a migratory pronucleus. The remaining three located outside of the PC degenerate. The migratory pronuclei are then exchanged between two conjugants and fuse with the stationary pronuclei to form synkarya, which undergo three successive divisions (postzygotic divisions). However, little is known about the surviving mechanism of the PC nuclei. In the current study, stage-specific appearance of cytoplasmic microtubules (cMTs) was indicated during the third prezygotic division by immunofluorescence labeling with anti-alpha tubulin antibodies surrounding the surviving nuclei, including the PC nuclei and the two types of prospective pronuclei. This suggested that cMTs were involved in the formation of a physical barrier, whose function may relate to sequestering and protecting the surviving nuclei from the major cytoplasm, where degeneration of extra-meiotic products occurs, another important nuclear event during the third prezygotic division.
Alyaa M Abdel-Haleem
Full Text Available Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale metabolic models (GeMMs of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1, choline, and pantothenate (vitamin B5 metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.
Xie, Liang; Duncan, Michael B; Pahler, Jessica; Sugimoto, Hikaru; Martino, Margot; Lively, Julie; Mundel, Thomas; Soubasakos, Mary; Rubin, Kristofer; Takeda, Takaaki; Inoue, Masahiro; Lawler, Jack; Hynes, Richard O; Hanahan, Douglas; Kalluri, Raghu
Whereas the roles of proangiogenic factors in carcinogenesis are well established, those of endogenous angiogenesis inhibitors (EAIs) remain to be fully elaborated. We investigated the roles of three EAIs during de novo tumorigenesis to further test the angiogenic balance hypothesis, which suggests that blood vessel development in the tumor microenvironment can be governed by a net loss of negative regulators of angiogenesis in addition to the well-established principle of up-regulated angiogenesis inducers. In a mouse model of pancreatic neuroendocrine cancer, administration of endostatin, thrombospondin-1, and tumstatin peptides, as well as deletion of their genes, reveal neoplastic stage-specific effects on angiogenesis, tumor progression, and survival, correlating with endothelial expression of their receptors. Deletion of tumstatin and thrombospondin-1 in mice lacking the p53 tumor suppressor gene leads to increased incidence and reduced latency of angiogenic lymphomas associated with diminished overall survival. The results demonstrate that EAIs are part of a balance mechanism regulating tumor angiogenesis, serving as intrinsic microenvironmental barriers to tumorigenesis.
Full Text Available Malaria parasites (Plasmodium spp. encounter markedly different (nutritional environments during their complex life cycles in the mosquito and human hosts. Adaptation to these different host niches is associated with a dramatic rewiring of metabolism, from a highly glycolytic metabolism in the asexual blood stages to increased dependence on tricarboxylic acid (TCA metabolism in mosquito stages. Here we have used stable isotope labelling, targeted metabolomics and reverse genetics to map stage-specific changes in Plasmodium berghei carbon metabolism and determine the functional significance of these changes on parasite survival in the blood and mosquito stages. We show that glutamine serves as the predominant input into TCA metabolism in both asexual and sexual blood stages and is important for complete male gametogenesis. Glutamine catabolism, as well as key reactions in intermediary metabolism and CoA synthesis are also essential for ookinete to oocyst transition in the mosquito. These data extend our knowledge of Plasmodium metabolism and point towards possible targets for transmission-blocking intervention strategies. Furthermore, they highlight significant metabolic differences between Plasmodium species which are not easily anticipated based on genomics or transcriptomics studies and underline the importance of integration of metabolomics data with other platforms in order to better inform drug discovery and design.
Takahara, Hiroyuki; Dolf, Andreas; Endl, Elmar; O'Connell, Richard
Generation of stage-specific cDNA libraries is a powerful approach to identify pathogen genes that are differentially expressed during plant infection. Biotrophic pathogens develop specialized infection structures inside living plant cells, but sampling the transcriptome of these structures is problematic due to the low ratio of fungal to plant RNA, and the lack of efficient methods to isolate them from infected plants. Here we established a method, based on fluorescence-activated cell sorting (FACS), to purify the intracellular biotrophic hyphae of Colletotrichum higginsianum from homogenates of infected Arabidopsis leaves. Specific selection of viable hyphae using a fluorescent vital marker provided intact RNA for cDNA library construction. Pilot-scale sequencing showed that the library was enriched with plant-induced and pathogenicity-related fungal genes, including some encoding small, soluble secreted proteins that represent candidate fungal effectors. The high purity of the hyphae (94%) prevented contamination of the library by sequences derived from host cells or other fungal cell types. RT-PCR confirmed that genes identified in the FACS-purified hyphae were also expressed in planta. The method has wide applicability for isolating the infection structures of other plant pathogens, and will facilitate cell-specific transcriptome analysis via deep sequencing and microarray hybridization, as well as proteomic analyses.
Abdel-Haleem, Alyaa M.
Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale models (GEMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1), choline, and pantothenate (vitamin B5) metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.
Xie, Liang; Duncan, Michael B.; Pahler, Jessica; Sugimoto, Hikaru; Martino, Margot; Lively, Julie; Mundel, Thomas; Soubasakos, Mary; Rubin, Kristofer; Takeda, Takaaki; Inoue, Masahiro; Lawler, Jack; Hynes, Richard O.; Hanahan, Douglas; Kalluri, Raghu
Whereas the roles of proangiogenic factors in carcinogenesis are well established, those of endogenous angiogenesis inhibitors (EAIs) remain to be fully elaborated. We investigated the roles of three EAIs during de novo tumorigenesis to further test the angiogenic balance hypothesis, which suggests that blood vessel development in the tumor microenvironment can be governed by a net loss of negative regulators of angiogenesis in addition to the well-established principle of up-regulated angiogenesis inducers. In a mouse model of pancreatic neuroendocrine cancer, administration of endostatin, thrombospondin-1, and tumstatin peptides, as well as deletion of their genes, reveal neoplastic stage-specific effects on angiogenesis, tumor progression, and survival, correlating with endothelial expression of their receptors. Deletion of tumstatin and thrombospondin-1 in mice lacking the p53 tumor suppressor gene leads to increased incidence and reduced latency of angiogenic lymphomas associated with diminished overall survival. The results demonstrate that EAIs are part of a balance mechanism regulating tumor angiogenesis, serving as intrinsic microenvironmental barriers to tumorigenesis. PMID:21622854
Bennuru, Sasisekhar; Cotton, James A.; Ribeiro, Jose M. C.; Grote, Alexandra; Harsha, Bhavana; Holroyd, Nancy; Mhashilkar, Amruta; Molina, Douglas M.; Randall, Arlo Z.; Shandling, Adam D.; Unnasch, Thomas R.; Ghedin, Elodie; Berriman, Matthew
ABSTRACT Onchocerciasis (river blindness) is a neglected tropical disease that has been successfully targeted by mass drug treatment programs in the Americas and small parts of Africa. Achieving the long-term goal of elimination of onchocerciasis, however, requires additional tools, including drugs, vaccines, and biomarkers of infection. Here, we describe the transcriptome and proteome profiles of the major vector and the human host stages (L1, L2, L3, molting L3, L4, adult male, and adult female) of Onchocerca volvulus along with the proteome of each parasitic stage and of its Wolbachia endosymbiont (wOv). In so doing, we have identified stage-specific pathways important to the parasite’s adaptation to its human host during its early development. Further, we generated a protein array that, when screened with well-characterized human samples, identified novel diagnostic biomarkers of O. volvulus infection and new potential vaccine candidates. This immunomic approach not only demonstrates the power of this postgenomic discovery platform but also provides additional tools for onchocerciasis control programs. PMID:27881553
Catley, Kefyn M.; Novick, Laura R.; Shade, Courtney K.
The authors argue that some diagrams in biology textbooks and the popular press presented as depicting evolutionary relationships suggest an inappropriate (anagenic) conception of evolutionary history. The goal of this research was to provide baseline data that begin to document how college students conceptualize the evolutionary relationships…
Pilar T. V. Florentino
Full Text Available Trypanosoma cruzi is the etiologic agent of Chagas’ disease. It is known that amastigotes derived from trypomastigotes in the extracellular milieu are infective in vitro and in vivo. Extracellular amastigotes (EAs have a stage-specific surface antigen called Ssp-4, a GPI-anchored glycoprotein that is secreted by the parasites. By immunoprecipitation with the Ssp-4-specific monoclonal antibodies (mAb 2C2 and 1D9, we isolated the glycoprotein from EAs. By mass spectrometry, we identified the core protein of Ssp-4 and evaluated mRNA expression and the presence of Ssp-4 carbohydrate epitopes recognized by mAb1D9. We demonstrated that the carbohydrate epitope recognized by mAb1D9 could promote host cell invasion by EAs. Although infectious EAs express lower amounts of Ssp-4 compared with less-infectious EAs (at the mRNA and protein levels, it is the glycosylation of Ssp-4 (identified by mAb1D9 staining only in infectious strains and recognized by galectin-3 on host cells that is the determinant of EA invasion of host cells. Furthermore, Ssp-4 is secreted by EAs, either free or associated with parasite vesicles, and can participate in host-cell interactions. The results presented here describe the possible role of a carbohydrate moiety of T. cruzi surface glycoproteins in host cell invasion by EA forms, highlighting the potential of these moieties as therapeutic and vaccine targets for the treatment of Chagas’ disease.
Florentino, Pilar T. V.; Real, Fernando; Orikaza, Cristina M.; da Cunha, Julia P. C.; Vitorino, Francisca N. L.; Cordero, Esteban M.; Sobreira, Tiago J. P.; Mortara, Renato A.
Trypanosoma cruzi is the etiologic agent of Chagas’ disease. It is known that amastigotes derived from trypomastigotes in the extracellular milieu are infective in vitro and in vivo. Extracellular amastigotes (EAs) have a stage-specific surface antigen called Ssp-4, a GPI-anchored glycoprotein that is secreted by the parasites. By immunoprecipitation with the Ssp-4-specific monoclonal antibodies (mAb) 2C2 and 1D9, we isolated the glycoprotein from EAs. By mass spectrometry, we identified the core protein of Ssp-4 and evaluated mRNA expression and the presence of Ssp-4 carbohydrate epitopes recognized by mAb1D9. We demonstrated that the carbohydrate epitope recognized by mAb1D9 could promote host cell invasion by EAs. Although infectious EAs express lower amounts of Ssp-4 compared with less-infectious EAs (at the mRNA and protein levels), it is the glycosylation of Ssp-4 (identified by mAb1D9 staining only in infectious strains and recognized by galectin-3 on host cells) that is the determinant of EA invasion of host cells. Furthermore, Ssp-4 is secreted by EAs, either free or associated with parasite vesicles, and can participate in host-cell interactions. The results presented here describe the possible role of a carbohydrate moiety of T. cruzi surface glycoproteins in host cell invasion by EA forms, highlighting the potential of these moieties as therapeutic and vaccine targets for the treatment of Chagas’ disease. PMID:29692765
Full Text Available Despite the application of numerous supplements to improve in vitro culture (IVC conditions of mammalian cells, studies regarding the effect of fetal bovine serum (FBS on mammalian early embryogenesis, particularly in relation to redox homeostasis, are lacking. Herein, we demonstrated that early development of in vitro-produced (IVP porcine embryos highly depends on the combination of FBS supplementation timing and embryonic reactive oxygen species (ROS requirements. Interestingly, FBS significantly reduced intracellular ROS levels in parthenogenetically activated (PA embryos regardless of the developmental stage. However, the beneficial effect of FBS on early embryogenesis was found only during the late phase (IVC 4-6 days treatment group. In particular, developmental competence parameters, such as blastocyst formation rate, cellular survival, total cell number and trophectoderm proportion, were markedly increased by FBS supplementation during the late IVC phase. In addition, treatment with FBS elevated antioxidant transcript levels during the late IVC phase. In contrast, supplementation with FBS during the entire period (1-6 days or during the early IVC phase (1-2 days greatly impaired the developmental parameters. Consistent with the results from PA embryos, the developmental competence of in vitro fertilization (IVF or somatic cell nuclear transfer (SCNT embryos were markedly improved by treatment with FBS during the late IVC phase. Moreover, the embryonic stage-specific effects of FBS were reversed by the addition of an oxidant and were mimicked by treatment with an antioxidant. These findings may increase our understanding of redox-dependent early embryogenesis and contribute to the large-scale production of high-quality IVP embryos.
Endo, Satoshi; Iwamoto, Kuninori; Fukuda, Hiroo
Tissue-specific overexpression of useful genes, which we can design according to their cause-and-effect relationships, often gives valuable gain-of-function phenotypes. To develop genetic tools in woody biomass engineering, we produced a collection of Arabidopsis lines that possess chimeric genes of a promoter of an early xylem differentiation stage-specific gene, Arabidopsis Tracheary Element Differentiation-related 4 (AtTED4) and late xylem development-associated genes, many of which are uncharacterized. The AtTED4 promoter directed the expected expression of transgenes in developing vascular tissues from young to mature stage. Of T2 lines examined, 42%, 49% and 9% were judged as lines with the nonrepeat type insertion, the simple repeat type insertion and the other repeat type insertion of transgenes. In 174 T3 lines, overexpression lines were confirmed for 37 genes, whereas only cosuppression lines were produced for eight genes. The AtTED4 promoter activity was high enough to overexpress a wide range of genes over wild-type expression levels, even though the wild-type expression is much higher than AtTED4 expression for several genes. As a typical example, we investigated phenotypes of pAtTED4::At5g60490 plants, in which both overexpression and cosuppression lines were included. Overexpression but not cosuppression lines showed accelerated xylem development, suggesting the positive role of At5g60490 in xylem development. Taken together, this study provides valuable results about behaviours of various genes expressed under an early xylem-specific promoter and about usefulness of their lines as genetic tools in woody biomass engineering. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Full Text Available Abstract Background The pathogenic mold Aspergillus fumigatus is the most frequent infectious cause of death in severely immunocompromised individuals such as leukemia and bone marrow transplant patients. Germination of inhaled conidia (asexual spores in the host is critical for the initiation of infection, but little is known about the underlying mechanisms of this process. Results To gain insights into early germination events and facilitate the identification of potential stage-specific biomarkers and vaccine candidates, we have used quantitative shotgun proteomics to elucidate patterns of protein abundance changes during early fungal development. Four different stages were examined: dormant conidia, isotropically expanding conidia, hyphae in which germ tube emergence has just begun, and pre-septation hyphae. To enrich for glycan-linked cell wall proteins we used an alkaline cell extraction method. Shotgun proteomic resulted in the identification of 375 unique gene products with high confidence, with no evidence for enrichment of cell wall-immobilized and secreted proteins. The most interesting discovery was the identification of 52 proteins enriched in dormant conidia including 28 proteins that have never been detected in the A. fumigatus conidial proteome such as signaling protein Pil1, chaperones BipA and calnexin, and transcription factor HapB. Additionally we found many small, Aspergillus specific proteins of unknown function including 17 hypothetical proteins. Thus, the most abundant protein, Grg1 (AFUA_5G14210, was also one of the smallest proteins detected in this study (M.W. 7,367. Among previously characterized proteins were melanin pigment and pseurotin A biosynthesis enzymes, histones H3 and H4.1, and other proteins involved in conidiation and response to oxidative or hypoxic stress. In contrast, expanding conidia, hyphae with early germ tubes, and pre-septation hyphae samples were enriched for proteins responsible for
Joosten, Reinoud A.M.G.; Roorda, Berend
We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary
Gallot-Lavallée, Lucie; Blanc, Guillaume; Claverie, Jean-Michel
Chrysochromulina ericina virus CeV-01B (CeV) was isolated from Norwegian coastal waters in 1998. Its icosahedral particle is 160 nm in diameter and encloses a 474-kb double-stranded DNA (dsDNA) genome. This virus, although infecting a microalga (the haptophyceae Haptolina ericina , formerly Chrysochromulina ericina ), is phylogenetically related to members of the Mimiviridae family, initially established with the acanthamoeba-infecting mimivirus and megavirus as prototypes. This family was later split into two genera ( Mimivirus and Cafeteriavirus ) following the characterization of a virus infecting the heterotrophic stramenopile Cafeteria roenbergensis (CroV). CeV, as well as two of its close relatives, which infect the unicellular photosynthetic eukaryotes Phaeocystis globosa (Phaeocystis globosa virus [PgV]) and Aureococcus anophagefferens (Aureococcus anophagefferens virus [AaV]), are currently unclassified by the International Committee on Viral Taxonomy (ICTV). The detailed comparative analysis of the CeV genome presented here confirms the phylogenetic affinity of this emerging group of microalga-infecting viruses with the Mimiviridae but argues in favor of their classification inside a distinct clade within the family. Although CeV, PgV, and AaV share more common features among them than with the larger Mimiviridae , they also exhibit a large complement of unique genes, attesting to their complex evolutionary history. We identified several gene fusion events and cases of convergent evolution involving independent lateral gene acquisitions. Finally, CeV possesses an unusual number of inteins, some of which are closely related despite being inserted in nonhomologous genes. This appears to contradict the paradigm of allele-specific inteins and suggests that the Mimiviridae are especially efficient in spreading inteins while enlarging their repertoire of homing genes. IMPORTANCE Although it infects the microalga Chrysochromulina ericina , CeV is more closely
A multilocus approach to assessing co-evolutionary relationships between Steinernema spp. (Nematoda: Steinernematidae) and their bacterial symbionts Xenorhabdus spp. (gamma-Proteobacteria: Enterobacteriaceae).
Lee, Ming-Min; Stock, S Patricia
Nematodes of the genus Steinernema Travassos, 1927 (Nematoda: Steinernematidae) and their associated bacteria, Xenorhabdus spp. (gamma-Proteobacteria), are an emergent model of terrestrial animal-microbe symbiosis. Interest in this association initially arose out of their potential as biocontrol agents against insect pests, but, despite advances in their field application and the growing popularity of this model system, relatively little has been published to uncover the evolutionary facets of this beneficial partnership. This study adds to the body of knowledge regarding nematode-bacteria symbiosis by proposing a possible scenario for their historical association in the form of a cophylogenetic hypothesis. Topological and likelihood based testing methods were employed to reconstruct a history of association between 30 host-symbiont pairs and to gauge the level of similarity between their inferred phylogenetic patterns.
Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General Article Volume 21 Issue 9 September 2016 pp 803- ... Keywords. Evolutionary game theory, evolutionary stable state, conflict, cooperation, biological games.
ABBOTT, B. D., LEFFLER, K.E. AND BUCKALEW, A.R, Reproductive Toxicology Division, NHEERL, ORD, US EPA, Research Triangle Park, North Carolina. Retinoic acid induction of cleft palate (CP) in EGF and TGF knockout mice: Stage specific influences of growth factor expression.<...
Nakamura, Y.; de Paiva Alves, E.; Veenstra, G.J.C.; Hoppler, S.
Key signalling pathways, such as canonical Wnt/beta-catenin signalling, operate repeatedly to regulate tissue- and stage-specific transcriptional responses during development. Although recruitment of nuclear beta-catenin to target genomic loci serves as the hallmark of canonical Wnt signalling,
Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S
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.
Li, Wuzhao; Wang, Lei; Cai, Xingjuan
and affect each other in many ways. The relationships include competition, predation, parasitism, mutualism and pythogenesis. In this paper, we consider the five relationships between solutions to propose a co-evolutionary algorithm termed species co-evolutionary algorithm (SCEA). In SCEA, five operators...
An Armillaria survey in Mexico: A basis for determining evolutionary relationships, assessing potentially invasive pathogens, evaluating future impacts of climate change, and developing international collaborations in forest pathology
Phil Cannon; Ned B. Klopfenstein; Mee-Sook Kim; John W. Hanna; Dionicio Alvarado. Rosales
In September 2007, a collaborative effort was made to survey Armillaria species in three general areas of south-central Mexico. Collected Armillaria isolates will be subjected to DNA analyses to examine genetic relationships with other Armillaria species. These studies will provide baseline information for examining evolution of Armillaria...
Full Text Available BACKGROUND: Cyclosporin A (CsA has important anti-microbial activity against parasites of the genus Leishmania, suggesting CsA-binding cyclophilins (CyPs as potential drug targets. However, no information is available on the genetic diversity of this important protein family, and the mechanisms underlying the cytotoxic effects of CsA on intracellular amastigotes are only poorly understood. Here, we performed a first genome-wide analysis of Leishmania CyPs and investigated the effects of CsA on host-free L. donovani amastigotes in order to elucidate the relevance of these parasite proteins for drug development. METHODOLOGY/PRINCIPAL FINDINGS: Multiple sequence alignment and cluster analysis identified 17 Leishmania CyPs with significant sequence differences to human CyPs, but with highly conserved functional residues implicated in PPIase function and CsA binding. CsA treatment of promastigotes resulted in a dose-dependent inhibition of cell growth with an IC50 between 15 and 20 microM as demonstrated by proliferation assay and cell cycle analysis. Scanning electron microscopy revealed striking morphological changes in CsA treated promastigotes reminiscent to developing amastigotes, suggesting a role for parasite CyPs in Leishmania differentiation. In contrast to promastigotes, CsA was highly toxic to amastigotes with an IC50 between 5 and 10 microM, revealing for the first time a direct lethal effect of CsA on the pathogenic mammalian stage linked to parasite thermotolerance, independent from host CyPs. Structural modeling, enrichment of CsA-binding proteins from parasite extracts by FPLC, and PPIase activity assays revealed direct interaction of the inhibitor with LmaCyP40, a bifunctional cyclophilin with potential co-chaperone function. CONCLUSIONS/SIGNIFICANCE: The evolutionary expansion of the Leishmania CyP protein family and the toxicity of CsA on host-free amastigotes suggest important roles of PPIases in parasite biology and implicate
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.
Carmen E Contreras
Full Text Available The evaluation of new antimalarial agents using older methods of monitoring sensitivity to antimalarial drugs are laborious and poorly suited to discriminate stage-specific activity. We used flow cytometry to study the effect of established antimalarial compounds, cysteine protease inhibitors, and a quinolone against asexual stages of Plasmodium falciparum. Cultured P. falciparum parasites were treated for 48 h with different drug concentrations and the parasitemia was determined by flow cytometry methods after DNA staining with propidium iodide. P. falciparum erythrocytic life cycle stages were readily distinguished by flow cytometry. Activities of established and new antimalarial compounds measured by flow cytometry were equivalent to results obtained with microscopy and metabolite uptake assays. The antimalarial activity of all compounds was higher against P. falciparum trophozoite stages. Advantages of flow cytometry analysis over traditional assays included higher throughput for data collection, insight into the stage-specificity of antimalarial activity avoiding use of radioactive isotopes.
Medzihradszky, K F; Gibson, B W; Kaur, S; Yu, Z H; Medzihradszky, D; Burlingame, A L; Bass, N M
The primary structure of a fatty-acid-binding protein (FABP) isolated from the liver of the nurse shark (Ginglymostoma cirratum) was determined by high-performance tandem mass spectrometry (employing multichannel array detection) and Edman degradation. Shark liver FABP consists of 132 amino acids with an acetylated N-terminal valine. The chemical molecular mass of the intact protein determined by electrospray ionization mass spectrometry (Mr = 15124 +/- 2.5) was in good agreement with that calculated from the amino acid sequence (Mr = 15121.3). The amino acid sequence of shark liver FABP displays significantly greater similarity to the FABP expressed in mammalian heart, peripheral nerve myelin and adipose tissue (61-53% sequence similarity) than to the FABP expressed in mammalian liver (22% similarity). Phylogenetic trees derived from the comparison of the shark liver FABP amino acid sequence with the members of the mammalian fatty-acid/retinoid-binding protein gene family indicate the initial divergence of an ancestral gene into two major subfamilies: one comprising the genes for mammalian liver FABP and gastrotropin, the other comprising the genes for mammalian cellular retinol-binding proteins I and II, cellular retinoic-acid-binding protein myelin P2 protein, adipocyte FABP, heart FABP and shark liver FABP, the latter having diverged from the ancestral gene that ultimately gave rise to the present day mammalian heart-FABP, adipocyte FABP and myelin P2 protein sequences. The sequence for intestinal FABP from the rat could be assigned to either subfamily, depending on the approach used for phylogenetic tree construction, but clearly diverged at a relatively early evolutionary time point. Indeed, sequences proximately ancestral or closely related to mammalian intestinal FABP, liver FABP, gastrotropin and the retinoid-binding group of proteins appear to have arisen prior to the divergence of shark liver FABP and should therefore also be present in elasmobranchs
Kato, Mihoko; Sternberg, Paul W
Cell migration is a common event during organogenesis, yet little is known about how migration is temporally coordinated with organ development. We are investigating stage-specific programs of cell migration using the linker cell (LC), a migratory cell crucial for male gonadogenesis of C. elegans. During the L3 and L4 larval stages of wild-type males, the LC undergoes changes in its position along the migratory route, in transcriptional regulation of the unc-5 netrin receptor and zmp-1 zinc matrix metalloprotease, and in cell morphology. We have identified the tailless homolog nhr-67 as a cell-autonomous, stage-specific regulator of timing in LC migration programs. In nhr-67-deficient animals, each of the L3 and L4 stage changes is either severely delayed or never occurs, yet LC development before the early L3 stage or after the mid-L4 stage occurs with normal timing. We propose that there is a basal migration program utilized throughout LC migration that is modified by stage-specific regulators such as nhr-67.
Backer, L.C.; Sontag, M.R.; Allen, J.W.
Synaptonemal complexes (SCs) reveal mutagen-induced effects in germ cell meiotic chromosomes. The study was aimed at characterizing relationships between SC and metaphase I chromosome damage following radiation exposure at various stages of spermatogenesis. Male mice were irradiated with doses of 0, 2, or 4 Gy, and spermatocytes were harvested at times consistent with earlier exposures as spermatogonial stem cells, preleptotene cells (premeiotic DNA synthesis), or meiotic prophase cells. After stem-cell exposure, twice as many rearrangements were observed in SCs as in metaphase I chromosomes. Irradiation during premeiotic DNA synthesis resulted in dose-related increases in SC breakage and rearrangements (including novel forms) and in metaphase chromosomal aberrations. Following prophase exposure, various types and levels of SC and metaphase damage were observed. Irradiation of zygotene cells led to high frequencies of chromosome multivalents in metaphase I without a correspondingly high level of damage in preceding prophase SCs. Thus, irradiation of premeiotic and meiotic cells results in variable relationships between SC and metaphase chromosome damage
Roorda, Berend; Joosten, Reinoud
We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary dynamics. For instance, each attractive evolutionarily stable strategy is an attractive evolutionarily stable equilibrium for certain barycentric ray-projection dynamics, and vice versa.
Fishman, Michael A
In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. Copyright © 2016 Elsevier Ltd. All rights reserved.
Geoffroy's side-necked turtle [Phrynops geoffroanus (Schweigger, 1812), Testudines: Chelidae] as a model for evolutionary ecotoxicology: relationship between environmental contamination, conditions and genetic variability.
Venancio, L P R; Zuccari, D A P C; Bonini-Domingos, C R
The objective of this study was to evaluate the role of human activity factors, such as environmental contamination and habitat changes, as drivers for changing the physiological, biochemical, and genetic diversity of Geoffroy's side-necked turtle populations in one of the most impacted watersheds in southeastern Brazil. The impact of chemical and organic contamination was determined by ecotoxicological analyses to assess the action of some of the major components involved in protection against oxidative stress, phase I and II detoxification metabolism, and antioxidant capacity. The results indicated the influence of domestic and industrial effluents on detoxification metabolism and oxidative stress. However, in spite of increased activity and effect of EROD (CYP1A1) and glutathione S-transferase (GST) activity, GST average values in the urban area agreed with those expected for hypoxic conditions according to the literature. This observation suggests that increased GST in response to ROS production due to the presence of pollutants increases the antioxidant defense network, controlling the oxidative damage caused by hypoxia and reperfusion. To determine the conditions that are reflected in individual ability (fitness), we evaluated the mathematical relationship between weight and length, and found that changes in body shape and weight increase, allowing inferences about animal health and welfare. The data obtained indicate differences in conditions that are associated with the area, but also with sex and reproductive period, and contamination gradient, indicating a strong influence of environmental stressors on the physiology of the specimens. The evaluation of genetic structure among populations of Preto River and Felicidade Stream, based on microsatellites, demonstrated that there was no genetic differentiation, due to extensive gene flow between the areas and high genetic diversity. However, after analysis of intrapopulation structure, we observed the existence
Charrel, R.N.; Brault, A.C.; Gallian, P.; Lemasson, J.-J.; Murgue, B.; Murri, S.; Pastorino, B.; Zeller, H.; Chesse, R. de; Micco, P. de; Lamballerie, X. de
Little is known about the genetic relationships between European and other Old-World strains of West Nile virus (WNV) and persistence of WNV North of Mediterranean. We characterized the complete genomes of three WNV strains from France (horse-2000), Tunisia (human-1997) and Kenya (mosquito-1998), and the envelope, NS3 and NS5 genes of the Koutango virus. Phylogenetic analyses including all available full-length sequences showed that: (1) Koutango virus is a distant variant of WNV; (2) the three characterized strains belong to lineage 1, clade 1a; (3) the Tunisian strain roots the lineage of viruses introduced in North America. We established that currently available partial envelope sequences do not generate reliable phylogenies. Accordingly, establishing a large WNV sequence database is pivotal for the understanding of spatial and temporal epidemiology of this virus. For rapid completion of that purpose, colinearized E-NS3-NS5 gene sequences were shown to constitute a valuable surrogate for complete sequences
Liu, Jian; Zhang, Shouzhou; Nagalingum, Nathalie S; Chiang, Yu-Chung; Lindstrom, Anders J; Gong, Xun
The gymnosperm genus Cycas is the sole member of Cycadaceae, and is the largest genus of extant cycads. There are about 115 accepted Cycas species mainly distributed in the paleotropics. Based on morphology, the genus has been divided into six sections and eight subsections, but this taxonomy has not yet been tested in a molecular phylogenetic framework. Although the monophyly of Cycas is broadly accepted, the intrageneric relationships inferred from previous molecular phylogenetic analyses are unclear due to insufficient sampling or uninformative DNA sequence data. In this study, we reconstructed a phylogeny of Cycas using four chloroplast intergenic spacers and seven low-copy nuclear genes and sampling 90% of extant Cycas species. The maximum likelihood and Bayesian inference phylogenies suggest: (1) matrices of either concatenated cpDNA markers or of concatenated nDNA lack sufficient informative sites to resolve the phylogeny alone, however, the phylogeny from the combined cpDNA-nDNA dataset suggests the genus can be roughly divided into 13 clades and six sections that are in agreement with the current classification of the genus; (2) although with partial support, a clade combining sections Panzhihuaenses + Asiorientales is resolved as the earliest diverging branch; (3) section Stangerioides is not monophyletic because the species resolve as a grade; (4) section Indosinenses is not monophyletic as it includes Cycas macrocarpa and C. pranburiensis from section Cycas; (5) section Cycas is the most derived group and its subgroups correspond with geography. Copyright © 2018 Elsevier Inc. All rights reserved.
and metacyclic forms. Further they show that although gut binding may be necessary for parasite establishment, in several vector-parasite pairs the specificity of such in vitro binding alone is insufficient to explain overall vector specificity. Other significant barriers to development must exist in certain refractory Leishmania parasite-sand fly vector combinations. A re-appraisal of the specificity of the Leishmania-sand fly relationship is required.
Mar 15, 2014 ... ... of events: 'Entities that were capable of independent replication ... There have been many major evolutionary events that this definition of .... selection at level x to exclusive selection at x – will probably require a multiplicity ...
Smrithi; Devdas; Ashok; Meghashree; Aarathi
Interpersonal Attraction is the attraction between two people, which leads to friendships and even romantic relationships. Although Interpersonal Attraction has been a long - standing concept, only recently it is being studied regarding its neurobiological and socio evolutionary basis. It is now a major area of research in Social as well as Evolutionary Psychology.
Gokhale, Chaitanya S.; Traulsen, Arne
Evolutionary game theory has become one of the most diverse and far reaching theories in biology. Applications of this theory range from cell dynamics to social evolution. However, many applications make it clear that inherent non-linearities of natural systems need to be taken into account. One way of introducing such non-linearities into evolutionary games is by the inclusion of multiple players. An example is of social dilemmas, where group benefits could e.g.\\ increase less than linear wi...
Several methods to analyze aspects of evolution are developed, that depend on the availability of complete genomes. While I consistently find a phylogenetic signal using many approaches, a question that is winning concern is how these evolutionary relationships should be interpreted. Since Darwin’s
Mark J Bailey
Full Text Available Introduction: Ovarian cancer is the leading cause of death from gynecological cancer. Non-specific symptoms early in disease and the lack of specific biomarkers hinder early diagnosis. Multi-marker blood screening tests have shown promise for improving identification of early stage disease; however, available tests lack sensitivity, and specificity. Materials and Methods: In this study, pooled deeply-depleted plasma from women with Stage 1, 2 or 3 ovarian cancer and healthy controls were used to compare the 2-dimensional gel electrophoresis (2-DE protein profiles and identify potential novel markers of ovarian cancer progression. Results/Discussion: Stage-specific variation in biomarker expression was observed. For example, apolipoprotein A1 expression is relatively low in control and Stage 1, but shows a substantial increase in Stage 2 and 3, thus, potential of utility for disease confirmation rather than early detection. A better marker for early stage disease was tropomyosin 4 (TPM4. The expression of TPM4 increased by 2-fold in Stage 2 before returning to "normal" levels in Stage 3 disease. Multiple isoforms were also identified for some proteins and in some cases, displayed stage-specific expression. An interesting example was fibrinogen alpha, for which 8 isoforms were identified. Four displayed a moderate increase at Stage 1 and a substantial increase for Stages 2 and 3 while the other 4 showed only moderate increases. Conclusion: Herein is provided an improved summary of blood protein profiles for women with ovarian cancer stratified by stage.
Baer, B; Millar, A H
Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein
Gibson, Mhairi A; Lawson, David W
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.
Gibson, Mhairi A; Lawson, David W
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. PMID:25684561
The North American Vaccinium section Cyanococcus includes the ecologically and economically important blueberry species, Vaccinium corymbosum (highbush blueberry), Vaccinium angustifolium (lowbush blueberry), Vaccinium myrtilloides (velvet-leaf blueberry), and Vaccinium virgatum (rabbiteye blueberry...
Igic, Boris; Kohn, Joshua R.
T2-type RNases are responsible for self-pollen recognition and rejection in three distantly related families of flowering plants—the Solanaceae, Scrophulariaceae, and Rosaceae. We used phylogenetic analyses of 67 T2-type RNases together with information on intron number and position to determine whether the use of RNases for self-incompatibility in these families is homologous or convergent. All methods of phylogenetic reconstruction as well as patterns of variation in intron structure find that all self-incompatibility RNases along with non-S genes from only two taxa form a monophyletic clade. Several lines of evidence suggest that the best interpretation of this pattern is homology of self-incompatibility RNases from the Scrophulariaceae, Solanaceae, and Rosaceae. Because the most recent common ancestor of these three families is the ancestor of ≈75% of dicot families, our results indicate that RNase-based self-incompatibility was the ancestral state in the majority of dicots. PMID:11698683
Van Winkle, Lon J.
This laboratory exercise integrates the topics of cell structure, classification of living organisms, and evolution. It is suitable for secondary or college biology courses and was used in an interdisciplinary science course for nonscience majors. (BB)
Bouwman, Abigail; Rühli, Frank
Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.
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...... kinds of evolutionary algorithms, have been prudently analyzed. This analysis was followed by a thorough analysis of various issues involved in stochastic local search algorithms. An interesting survey of various technological and industrial applications in mechanical engineering and design has been...... 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...
Wong, Daniel Fu Keung
A qualitative study was undertaken to explore the stage-specific and culture-specific coping strategies used by Mainland Chinese immigrants in Hong Kong to handle psychosocial stressors experienced during the resettlement stage of the migration process. While direct action coping strategies of problem-solving and compromise were used by immigrants to deal with recurring, daily resettlement difficulties, cognitive strategies of positive comparisons and positive and optimistic thinking were utilized to change the meanings of these difficulties. Emotion-focused coping of acceptance and avoidance strategies were culture-specific, and were useful in reducing the stress associated with the resettlement difficulties encountered. It was also found that strategies such as acceptance, compromise and avoidance might have deleterious effects on the longer-term adjustment of immigrants. Implications for services and counseling for the immigrants were suggested.
Torres-Duarte, Cristina; Ramos-Torres, Karla M; Rahimoff, René; Cherr, Gary N
The effects of exposure to either soluble copper (copper sulfate) or copper oxide nanoparticles (nano-CuO) during specific early developmental stages of sea urchin embryos were analyzed. Soluble copper caused significant malformations in embryos (skeletal malformations, delayed development or gut malformations) when present at any given stage, while cleavage stage was the most sensitive to nano-CuO exposure causing skeletal malformations and decreased total antioxidant capacity. The stage specificity was linked to higher endocytic activity during the first hours of development that leads to higher accumulation of copper in specific cells critical for development. Results indicate that nano-CuO results in higher accumulation of copper inside of embryos and this intracellular copper is more persistent as compared to soluble copper. The possible implications later in development are discussed. Copyright © 2017 Elsevier B.V. All rights reserved.
Full Text Available The human embryonic, fetal and adult β-like globin genes provide a paradigm for tissue- and developmental stage-specific gene regulation. The fetal γ-globin gene is expressed in fetal erythroid cells but is repressed in adult erythroid cells. The molecular mechanism underlying this transcriptional switch during erythroid development is not completely understood. Here, we used a combination of in vitro and in vivo assays to dissect the molecular assemblies of the active and the repressed proximal γ-globin promoter complexes in K562 human erythroleukemia cell line and primary human fetal and adult erythroid cells. We found that the proximal γ-globin promoter complex is assembled by a developmentally regulated, general transcription activator NF-Y bound strongly at the tandem CCAAT motifs near the TATA box. NF-Y recruits to neighboring DNA motifs the developmentally regulated, erythroid transcription activator GATA-2 and general repressor BCL11A, which in turn recruit erythroid repressor GATA-1 and general repressor COUP-TFII to form respectively the NF-Y/GATA-2 transcription activator hub and the BCL11A/COUP-TFII/GATA-1 transcription repressor hub. Both the activator and the repressor hubs are present in both the active and the repressed γ-globin promoter complexes in fetal and adult erythroid cells. Through changes in their levels and respective interactions with the co-activators and co-repressors during erythroid development, the activator and the repressor hubs modulate erythroid- and developmental stage-specific transcription of γ-globin gene.
Baragona, Roberto; Poli, Irene
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
Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca
Analyzing evolutionary relationships requires that students have a thorough understanding of evidence and of how scientists use evidence to develop these relationships. In this lesson sequence, students work in groups to process many different lines of evidence of evolutionary relationships between ungulates, then construct a scientific argument…
Svensson, Erik I
Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated by Ernst Mayr. They have also motivated some biologists and philosophers to argue for an Extended Evolutionary Synthesis (EES). The EES will supposedly expand the scope of the Modern Synthesis (MS) and SET, which has been characterized as gene-centred, relying primarily on natural selection and largely neglecting reciprocal causation. Here, I critically examine these claims, with a special focus on the last conjecture. I conclude that reciprocal causation has long been recognized as important by naturalists, ecologists and evolutionary biologists working in the in the MS tradition, although it it could be explored even further. Numerous empirical examples of reciprocal causation in the form of positive and negative feedback are now well known from both natural and laboratory systems. Reciprocal causation have also been explicitly incorporated in mathematical models of coevolutionary arms races, frequency-dependent selection, eco-evolutionary dynamics and sexual selection. Such dynamic feedback were already recognized by Richard Levins and Richard Lewontin in their bok The Dialectical Biologist . Reciprocal causation and dynamic feedback might also be one of the few contributions of dialectical thinking and Marxist philosophy in evolutionary theory. I discuss some promising empirical and analytical tools to study reciprocal causation and the implications for the EES. Finally, I briefly discuss how quantitative genetics can be adapated to studies of reciprocal causation, constructive inheritance and phenotypic plasticity and suggest that the flexibility of this approach
Coelho de Souza, Fernanda; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J. W.; Chave, Jerome; Galbraith, David R.; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R. Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E. O. C.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard C, Gerardo A.; Baraloto, Christopher; Barroso, Jorcely G.; Bonal, Damien; Boot, Rene G. A.; Camargo, José L. C.; Comiskey, James A.; Valverde, Fernando Cornejo; de Camargo, Plínio B.; Di Fiore, Anthony; Erwin, Terry L.; Feldpausch, Ted R.; Ferreira, Leandro; Fyllas, Nikolaos M.; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N.; Killeen, Timothy J.; Laurance, William F.; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E.; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Marimon-Junior, Ben H.; Mendoza, Casimiro; Morandi, Paulo; Neill, David A.; Vargas, Percy Núñez; Oliveira, Edmar A.; Lenza, Eddie; Palacios, Walter A.; Peñuela-Mora, Maria C.; Pipoly, John J.; Pitman, Nigel C. A.; Prieto, Adriana; Quesada, Carlos A.; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P.; Silveira, Marcos; ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M. F.; van der Meer, Peter J.; Vasquez, Rodolfo V.; Vieira, Simone A.; Vilanova, Emilio; Vos, Vincent A.; Wang, Ophelia; Young, Kenneth R.; Zagt, Roderick J.; Baker, Timothy R.
Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. PMID:27974517
Coelho de Souza, Fernanda; Dexter, Kyle G; Phillips, Oliver L; Brienen, Roel J W; Chave, Jerome; Galbraith, David R; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E O C; Araujo-Murakami, Alejandro; Arets, Eric J M M; Aymard C, Gerardo A; Baraloto, Christopher; Barroso, Jorcely G; Bonal, Damien; Boot, Rene G A; Camargo, José L C; Comiskey, James A; Valverde, Fernando Cornejo; de Camargo, Plínio B; Di Fiore, Anthony; Elias, Fernando; Erwin, Terry L; Feldpausch, Ted R; Ferreira, Leandro; Fyllas, Nikolaos M; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N; Killeen, Timothy J; Laurance, William F; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S; Marimon-Junior, Ben H; Mendoza, Casimiro; Morandi, Paulo; Neill, David A; Vargas, Percy Núñez; Oliveira, Edmar A; Lenza, Eddie; Palacios, Walter A; Peñuela-Mora, Maria C; Pipoly, John J; Pitman, Nigel C A; Prieto, Adriana; Quesada, Carlos A; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P; Silveira, Marcos; Stropp, Juliana; Ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M F; van der Meer, Peter J; Vasquez, Rodolfo V; Vieira, Simone A; Vilanova, Emilio; Vos, Vincent A; Wang, Ophelia; Young, Kenneth R; Zagt, Roderick J; Baker, Timothy R
Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. © 2016 The Authors.
Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.
Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution 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 others to speed the development of evolutionary molecular medicine. PMID:22544168
1968-01-011. 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
Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.
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
Mora, Antonio M.; Squillero, Giovanni; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Smith, Stephen L; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Mora, Antonio M.; Squillero, Giovanni; Jan, Mathieu; Matthias, M; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Esparcia-Alcazar, Anna I; Silva, Sara; Agapitos, Alexandros; Cotta, Carlos; De Falco, Ivanoe; Cioppa, Antonio Della; Diwold, Konrad; Ekart, Aniko; Tarantino, Ernesto; Vega, Francisco Fernandez De; Burelli, Paolo; Sim, Kevin; Cagnoni, Stefano; Simoes, Anabela; Merelo, J.J.; Urquhart, Neil; Haasdijk, Evert; Zhang, Mengjie; Squillero, Giovanni; Eiben, A E; Tettamanzi, Andrea G B; Glette, Kyrre; Rohlfshagen, Philipp; Schaefer, Robert; Caserta, Marco; Ramirez, Adriana; Voß, Stefan
The application of genetic and evolutionary computation to problems in medicine has increased rapidly over the past five years, but there are specific issues and challenges that distinguish it from other real-world applications. Obtaining reliable and coherent patient data, establishing the clinical
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.
Gangestad, S.W.; Tybur, J.M.
Functional approaches in psychology - which ask what behavior is good for - are almost as old as scientific psychology itself. Yet sophisticated, generative functional theories were not possible until developments in evolutionary biology in the mid-20th century. Arising in the last three decades,
Biochemical information has been crucial for the development of evolutionary biology. On the one hand, the sequence information now appearing is producing a huge increase in the amount of data available for phylogenetic analysis; on the other hand, and perhaps more fundamentally, it allows understanding of the ...
Hindi and English. Port 1. Resonance, Vo1.7 ... they use. Of course, many evolutionary biologists do work with fossils or DNA, or both, but there are also large numbers of ... The first major division that I like to make is between studies focussed ...
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…
Bertolini, L.; de Roo, G.; Silva, E.A.
Coping with uncertainty is a defining challenge for spatial planners. Accordingly, most spatial planning theories and methods are aimed at reducing uncertainty. However, the question is what should be done when this seems impossible? This chapter proposes an evolutionary interpretation of spatial
Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon
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...
Full Text Available CCCTC-binding factor (CTCF is largely responsible for the 3D architecture of the genome, in concert with the action of cohesin, through the creation of long-range chromatin loops. Cohesin is hypothesized to be the main driver of these long-range chromatin interactions by the process of loop extrusion. Here, we performed ChIP-seq for CTCF and cohesin in two stages each of T and B cell differentiation and examined the binding pattern in all six antigen receptor (AgR loci in these lymphocyte progenitors and in mature T and B cells, ES cells, and fibroblasts. The four large AgR loci have many bound CTCF sites, most of which are only occupied in lymphocytes, while only the CTCF sites at the end of each locus near the enhancers or J genes tend to be bound in non-lymphoid cells also. However, despite the generalized lymphocyte restriction of CTCF binding in AgR loci, the Igκ locus is the only locus that also shows significant lineage-specificity (T vs. B cells and developmental stage-specificity (pre-B vs. pro-B in CTCF binding. We show that cohesin binding shows greater lineage- and stage-specificity than CTCF at most AgR loci, providing more specificity to the loops. We also show that the culture of pro-B cells in IL7, a common practice to expand the number of cells before ChIP-seq, results in a CTCF-binding pattern resembling pre-B cells, as well as other epigenetic and transcriptional characteristics of pre-B cells. Analysis of the orientation of the CTCF sites show that all sites within the large V portions of the Igh and TCRβ loci have the same orientation. This suggests either a lack of requirement for convergent CTCF sites creating loops, or indicates an absence of any loops between CTCF sites within the V region portion of those loci but only loops to the convergent sites at the D-J-enhancer end of each locus. The V region portions of the Igκ and TCRα/δ loci, by contrast, have CTCF sites in both orientations, providing many options for
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...
Evolutionary algorithms (EAs) are becoming increasingly attractive for researchers from various disciplines, such as operations research, computer science, industrial engineering, electrical engineering, social science, economics, etc. This book presents an insightful, comprehensive, and up-to-date treatment of EAs, such as genetic algorithms, differential evolution, evolution strategy, constraint optimization, multimodal optimization, multiobjective optimization, combinatorial optimization, evolvable hardware, estimation of distribution algorithms, ant colony optimization, particle swarm opti
Chen, Binbin; Platt, Manu O
Cathepsins K, L, and S are cysteine proteases upregulated in cancer and proteolyze extracellular matrix to facilitate metastasis, but difficulty distinguishing specific cathepsin activity in complex tissue extracts confounds scientific studies and employing them for use in clinical diagnoses. Here, we have developed multiplex cathepsin zymography to profile cathepsins K, L, and S activity in 10 μg human breast, lung, and cervical tumors by exploiting unique electrophoretic mobility and renaturation properties. Frozen breast, lung, and cervix cancer tissue lysates and normal organ tissue lysates from the same human patients were obtained (28 breast tissues, 23 lung tissues, and 23 cervix tissues), minced and homogenized prior to loading for cathepsin gelatin zymography to determine enzymatic activity. Cleared bands of cathepsin activity were identified and validated in tumor extracts and detected organ- and stage-specific differences in activity. Cathepsin K was unique compared to cathepsins L and S. It was significantly higher for all cancers even at the earliest stage tested (stage I for lung and cervix (n = 6, p zymography, yielded 100% sensitivity and specificity for 20 breast tissue samples tested (10 normal; 10 tumor) in part due to the consistent absence of cathepsin K in normal breast tissue across all patients. To summarize, this sensitive assay provides quantitative outputs of cathepsins K, L, and S activities from mere micrograms of tissue and has potential use as a supplement to histological methods of clinical diagnoses of biopsied human tissue.
Shen, Ru; Zhao, Ling-Li; Yu, Zhen; Zhang, Cheng; Chen, Yuan-Hua; Wang, Hua; Zhang, Zhi-Hui; Xu, De-Xiang
Di (2-ethylhexyl) phthalate (DEHP) is male developmental toxicant that impairs testis development with reduced anogenital distance. The present study aimed to investigate whether maternal DEHP exposure during pregnancy causes intrauterine growth restriction (IUGR) in a gender-specific manner and to identify the critical window of DEHP-induced fetal IUGR. Pregnant mice were administered with DEHP (0, 50 or 200mg/kg) by gavage. Fetal IUGR was observed not only in males but also in females when litters were exposed to DEHP on gestational day (GD)0-GD17. Interestingly, fetal weight and crown-rump length were reduced, markedly in dams with DEHP on GD13-GD17, slightly in dams with on GD7-GD12, but not in dams with on GD0-GD6. Further analysis showed that maternal DEHP exposure on GD7-GD12 inhibited cell proliferation, lowered placental weight, and reduced blood sinusoid area in placental labyrinth layer. These results suggest that maternal DEHP exposure induces IUGR in a stage-specific but gender-independent manner. Copyright © 2016 Elsevier Inc. All rights reserved.
Katagiri, Yohko U.; Kiyokawa, Nobutaka; Nakamura, Kyoko; Takenouchi, Hisami; Taguchi, Tomoko; Okita, Hajime; Umezawa, Akihiro; Fujimoto, Junichiro
We previously produced monoclonal antibodies against the detergent-insoluble microdomain, i.e., the raft microdomain, of the human renal cancer cell line ACHN. Raft.2, one of these monoclonal antibodies, recognizes sialosyl globopentaosylceramide, which has the stage-specific embryonic antigen (SSEA)-4 epitope. Although the mouse embryonal carcinoma (EC) cell line F9 does not express SSEA-4, some F9 cells stained with Raft.2. Western analysis and matrix-assisted laser desorption ionization-time of flight mass spectrometry identified the Raft.2 binding molecule as laminin binding protein (LBP), i.e., 34/67 laminin receptor. Weak acid treatment or digestion with Clostridium perfringens sialidase reduced Raft.2 binding to LBP on nitrocellulose sheets and [ 14 C]galactose was incorporated into LBP, indicating LBP to have a sialylated carbohydrate moiety. Subcellular localization analysis by sucrose density-gradient centrifugation and examination by confocal microscopy revealed LBP to be localized on the outer surface of the plasma membrane. An SSEA-4-positive human EC cell line, NCR-G3 cells, also expressed Raft.2-binding LBP
Paulo M G Rodrigues
Full Text Available Nibrin (NBN or NBS1 and ATM are key factors for DNA Double Strand Break (DSB signaling and repair. Mutations in NBN or ATM result in Nijmegen Breakage Syndrome and Ataxia telangiectasia. These syndromes share common features such as radiosensitivity, neurological developmental defects and cancer predisposition. However, the functional synergy of Nbn and Atm in different tissues and developmental stages is not yet understood. Here, we show in vivo consequences of conditional inactivation of both genes in neural stem/progenitor cells using Nestin-Cre mice. Genetic inactivation of Atm in the central nervous system of Nbn-deficient mice led to reduced life span and increased DSBs, resulting in increased apoptosis during neural development. Surprisingly, the increase of DSBs and apoptosis was found only in few tissues including cerebellum, ganglionic eminences and lens. In sharp contrast, we showed that apoptosis associated with Nbn deletion was prevented by simultaneous inactivation of Atm in developing retina. Therefore, we propose that Nbn and Atm collaborate to prevent DSB accumulation and apoptosis during development in a tissue- and developmental stage-specific manner.
Full Text Available Highly coordinated transcription networks orchestrate the self-renewal of pluripotent stem cell and the earliest steps of mammalian development. KRAB-containing zinc finger proteins represent the largest group of transcription factors encoded by the genomes of higher vertebrates including mice and humans. Together with their putatively universal cofactor KAP1, they have been implicated in events as diverse as the silencing of endogenous retroelements, the maintenance of imprinting and the pluripotent self-renewal of embryonic stem cells, although the genomic targets and specific functions of individual members of this gene family remain largely undefined. Here, we first generated a list of Ensembl-annotated KRAB-containing genes encoding the mouse and human genomes. We then defined the transcription levels of these genes in murine early embryonic cells. We found that the majority of KRAB-ZFP genes are expressed in mouse pluripotent stem cells and other early progenitors. However, we also identified distinctively cell- or stage-specific patterns of expression, some of which are pluripotency-restricted. Finally, we determined that individual KRAB-ZFP genes exhibit highly distinctive modes of expression, even when grouped in genomic clusters, and that these cannot be correlated with the presence of prototypic repressive or activating chromatin marks. These results pave the way to delineating the role of specific KRAB-ZFPs in early embryogenesis.
Roe, John H.; Hopkins, William A.; Jackson, Brian P.
Information on species-and stage-specific patterns of contaminant accumulation is generally lacking for amphibians, yet such information could provide valuable knowledge on how amphibians interact with contaminants. We assessed concentrations of As, Cd, Cu, Ni, Pb, Se, Sr, and Zn in whole bodies of larval, recently metamorphosed, and adult life stages in Bufo terrestris and Rana sphenocephala from a site that currently receives coal combustion waste (CCW) discharge, a site where CCW was formerly discharged that has undergone natural attenuation for 30 years, and a nearby reference site. For the majority of elements (As, Cd, Cu, Ni, Pb, Zn), concentrations were highest in larvae, but Se and Sr concentrations remained elevated in later life stages, likely because these elements are S and Ca analogs, respectively, and are thus retained throughout structural changes during metamorphosis. Element concentrations were generally higher in B. terrestris than in R. sphenocephala. Concentrations of As, Se, and Sr were up to 11-35 times higher in metamorphs emigrating from CCW-polluted wetlands compared to unpolluted wetlands, suggesting metamorphosed amphibians can transport trace elements from aquatic disposal basins to nearby uncontaminated terrestrial habitats. In addition, anurans utilizing naturally revegetated sites up to 30 years after CCW disposal ceases are exposed to trace elements, although to a lesser degree than sites where CCW is currently discharged. - Results suggest that metamorphosed amphibians can transport trace elements from aquatic disposal basins to non-contaminated habitats
Roe, John H. [University of Georgia, Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802 (United States); Hopkins, William A. [University of Georgia, Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802 (United States)]. E-mail: firstname.lastname@example.org; Jackson, Brian P. [University of Georgia, Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802 (United States)
Information on species-and stage-specific patterns of contaminant accumulation is generally lacking for amphibians, yet such information could provide valuable knowledge on how amphibians interact with contaminants. We assessed concentrations of As, Cd, Cu, Ni, Pb, Se, Sr, and Zn in whole bodies of larval, recently metamorphosed, and adult life stages in Bufo terrestris and Rana sphenocephala from a site that currently receives coal combustion waste (CCW) discharge, a site where CCW was formerly discharged that has undergone natural attenuation for 30 years, and a nearby reference site. For the majority of elements (As, Cd, Cu, Ni, Pb, Zn), concentrations were highest in larvae, but Se and Sr concentrations remained elevated in later life stages, likely because these elements are S and Ca analogs, respectively, and are thus retained throughout structural changes during metamorphosis. Element concentrations were generally higher in B. terrestris than in R. sphenocephala. Concentrations of As, Se, and Sr were up to 11-35 times higher in metamorphs emigrating from CCW-polluted wetlands compared to unpolluted wetlands, suggesting metamorphosed amphibians can transport trace elements from aquatic disposal basins to nearby uncontaminated terrestrial habitats. In addition, anurans utilizing naturally revegetated sites up to 30 years after CCW disposal ceases are exposed to trace elements, although to a lesser degree than sites where CCW is currently discharged. - Results suggest that metamorphosed amphibians can transport trace elements from aquatic disposal basins to non-contaminated habitats.
Roe, J.H.; Hopkins, W.A.; Jackson, B.P. [University of Georgia, Aiken, SC (US)
Information on species- and stage-specific patterns of contaminant accumulation is generally lacking for amphibians, yet such information could provide valuable knowledge on how amphibians interact with contaminants. We assessed concentrations of As, Cd, Cu, Ni, Pb, Se, Sr, and Zn in whole bodies of larval, recently metamorphosed, and adult life stages in Bufo terrestris and Rana sphenocephala from a site that currently receives coal combustion waste (CCW) discharge, a site where CCW was formerly discharged that has undergone natural attenuation for 30 years, and a nearby reference site. For the majority of elements (As, Cd, Cu, Ni, Pb, Zn), concentrations were highest in larvae, but Se and Sr concentrations remained elevated in later life stages, likely because these elements are S and Ca analogs, respectively, and are thus retained throughout structural changes during metamorphosis. Element concentrations were generally higher in B. terrestris than in R. sphenocephala. Concentrations of As, Se, and Sr were up to 11-35 times higher in metamorphs emigrating from CCW-polluted wetlands compared to unpolluted wetlands, suggesting metamorphosed amphibians can transport trace elements from aquatic disposal basins to nearby uncontaminated terrestrial habitats. In addition, anurans utilizing naturally revegetated sites up to 30 years after CCW disposal ceases are exposed to trace elements, although to a lesser degree than sites where CCW is currently discharged.
Szabó, György; Fáth, Gábor
Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.
Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R
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 often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).
McAvoy, Alex; Hauert, Christoph
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. PMID:26308326
Ko, Il Sun; Choi, So Young; Kim, Jin Sook
This study was done to clarify attributes, antecedents, and consequences of spirituality. Rodgers's evolutionary concept analysis was used to analyze fifty seven studies from the literature related to spirituality as it appears in systematic literature reviews of theology, medicine, counseling & psychology, social welfare, and nursing. Spirituality was found to consist of two dimensions and eight attributes: 1) vertical dimension: 'intimacy and connectedness with God' and 'holy life and belief', 2) horizontal dimension: 'self-transcendence', 'meaning and purpose in life', 'self-integration', and 'self-creativity' in relationship with self, 'connectedness' and 'trust' in relationship with others·neighbors·nature. Antecedents of spirituality were socio-demographic, religious, psychological, and health related characteristics. Consequences of spirituality were positive and negative. Being positive included 'life centered on God' in vertical dimension, and among horizontal dimension 'joy', 'hope', 'wellness', 'inner peace', and 'self-actualization' in relationship with self, 'doing in love' and 'extended life toward neighbors and the world' in relationship with others·neighbors·nature. Being negative was defined as having 'guilt', 'inner conflict', 'loneliness', and 'spiritual distress'. Facilitators of spirituality were stressful life events and experiences. Spirituality is a multidimensional concept. Unchangeable attributes of spirituality are 'connectedness with God', 'self-transcendence', 'meaning of life' and 'connectedness with others·nature'. Unchangeable consequences of spirituality are 'joy' and 'hope'. The findings suggest that the dimensional framework of spirituality can be used to assess the current spiritual state of patients. Based on these results, the development of a Korean version of the scale measuring spirituality is recommended. © 2017 Korean Society of Nursing Science
Full Text Available Major construction projects have a great influence on the national economy and society, wherein cooperative relationship between construction suppliers plays an increasingly significant role in the overall supply chain system. However, the relationships between suppliers are noncontractual, multistage, dynamic, and complicated. To gain a deeper insight into the suppliers’ cooperative relationships, an evolutionary game model is developed to explore the cooperation tendency of multisuppliers. A replicator dynamic system is further formulated to investigate the evolutionary stable strategies of multisuppliers. Then, fourteen “when-then” type scenarios are concluded and classified into six different evolutionary tracks. Meanwhile, the critical influencing factors are identified. The results show that the suppliers’ production capacity, owner-supplier contract, and the owner’s incentive mechanism influence the cooperation tendency of suppliers directly. The managerial implications contribute to insightful references for a more stable cooperative relationship between the owner and suppliers.
Full Text Available Rice false smut, a fungal disease caused by Ustilaginoidea virens is becoming a severe detriment to rice production worldwide. However, little is known about the molecular response of rice to attacks by the smut pathogen. In this article, we define the initial infection process as having three stages: initial colonization on the pistil (stage 1, S1, amplification on the anther (stage 2, S2 and sporulation in the anther chambers (stage 3, S3. Based on the transcriptome of rice hosts in response to U. virens in two separate years, we identified 126, 204, and 580 specific regulated genes in their respective stages S1, S2, and S3, respectively, by excluding common expression patterns in other openly biotic/abiotic databases using bioinformatics. As the disease progresses, several stage-specific biological processes (BP terms were distinctively enriched: "Phosphorylation" in stage S1, "PCD" in S2, and "Cell wall biogenesis" in S3, implying a concise signal cascade indicative of the tactics that smut pathogens use to control host rice cells during infection. 113 regulated genes were coexpressed among the three stages. They shared highly conserved promoter cis-element in the promoters in response to the regulation of WRKY and Myb for up-regulation, and ABA and Ca2+ for down regulation, indicating their potentially critical roles in signal transduction during rice-U. virens interaction. We further analyzed seven highly regulated unique genes; four were specific to pollen development, implying that pollen-related genes play critical roles in the establishment of rice susceptibility to U. virens. To my knowledge, this is the first report about probing of molecular response of rice to smut pathogen infection, which will greatly expand our understanding of the molecular events surrounding infection by rice false smut.
Cashman, J D; Clark-Lewis, I; Eaves, A C; Eaves, C J
Nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice transplanted with human cord blood or adult marrow cells and injected 6 weeks posttransplant with 2 daily doses of transforming growth factor-beta(1) (TGF-beta(1)), monocyte chemoattractant protein-1 (MCP-1), or a nonaggregating form of macrophage inflammatory protein-1alpha (MIP-1alpha) showed unique patterns of inhibition of human progenitor proliferation 1 day later. TGF-beta(1) was active on long-term culture initiating cells (LTC-IC) and on primitive erythroid and granulopoietic colony-forming cells (HPP-CFC), but had no effect on mature CFC. MCP-1 inhibited the cycling of both types of HPP-CFC but not LTC-IC. MIP-1alpha did not inhibit either LTC-IC or granulopoietic HPP-CFC but was active on erythroid HPP-CFC and mature granulopoietic CFC. All of these responses were independent of the source of human cells transplanted. LTC-IC of either human cord blood or adult marrow origin continue to proliferate in NOD/SCID mice for many weeks, although the turnover of all types of human CFC in mice transplanted with adult human marrow (but not cord blood) is downregulated after 6 weeks. Interestingly, administration of either MIP-1beta, an antagonist of both MIP-1alpha and MCP-1 or MCP-1(9-76), an antagonist of MCP-1 (and MCP-2 and MCP-3), into mice in which human marrow-derived CFC had become quiescent, caused the rapid reactivation of these progenitors in vivo. These results provide the first definition of stage-specific inhibitors of human hematopoietic progenitor cell cycling in vivo. In addition they show that endogenous chemokines can contribute to late graft failure, which can be reversed by the administration of specific antagonists.
Austen L. Krill
Full Text Available Cognitive neuroscience, the study of brain-behavior relationships, has long attempted to map the brain. The discipline is flourishing, with an increasing number of functional neuroimaging studies appearing in the scientific literature daily. Unlike biology and even psychology, the cognitive neurosciences have only recently begun to apply evolutionary meta-theory and methodological guidance. Approaching cognitive neuroscience from an evolutionary perspective allows scientists to apply biologically based theoretical guidance to their investigations and can be conducted in both humans and nonhuman animals. In fact, several investigations of this sort are underway in laboratories around the world. This paper and two new volumes (Platek, Keenan, and Shackelford [Eds.], 2007; Platek and Shackelford [Eds.], under contract represent the first formal attempts to document the burgeoning field of evolutionary cognitive neuroscience. Here, we briefly review the current state of the science of evolutionary cognitive neuroscience, the methods available to the evolutionary cognitive neuroscientist, and what we foresee as the future directions of the discipline.
of population performance will increase in frequency. Yield, one of the fundamental agronomic variables, is not an individual, but a population characteristic. A farmer wants a high yield per hectare; he is not interested in the performance of individual plants. When individual selection and population...... 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...
Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian
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...
Kutschera, Ulrich; Niklas, Karl J.
Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin’s son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin’s work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.
Ellers, Jacintha; Kiers, E Toby; Currie, Cameron R; McDonald, Bradon R; Visser, Bertanne
Loss of traits can dramatically alter the fate of species. Evidence is rapidly accumulating that the prevalence of trait loss is grossly underestimated. New findings demonstrate that traits can be lost without affecting the external phenotype, provided the lost function is compensated for by species interactions. This is important because trait loss can tighten the ecological relationship between partners, affecting the maintenance of species interactions. Here, we develop a new perspective on so-called `compensated trait loss' and how this type of trait loss may affect the evolutionary dynamics between interacting organisms. We argue that: (1) the frequency of compensated trait loss is currently underestimated because it can go unnoticed as long as ecological interactions are maintained; (2) by analysing known cases of trait loss, specific factors promoting compensated trait loss can be identified and (3) genomic sequencing is a key way forwards in detecting compensated trait loss. We present a comprehensive literature survey showing that compensated trait loss is taxonomically widespread, can involve essential traits, and often occurs as replicated evolutionary events. Despite its hidden nature, compensated trait loss is important in directing evolutionary dynamics of ecological relationships and has the potential to change facultative ecological interactions into obligatory ones. © 2012 Blackwell Publishing Ltd/CNRS.
Kutschera, Ulrich; Niklas, Karl J
Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin's son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin's work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.
Bickham, John W
Evolutionary Toxicology is the study of the effects of chemical pollutants on the genetics of natural populations. Research in Evolutionary Toxicology uses experimental designs familiar to the ecotoxicologist with matched reference and contaminated sites and the selection of sentinel species. It uses the methods of molecular genetics and population genetics, and is based on the theories and concepts of evolutionary biology and conservation genetics. Although it is a relatively young field, interest is rapidly growing among ecotoxicologists and more and more field studies and even controlled laboratory experiments are appearing in the literature. A number of population genetic impacts have been observed in organisms exposed to pollutants which I refer to here as the four cornerstones of Evolutionary Toxicology. These include (1) genome-wide changes in genetic diversity, (2) changes in allelic or genotypic frequencies caused by contaminant-induced selection acting at survivorship loci, (3) changes in dispersal patterns or gene flow which alter the genetic relationships among populations, and (4) changes in allelic or genotypic frequencies caused by increased mutation rates. It is concluded that population genetic impacts of pollution exposure are emergent effects that are not necessarily predictable from the mode of toxicity of the pollutant. Thus, to attribute an effect to a particular contaminant requires a careful experimental design which includes selection of appropriate reference sites, detailed chemistry analyses of environmental samples and tissues, and the use of appropriate biomarkers to establish exposure and effect. This paper describes the field of Evolutionary Toxicology and discusses relevant field studies and their findings. © Springer Science+Business Media, LLC 2011
Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E
Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660
Fogel, David B.
Evolutionary computation is becoming a common technique for solving difficult, real-world problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as their ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine.
Aurass, Philipp; Gerlach, Thomas; Becher, Dörte; Voigt, Birgit; Karste, Susanne; Bernhardt, Jörg; Riedel, Katharina; Hecker, Michael; Flieger, Antje
their phase specific function. The distinct temporal or spatial presence of such proteins might have important implications for functional assignments in the future or for use as life-stage specific markers for pathogen analysis. PMID:26545400
Höfner, Thomas; Klein, Corinna; Eisen, Christian; Rigo-Watermeier, Teresa; Haferkamp, Axel; Sprick, Martin R
The long-term propagation of basal prostate progenitor cells ex vivo has been very difficult in the past. The development of novel methods to expand prostate progenitor cells in vitro allows determining their cell surface phenotype in greater detail. Mouse (Lin(-)Sca-1(+) CD49f(+) Trop2(high)-phenotype) and human (Lin(-) CD49f(+) TROP2(high)) basal prostate progenitor cells were expanded in vitro. Human and mouse cells were screened using 242 anti-human or 176 antimouse monoclonal antibodies recognizing the cell surface protein profile. Quantitative expression was evaluated at the single-cell level using flow cytometry. Differentially expressed cell surface proteins were evaluated in conjunction with the known CD49f(+)/TROP2(high) phenotype of basal prostate progenitor cells and characterized by in vivo sandwich-transplantation experiments using nude mice. The phenotype of basal prostate progenitor cells was determined as CD9(+)/CD24(+)/CD29(+)/CD44(+)/CD47(+)/CD49f(+)/CD104(+)/CD147(+)/CD326(+)/Trop2(high) of mouse as well as human origin. Our analysis revealed several proteins, such as CD13, Syndecan-1 and stage-specific embryonal antigens (SSEAs), as being differentially expressed on murine and human CD49f(+) TROP2(+) basal prostate progenitor cells. Transplantation experiments suggest that CD49f(+) TROP2(high) SSEA-4(high) human prostate basal progenitor cells to be more potent to regenerate prostate tubules in vivo as compared with CD49f(+) TROP2(high) or CD49f(+) TROP2(high) SSEA-4(low) cells. Determination of the cell surface protein profile of functionally defined murine and human basal prostate progenitor cells reveals differentially expressed proteins that may change the potency and regenerative function of epithelial progenitor cells within the prostate. SSEA-4 is a candidate cell surface marker that putatively enables a more accurate identification of the basal PESC lineage. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by
Williams, Tegan A; Bonham, Luke A; Bernier, Nicholas J
The capacity for early life environmental stressors to induce programming effects on the endocrine stress response in fish is largely unknown. In this study we determined the effects of high environmental ammonia (HEA) exposure on the stress response in larval zebrafish, assessed the tolerance of embryonic and larval stages to HEA, and evaluated whether early life HEA exposure has long-term consequences on the cortisol response to a novel stressor. Exposure to 500-2000μM NH 4 Cl for 16h did not affect the gene expression of corticotropin-releasing factor (CRF) system components in 1day post-fertilization (dpf) embryos, but differentially increased crfa, crfb and CRF binding protein (crfbp) expression and stimulated both dose- and time-dependent increases in the whole body cortisol of 5dpf larvae. Pre-acclimation to HEA at 1dpf did not affect the cortisol response to a subsequent NH 4 Cl exposure at 5dpf. In contrast, pre-acclimation to HEA at 5dpf caused a small but significant reduction in the cortisol response to a second NH 4 Cl exposure at 10dpf. While continuous exposure to 500-2000μM NH 4 Cl between 0 and 5dpf had a modest effect on mean survival time, exposure to 400-1000μM NH 4 Cl between 10 and 14dpf decreased mean survival time in a dose-dependent manner. Moreover, pre-acclimation to HEA at 5dpf significantly decreased the risk of mortality to continuous NH 4 Cl exposure between 10 and 14dpf. Finally, while HEA at 1dpf did not affect the cortisol stress response to a novel vortex stressor at 5dpf, the same HEA treatment at 5dpf abolished vortex stressor-induced increases in whole body cortisol at 10 and 60dpf. Together these results show that the impact of HEA on the cortisol stress response during development is life-stage specific and closely linked to ammonia tolerance. Further, we demonstrate that HEA exposure at the larval stage can have persistent effects on the capacity to respond to stressors in later life. Copyright © 2017 Elsevier Inc. All
Fisher, D N; McAdam, A G
The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals' network traits, representing some aspect of their social phenotype, relate to their fitness. Meanwhile, quantitative geneticists have demonstrated that traits expressed in a social context can depend on the phenotypes and genotypes of interacting partners, leading to influences of the social environment on the traits and fitness of individuals and the evolutionary trajectories of populations. Therefore, both fields are investigating similar topics, yet have arrived at these points relatively independently. We review how these approaches are diverged, and yet how they retain clear parallelism and so strong potential for complementarity. This demonstrates that, despite separate bodies of theory, advances in one might inform the other. Techniques in network analysis for quantifying social phenotypes, and for identifying community structure, should be useful for those studying the relationship between individual behaviour and group-level phenotypes. Entering social association matrices into quantitative genetic models may also reduce bias in heritability estimates, and allow the estimation of the influence of social connectedness on trait expression. Current methods for measuring natural selection in a social context explicitly account for the fact that a trait is not necessarily the property of a single individual, something the network approaches have not yet considered when relating network metrics to individual fitness. Harnessing evolutionary models that consider traits affected by genes in other individuals (i.e. indirect genetic
Darwin's principle of evolution by natural selection is readily casted into a mathematical formalism. Molecular biology revealed the mechanism of mutation and provides the basis for a kinetic theory of evolution that models correct reproduction and mutation as parallel chemical reaction channels. A result of the kinetic theory is the existence of a phase transition in evolution occurring at a critical mutation rate, which represents a localization threshold for the population in sequence space. Occurrence and nature of such phase transitions depend critically on fitness landscapes. The fitness landscape being tantamount to a mapping from sequence or genotype space into phenotype space is identified as the true source of complexity in evolution. Modeling evolution as a stochastic process is discussed and neutrality with respect to selection is shown to provide a major challenge for understanding evolutionary processes (author)
Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.
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.
Kleshnina, Maria; Filar, Jerzy A; Ejov, Vladimir; McKerral, Jody C
The adaptation process of a species to a new environment is a significant area of study in biology. As part of natural selection, adaptation is a mutation process which improves survival skills and reproductive functions of species. Here, we investigate this process by combining the idea of incompetence with evolutionary game theory. In the sense of evolution, incompetence and training can be interpreted as a special learning process. With focus on the social side of the problem, we analyze the influence of incompetence on behavior of species. We introduce an incompetence parameter into a learning function in a single-population game and analyze its effect on the outcome of the replicator dynamics. Incompetence can change the outcome of the game and its dynamics, indicating its significance within what are inherently imperfect natural systems.
Agenor, Christine; Conner, Norma; Aroian, Karen
Mental health is an important measure of public health (WHO, 2004); however, nursing practice and research continues to prioritize mental illness, rather than well-being (Wand, 2011). Flourishing is a recent concept in the field of well-being. The term has been used sparingly in nursing practice and research, and conceptual clarification is needed to promote comprehensive understanding of the phenomenon. The purpose of this study is to critically analyze flourishing, assess the maturity of the concept, and provide recommendations for future research, education, and practice. The concept of flourishing was analyzed using the evolutionary approach to concept analysis (Rodgers, 2000). A search for articles on flourishing within the context of well-being was conducted through CINAHL, MEDLINE, and PsycINFO. A sample of 32 articles and 1 book was reviewed. Data were reviewed for concept attributes, antecedents, consequences, surrogate terms and related concepts. Four models of flourishing were identified with six overlapping attributes: meaning, positive relationships, engagement, competence, positive emotion, and self-esteem. Limited longitudinal and predictive studies have been conducted, but there is evidence for several antecedents and outcomes of flourishing. Research is ongoing primarily in psychology and sociology and is lacking in other disciplines. The concept of flourishing is immature; however, evidence is building for related concepts. A lack of consistent terminology regarding flourishing prevents knowledge development of flourishing as a distinct concept. Further multidisciplinary research is needed to establish standard operational and conceptual definitions and develop effective interventions.
Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne
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.
Boschma, R.A.; Frenken, K.
This paper aims to provide the outlines of an evolutionary economic geography of industry location. We discuss two evolutionary explanations of industry location, that is, one that concentrates on spin-offs, and one that focuses attention on knowledge and agglomeration economies. We claim that both
These discussions included, among others, the possible consequences of nonDNA-based inheritance—epigenetics and cultural evolution, niche construction, and developmental mechanisms on our understanding of the evolutionary process, speciation, complexity in biology, and constructing a formal evolutionary theory.
We are delighted to bring to the readers, a set of peer-reviewed papers on evolutionary biology, published as a special issue of the Journal of Genetics. These papers emanated from ruminations upon and discussions at the Foundations of. Evolutionary Theory: the Ongoing Synthesis meeting at Coorg, India, in February ...
Nie, Pu-Yan; Zhang, Pei-Ai
Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.
Boschma, R.A.; Frenken, K.; Puranam, Krishna Kishore; Ravi Kumar Jain B., xx
This paper is written as the first chapter of an edited volume on evolutionary economics and economic geography (Frenken, K., editor, Applied Evolutionary Economics and Economic Geography, Cheltenham: Edward Elgar, expected publication date February 2007). The paper reviews empirical applications of
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.
Scholte, Larissa L S; Pascoal-Xavier, Marcelo A; Nahum, Laila A
Helminths include free-living and parasitic Platyhelminthes and Nematoda which infect millions of people worldwide. Some Platyhelminthes species of blood flukes ( Schistosoma haematobium, Schistosoma japonicum , and Schistosoma mansoni ) and liver flukes ( Clonorchis sinensis and Opisthorchis viverrini ) are known to be involved in human cancers. Other helminths are likely to be carcinogenic. Our main goals are to summarize the current knowledge of human cancers caused by Platyhelminthes, point out some helminth and human biomarkers identified so far, and highlight the potential contributions of phylogenetics and molecular evolution to cancer research. Human cancers caused by helminth infection include cholangiocarcinoma, colorectal hepatocellular carcinoma, squamous cell carcinoma, and urinary bladder cancer. Chronic inflammation is proposed as a common pathway for cancer initiation and development. Furthermore, different bacteria present in gastric, colorectal, and urogenital microbiomes might be responsible for enlarging inflammatory and fibrotic responses in cancers. Studies have suggested that different biomarkers are involved in helminth infection and human cancer development; although, the detailed mechanisms remain under debate. Different helminth proteins have been studied by different approaches. However, their evolutionary relationships remain unsolved. Here, we illustrate the strengths of homology identification and function prediction of uncharacterized proteins from genome sequencing projects based on an evolutionary framework. Together, these approaches may help identifying new biomarkers for disease diagnostics and intervention measures. This work has potential applications in the field of phylomedicine (evolutionary medicine) and may contribute to parasite and cancer research.
Hummert, Sabine; Bohl, Katrin; Basanta, David; Deutsch, Andreas; Werner, Sarah; Theissen, Günter; Schroeter, Anja; Schuster, Stefan
In two papers we review game theory applications in biology below the level of cognitive living beings. It can be seen that evolution and natural selection replace the rationality of the actors appropriately. Even in these micro worlds, competing situations and cooperative relationships can be found and modeled by evolutionary game theory. Also those units of the lowest levels of life show different strategies for different environmental situations or different partners. We give a wide overview of evolutionary game theory applications to microscopic units. In this first review situations on the cellular level are tackled. In particular metabolic problems are discussed, such as ATP-producing pathways, secretion of public goods and cross-feeding. Further topics are cyclic competition among more than two partners, intra- and inter-cellular signalling, the struggle between pathogens and the immune system, and the interactions of cancer cells. Moreover, we introduce the theoretical basics to encourage scientists to investigate problems in cell biology and molecular biology by evolutionary game theory.
Larissa L. S. Scholte
Full Text Available Helminths include free-living and parasitic Platyhelminthes and Nematoda which infect millions of people worldwide. Some Platyhelminthes species of blood flukes (Schistosoma haematobium, Schistosoma japonicum, and Schistosoma mansoni and liver flukes (Clonorchis sinensis and Opisthorchis viverrini are known to be involved in human cancers. Other helminths are likely to be carcinogenic. Our main goals are to summarize the current knowledge of human cancers caused by Platyhelminthes, point out some helminth and human biomarkers identified so far, and highlight the potential contributions of phylogenetics and molecular evolution to cancer research. Human cancers caused by helminth infection include cholangiocarcinoma, colorectal hepatocellular carcinoma, squamous cell carcinoma, and urinary bladder cancer. Chronic inflammation is proposed as a common pathway for cancer initiation and development. Furthermore, different bacteria present in gastric, colorectal, and urogenital microbiomes might be responsible for enlarging inflammatory and fibrotic responses in cancers. Studies have suggested that different biomarkers are involved in helminth infection and human cancer development; although, the detailed mechanisms remain under debate. Different helminth proteins have been studied by different approaches. However, their evolutionary relationships remain unsolved. Here, we illustrate the strengths of homology identification and function prediction of uncharacterized proteins from genome sequencing projects based on an evolutionary framework. Together, these approaches may help identifying new biomarkers for disease diagnostics and intervention measures. This work has potential applications in the field of phylomedicine (evolutionary medicine and may contribute to parasite and cancer research.
Aristotelous, Andreas C; Durrett, Richard
Inspired by the use of hybrid cellular automata in modeling cancer, we introduce a generalization of evolutionary games in which cells produce and absorb chemicals, and the chemical concentrations dictate the death rates of cells and their fitnesses. Our long term aim is to understand how the details of the interactions in a system with n species and m chemicals translate into the qualitative behavior of the system. Here, we study two simple 2×2 games with two chemicals and revisit the two and three species versions of the one chemical colicin system studied earlier by Durrett and Levin (1997). We find that in the 2×2 examples, the behavior of our new spatial model can be predicted from that of the mean field differential equation using ideas of Durrett and Levin (1994). However, in the three species colicin model, the system with diffusion does not have the coexistence which occurs in the lattices model in which sites interact with only their nearest neighbors. Copyright © 2014 Elsevier Inc. All rights reserved.
Lacquaniti, Francesco; Ivanenko, Yuri P; d'Avella, Andrea; Zelik, Karl E; Zago, Myrka
The identification of biological modules at the systems level often follows top-down decomposition of a task goal, or bottom-up decomposition of multidimensional data arrays into basic elements or patterns representing shared features. These approaches traditionally have been applied to mature, fully developed systems. Here we review some results from two other perspectives on modularity, namely the developmental and evolutionary perspective. There is growing evidence that modular units of development were highly preserved and recombined during evolution. We first consider a few examples of modules well identifiable from morphology. Next we consider the more difficult issue of identifying functional developmental modules. We dwell especially on modular control of locomotion to argue that the building blocks used to construct different locomotor behaviors are similar across several animal species, presumably related to ancestral neural networks of command. A recurrent theme from comparative studies is that the developmental addition of new premotor modules underlies the postnatal acquisition and refinement of several different motor behaviors in vertebrates.
Sanchez, Ernesto; Tonda, Alberto
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
Simison, W. Brian; Boore, Jeffrey L.
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.
Kisdi, E; Geritz, S A
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.
Whiteson, S.; Wiering, M.; van Otterlo, M.
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,
Evolutionary genetics straddles the two fundamental processes of life, ... of the genus Drosophila have been used extensively as model systems in experimental ... issue will prove interesting, informative and thought-provoking for both estab-.
Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi
The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.
R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22
a need for a technique by which the robot is able to acquire new behaviours automatically .... Evolutionary robotics is a comparatively new field of robotics research, which seems to ..... Technical Report: PCIA-94-04, Institute of Psychology,.
Eastwick, Paul W.
Evolutionary psychologists explore the adaptive function of traits and behaviors that characterize modern Homo sapiens. However, evolutionary psychologists have yet to incorporate the phylogenetic relationship between modern Homo sapiens and humans' hominid and pongid relatives (both living and extinct) into their theorizing. By considering the…
Full Text Available Economic agents are not always rational or farsighted and can make decisions according to simple behavioral rules that vary according to situation and can be studied using the tools of evolutionary game theory. Furthermore, such behavioral rules are themselves subject to evolutionary forces. Paying particular attention to the work of young researchers, this essay surveys the progress made over the last decade towards understanding these phenomena, and discusses open research topics of importance to economics and the broader social sciences.
An evolutionary perspective on attachment theory and psychoanalytic theory brings these two fields together in interesting ways. Application of the evolutionary principle of parent-offspring conflict to attachment theory suggests that attachment styles represent context-sensitive, evolved (adaptive) behaviors. In addition, an emphasis on offspring counter-strategies to adult reproductive strategies leads to consideration of attachment styles as overt manifestations of psychodynamic mediating processes, including the defense mechanisms of repression and reaction formation.
Martinac, Boris; Kloda, Anna
According to the recent revision, the universal phylogenetic tree is composed of three domains: Eukarya (eukaryotes), Bacteria (eubacteria) and Archaea (archaebacteria). Mechanosensitive (MS) ion channels have been documented in cells belonging to all three domains suggesting their very early appearance during evolution of life on Earth. The channels show great diversity in conductance, selectivity and voltage dependence, while sharing the property of being gated by mechanical stimuli exerted on cell membranes. In prokaryotes, MS channels were first documented in Bacteria followed by their discovery in Archaea. The finding of MS channels in archaeal cells helped to recognize and establish the evolutionary relationship between bacterial and archaeal MS channels and to show that this relationship extends to eukaryotic Fungi (Schizosaccharomyces pombe) and Plants (Arabidopsis thaliana). Similar to their bacterial and archaeal homologues, MS channels in eukaryotic cell-walled Fungi and Plants may serve in protecting the cellular plasma membrane from excessive dilation and rupture that may occur during osmotic stress. This review summarizes briefly some of the recent developments in the MS channel research field that may ultimately lead to elucidation of the biophysical and evolutionary principles underlying the mechanosensory transduction in living cells.
Belkum, van A.; Struelens, M.; Visser, de J.A.G.M.; Verburgh, H.; Tibayrenc., M.
Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing
A.F. van Belkum (Alex); M. Struelens; A. de Visser (Arjan); H.A. Verbrugh (Henri); M. Tibayrench
textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and
Bocxlaer, Van B.; Strong, E.E.
The anatomy, functional morphology and evolutionary ecology of the Viviparidae, and the subfamily Bellamyinae in particular, are incompletely known. Partly as a result, genealogical relationships within the family remain poorly understood. Because of this lack in knowledge, few informed hypotheses
Aktipis, C Athena; Nesse, Randolph M
New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.
Cotton, James A; Lilley, Catherine J; Jones, Laura M; Kikuchi, Taisei; Reid, Adam J; Thorpe, Peter; Tsai, Isheng J; Beasley, Helen; Blok, Vivian; Cock, Peter J A; Eves-van den Akker, Sebastian; Holroyd, Nancy; Hunt, Martin; Mantelin, Sophie; Naghra, Hardeep; Pain, Arnab; Palomares-Rius, Juan E; Zarowiecki, Magdalena; Berriman, Matthew; Jones, John T; Urwin, Peter E
Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.
Vanee, Niti; Fisher, Adam B; Fong, Stephen S
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.
Full Text Available The low rates of regular exercise and overall physical activity (PA in the general population represent a significant public health challenge. Previous research suggests that, for many people, exercise leads to a negative affective response and, in turn, reduced likelihood of future exercise. The purpose of this paper is to examine this exercise-affect-adherence relationship from an evolutionary perspective. Specifically, we argue that low rates of physical exercise in the general population are a function of the evolved human tendency to avoid unnecessary physical exertion. This innate tendency evolved because it allowed our evolutionary ancestors to conserve energy for physical activities that had immediate adaptive utility such as pursuing prey, escaping predators, and engaging in social and reproductive behaviors. The commonly observed negative affective response to exercise is an evolved proximate psychological mechanism through which humans avoid unnecessary energy expenditure. The fact that the human tendencies toward negative affective response to and avoidance of unnecessary physical activities are innate does not mean that they are unchangeable. Indeed, it is only because of human-engineered changes in our environmental conditions (i.e., it is no longer necessary for us to work for our food that our predisposition to avoid unnecessary physical exertion has become a liability. Thus, it is well within our capabilities to reengineer our environments to once again make PA necessary or, at least, to serve an immediate functional purpose. We propose a two-pronged approach to PA promotion based on this evolutionary functional perspective: First, to promote exercise and other physical activities that are perceived to have an immediate purpose, and second, to instill greater perceived purpose for a wider range of physical activities. We posit that these strategies are more likely to result in more positive (or at least less negative affective
Full Text Available A brief discussion of the genesis of evolutionary computation methods, their relationship to artificial intelligence, and the contribution of genetics and Darwin’s theory of natural evolution is provided. Then, the main evolutionary computation methods are illustrated: evolution strategies, genetic algorithms, estimation of distribution algorithms, differential evolution, and a brief description of some evolutionary behavior methods such as ant colony and particle swarm optimization. We also discuss the role of the genetic algorithm for multivariate probability distribution random generation, rather than as a function optimizer. Finally, some relevant applications of genetic algorithm to statistical problems are reviewed: selection of variables in regression, time series model building, outlier identification, cluster analysis, design of experiments.
Cotton, James A
Background: Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. Results: We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. Conclusions: The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens. 2014 Cotton et al.; licensee BioMed Central Ltd.
Brewer, Michael J; Anderson, Darwin J; Armstrong, J Scott
Verde plant bugs, Creontiades signatus Distant (Hemiptera: Miridae), were released onto caged cotton, Cossypium hirsutum L., for a 1-wk period to characterize the effects of insect density and bloom period of infestation on cotton injury and yield in 2011 and 2012, Corpus Christi, TX. When plants were infested during early bloom (10-11 nodes above first white flower), a linear decline in fruit retention and boll load and a linear increase in boll injury were detected as verde plant bug infestation levels increased from an average of 0.5 to 4 bugs per plant. Lint and seed yield per plant showed a corresponding decline. Fruit retention, boll load, and yield were not affected on plants infested 1 wk later at peak bloom (8-9 nodes above first white flower), even though boll injury increased as infestation levels increased. Second-year testing verified boll injury but not yield loss, when infestations occurred at peak bloom. Incidence of cotton boll rot, known to be associated with verde plant bug feeding, was low to modest (verde plant bug were important contributors to yield decline, damage potential was greatest during the early bloom period of infestation, and a simple linear response best described the yield response-insect density relationship at early bloom. Confirmation that cotton after peak bloom was less prone to verde plant bug injury and an early bloom-specific economic injury level were key findings that can improve integrated pest management decision-making for dryland cotton, at least under low-rainfall growing conditions.
Brown, C. R.
Full Text Available The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demographic rates, such as survival, fecundity, and age of first breeding, and biologists from both fields have a vested interest in good analytical machinery for the estimation and analysis of these demographic rates. In the EURING conferences, we have been striving since the mid 1980s to promote a quantitative understanding of demographic rates through interdisciplinary collaboration between ecologists and statisticians. From the ecological side, the principal impetus has come from population biology, and in particular from wildlife biology, but the importance of good quantitative insights into demographic processes has long been recognized by a number of evolutionary biologists (e.g., Nichols & Kendall, 1995; Clobert, 1995; Cooch et al., 2002. In organizing this session, we have aimed to create a forum for those committed to gaining the best possible understanding of evolutionary processes through the application of modern quantitative methods for the collection and interpretation of data on marked animal populations. Here we present a short overview of the material presented in the session on evolutionary biology and life histories. In a plenary talk, Brown & Brown (2004 explored how mark–recapture methods have allowed a better understanding of the evolution of group–living and alternative reproductive tactics in colonial cliff swallows (Petrochelidon pyrrhonota. By estimating the number of transient birds passing through colonies of different sizes, they
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.
An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. Copyright © 2016 Elsevier Ltd. All rights reserved.
Ursem, Rasmus Kjær
Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...
Molecular networks act as the backbone of molecular activities within cells, offering a unique opportunity to better understand the mechanism of diseases. While network data usually constitute only static network maps, integrating them with time course gene expression information can provide clues to the dynamic features of these networks and unravel the mechanistic driver genes characterizing cellular responses. Time course gene expression data allow us to broadly "watch" the dynamics of the system. However, one challenge in the analysis of such data is to establish and characterize the interplay among genes that are altered at different time points in the context of a biological process or functional category. Integrative analysis of these data sources will lead us a more complete understanding of how biological entities (e.g., genes and proteins) coordinately perform their biological functions in biological systems. In this paper, we introduced a novel network-based approach to extract functional knowledge from time-dependent biological processes at a system level using time course mRNA sequencing data in zebrafish embryo development. The proposed method was applied to investigate 1α, 25(OH)2D3-altered mechanisms in zebrafish embryo development. We applied the proposed method to a public zebrafish time course mRNA-Seq dataset, containing two different treatments along four time points. We constructed networks between gene ontology biological process categories, which were enriched in differential expressed genes between consecutive time points and different conditions. The temporal propagation of 1α, 25-Dihydroxyvitamin D3-altered transcriptional changes started from a few genes that were altered initially at earlier stage, to large groups of biological coherent genes at later stages. The most notable biological processes included neuronal and retinal development and generalized stress response. In addition, we also investigated the relationship among
Han, Mira V; Zmasek, Christian M
Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org.
Neil W. Blackstone
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.
This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…
This paper engages with the methodological debate on the contribution of Darwinism to Veblen's (1898) evolutionary research program for economics. I argue that ontological continuity, generalized Darwinism, and multi-level selection are necessary building blocks for an explanatory framework that can
Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 7. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology. Renee M Borges. General Article Volume 10 Issue 7 July 2005 pp 21-33. Fulltext. Click here to view fulltext PDF. Permanent link:
Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Evolutionary Biology Research in India. Information and Announcements Volume 5 Issue 10 October 2000 pp 102-104. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/005/10/0102-0104 ...
Against recent attempts to forge a reconciliation between constructionism and realism, I contend that, in psychology at least, stirring up conflict is a more fruitful strategy. To illustrate this thesis, I confront a school of psychology with strong realist leanings, evolutionary psychology, with
Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando
Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleo...
Prins, J.C.P.; Smant, G.; Jansen, R.C.
Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome
Carr, Catherine E; Christensen-Dalsgaard, Jakob
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...
Carlo Alberto Redi
Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....
Nov 24, 2017 ... q(t) of an allele at a locus among the gametes produced at time t, to its .... the importance of disease as an evolutionary factor, which is now a ..... VII. Selection intensity as a function of mortality rate. Proc. Camb. Philos. Soc.
Brodal, Gerth Sølfting; Fagerberg, Rolf; Pedersen, Christian Nørgaard Storm
Evolutionary trees describing the relationship for a set of species are central in evolutionary biology, and quantifying differences between evolutionary trees is therefore an important task. The quartet distance is a distance measure between trees previously proposed by Estabrook, McMorris, and ...... unrooted evolutionary trees of n species, where all internal nodes have degree three, in time O(n log n. The previous best algorithm for the problem uses time O(n 2).......Evolutionary trees describing the relationship for a set of species are central in evolutionary biology, and quantifying differences between evolutionary trees is therefore an important task. The quartet distance is a distance measure between trees previously proposed by Estabrook, Mc......Morris, and Meacham. The quartet distance between two unrooted evolutionary trees is the number of quartet topology differences between the two trees, where a quartet topology is the topological subtree induced by four species. In this paper we present an algorithm for computing the quartet distance between two...
Steele, James; Jordan, Peter; Cochrane, Ethan
Evolutionary approaches to cultural change are increasingly influential, and many scientists believe that a 'grand synthesis' is now in sight. The papers in this Theme Issue, which derives from a symposium held by the AHRC Centre for the Evolution of Cultural Diversity (University College London) in December 2008, focus on how the phylogenetic tree-building and network-based techniques used to estimate descent relationships in biology can be adapted to reconstruct cultural histories, where some degree of inter-societal diffusion will almost inevitably be superimposed on any deeper signal of a historical branching process. The disciplines represented include the three most purely 'cultural' fields from the four-field model of anthropology (cultural anthropology, archaeology and linguistic anthropology). In this short introduction, some context is provided from the history of anthropology, and key issues raised by the papers are highlighted.
Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt
Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.
Applied Evolutionary Economics and Economic Geography" aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and
... and Evolutionary Dynamics of Pathogens * 21 Keith A. Crandall and Marcos Pérez-Losada II. Evolutionary Genetics of Microbial Pathogens 4. Environmental and Social Influences on Infectious Disea...
The aim of the study was to report an evolutionary concept analysis of faith community nursing (FCN). FCN is a source of healthcare delivery in the USA which has grown in comprehensiveness and complexity. With increasing healthcare cost and a focus on access and prevention, FCN has extended beyond the physical walls of the faith community building. Faith communities and healthcare organizations invest in FCN and standardized training programs exist. Using Rodgers' evolutionary analysis, the literature was examined for antecedents, attributes, and consequences of the concept. This design allows for understanding the historical and social nature of the concept and how it changes over time. A search of databases using the keywords FCN, faith community nurse, parish nursing, and parish nurse was done. The concept of FCN was explored using research and theoretical literature. A theoretical definition and model were developed with relevant implications. The search results netted a sample of 124 reports of research and theoretical articles from multiple disciplines: medicine, education, religion and philosophy, international health, and nursing. Theoretical definition: FCN is a method of healthcare delivery that is centered in a relationship between the nurse and client (client as person, family, group, or community). The relationship occurs in an iterative motion over time when the client seeks or is targeted for wholistic health care with the goal of optimal wholistic health functioning. Faith integrating is a continuous occurring attribute. Health promoting, disease managing, coordinating, empowering and accessing health care are other essential attributes. All essential attributes occur with intentionality in a faith community, home, health institution and other community settings with fluidity as part of a community, national, or global health initiative. A new theoretical definition and corresponding conceptual model of FCN provides a basis for future nursing
Life stage-specific effects of the fungicide pyrimethanil and temperature on the snail Physella acuta (Draparnaud, 1805) disclose the pitfalls for the aquatic risk assessment under global climate change
Seeland, Anne; Albrand, Jennifer; Oehlmann, Jörg; Müller, Ruth
It can be suggested that the combined stress of pesticide pollution and suboptimal temperature influences the sensitivity of life stages of aquatic invertebrates differently. The embryo, juvenile, half- and full-life-cycle toxicity tests performed with the snail Physella acuta at different concentrations (0.06–0.5 or 1.0 mg L −1 ) of the model fungicide pyrimethanil at 15, 20 and 25 °C revealed, that pyrimethanil caused concentration-dependent effects at all test temperatures. Interestingly, the ecotoxicity of pyrimethanil was higher at lower (suboptimal) temperature for embryo hatching and F 1 reproduction, but its ecotoxicity for juvenile growth and F 0 reproduction increased with increasing temperature. The life-stage specific temperature-dependent ecotoxicity of pyrimethanil and the high fungicide susceptibility of the invasive snail clearly demonstrate the complexity of pesticide–temperature interactions and the challenge to draw conclusions for the risk of pesticides under the impact of global climate change. -- Highlights: ► Physella acuta reacts highly sensitively to exposure to pyrimethanil. ► The ecotoxicity of pyrimethanil is life-stage specific. ► Pyrimethanil and temperature stress influenced the development interactively. -- The aquatic risk of pesticides under climate change cannot be adequately assessed by recent strategies for the regular risk assessment of agrochemicals
Vale, Pedro F.; Wilson, Alastair J.; Best, Alex; Boots, Mike; Little, Tom J.
Victims of infection are expected to suffer increasingly as parasite population growth increases. Yet, under some conditions, faster growing parasites do not appear to cause more damage and infections can be quite tolerable. We studied these conditions by assessing how the relationship between parasite population growth and host health is sensitive to environmental variation. In experimental infections of the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa we show how easily an interaction can shift from a severe interaction, i.e. when host fitness declines substantially with each unit of parasite growth, to a tolerable relationship by changing only simple environmental variables: temperature and food availability. We explored the evolutionary and epidemiological implications of such a shift by modelling pathogen evolution and disease spread under different levels of infection severity, and find that environmental shifts that promote tolerance ultimately result in populations harbouring more parasitized individuals. We also find that the opportunity for selection, as indicated by the variance around traits, varied considerably with the environmental treatment. Thus our results suggest two mechanisms that could underlie co-evolutionary hot- and coldspots: spatial variation in tolerance and spatial variation in the opportunity for selection. PMID:21460572
Dolfsma, Wilfred; Leydesdorff, Loet
Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal
Evolutionary game theory has been viewed as an evolutionary repair of rational actor game theory in the hope that a population of boundedly rational players may attain convergence to classic rational solutions, such as the Nash Equilibrium, via some learning or evolutionary process. In this thesis
Zhu, Xuli; Jiang, Libo; Ye, Meixia; Sun, Lidan; Gragnoli, Claudia; Wu, Rongling
Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation. Copyright © 2016 Elsevier Ltd. All rights reserved.
Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón
Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.
Full Text Available As predicted by evolutionary economics, historical antecedents matter when it comes to the relationship between survival of entrants and organizational capabilities. Spinoff firms provide an exemplary case of such relationship where the founders’ pre-entry capabilities that are inherited from the parent firm increases their survival chances. Looking closer and deeper to the evolutionary spinoff success mechanisms, I examine three specific genetic features which make spinoff firms more advantageous compared to other entrants; namely 1 Genotype: Transfer of blueprint, 2 Phenotype: Organizational learning, and 3 Memes: Informal relations and social capital. A detailed theoretical analysis of each mechanism prevails how they function and provide sustainable competitive advantage to spinoff firms. Testable hypotheses are provided about each mechanism.
Dimopoulos, Christos; Papageorgis, Panagiotis; Boustras, George; Efstathiades, Christodoulos
This paper discusses the concept of ageing as this applies to the operation of Evolutionary Algorithms, and examines its relationship to the concept of ageing as this is understood for human beings. Evolutionary Algorithms constitute a family of search algorithms which base their operation on an analogy from the evolution of species in nature. The paper initially provides the necessary knowledge on the operation of Evolutionary Algorithms, focusing on the use of ageing strategies during the implementation of the evolutionary process. Background knowledge on the concept of ageing, as this is defined scientifically for biological systems, is subsequently presented. Based on this information, the paper provides a comparison between the two ageing concepts, and discusses the philosophical inspirations which can be drawn for human ageing based on the operation of Evolutionary Algorithms. Copyright © 2017 Elsevier B.V. All rights reserved.
First we introduce a simple model for the description of evolutionary algorithms, which is based on 2nd order partial differential equations for the distribution function of the individuals. Then we turn to the properties of Boltzmann's and Darwin's strategy. the next chapter is dedicated to the mathematical properties of Schroedinger operators. Both statements on the spectral density and their reproducibility during the simulation are summarized. The remaining of this chapter are dedicated to the analysis of the kernel as well as the dependence of the Schroedinger operator on the potential. As conclusion from the results of this chapter we obtain the classification of the strategies in dependence of the fitness. We obtain the classification of the evolutionary strategies, which are described by a 2nd order partial differential equation, in relation to their solution behaviour. Thereafter we are employed with the variation of the mutation distribution
Frederiksen, Peter; Jagtfelt, Tue
This article attempts to solve current problems of conceptual fragmentation within the field of evolutionary economics. One of the problems, as noted by a number of observers, is that the field suffers from an assemblage of fragmented and scattered concepts (Boschma and Martin 2010). A solution...... to this problem is proposed in the form of a model of exponential expansion. The model outlines the overall structure and function of the economy as exponential expansion. The pictographic model describes four axiomatic concepts and their exponential nature. The interactive, directional, emerging and expanding...... concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light...
Hochberg, Michael E; Thomas, Frédéric; Assenat, Eric; Hibner, Urszula
Evolutionary theory predicts that once an individual reaches an age of sufficiently low Darwinian fitness, (s)he will have reduced chances of keeping cancerous lesions in check. While we clearly need to better understand the emergence of precursor states and early malignancies as well as their mitigation by the microenvironment and tissue architecture, we argue that lifestyle changes and preventive therapies based in an evolutionary framework, applied to identified high-risk populations before incipient neoplasms become clinically detectable and chemoresistant lineages emerge, are currently the most reliable way to control or eliminate early tumours. Specifically, the relatively low levels of (epi)genetic heterogeneity characteristic of many if not most incipient lesions will mean a relatively limited set of possible adaptive traits and associated costs compared to more advanced cancers, and thus a more complete and predictable understanding of treatment options and outcomes. We propose a conceptual model for preventive treatments and discuss the many associated challenges.
Park, Shinkyu; Shamma, Jeff S.; Martins, Nuno C.
This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.
This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.
The morphological diversity of viruses which parasitize hyperthermophilic archaea thriving at temperatures > or = 80 degrees C appears to exceed that of viruses of prokaryotes living at lower temperatures. Based on assumptions of the existence of viruses in the prebiotic phase of evolution and hot origins of cellular life, we suggest that this remarkable diversity could have its source in ancestral diversity of viral morphotypes in hot environments. Attempts are made to trace evolutionary relationships of viruses of hyperthermophilic archaea with other viruses.
Love, Alan C
This paper focuses on abstraction as a mode of reasoning that facilitates a productive relationship between philosophy and science. Using examples from evolutionary developmental biology, I argue that there are two areas where abstraction can be relevant to science: reasoning explication and problem clarification. The value of abstraction is characterized in terms of methodology (modeling or data gathering) and epistemology (explanatory evaluation or data interpretation).
Pubertal development is subject to substantial heritability, but much variation remains to be explained, including fast changes over the last 150 years, that cannot be explained by changes of gene frequency in the population. This article discusses the influence of environmental factors to adjust maturational tempo in the service of fitness goals. Utilizing evolutionary development thinking (evo-devo), the author examines adolescence as an evolutionary life-history stage in its developmental context. The transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, social needs of adolescence and maturation toward youth and adulthood. Using Belsky's evolutionary theory of socialization, I show that familial psychosocial environment during the infancy-childhood and childhood-juvenility transitions foster a fast life-history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. The implications of the evo-devo framework for theory building, illuminates new directions in the understanding of precocious puberty other than a diagnosis of a disease.
David F. Bjorklund
Full Text Available Developmental thinking is gradually becoming integrated within mainstream evolutionary psychology. This is most apparent with respect to the role of parenting, with proponents of life history theory arguing that cognitive and behavioral plasticity early in life permits children to select different life history strategies, with such strategies being adaptive solutions to different fitness trade-offs. I argue that adaptations develop and are based on the highly plastic nature of infants’ and children’s behavior/cognition/brains. The concept of evolved probabilistic cognitive mechanisms is introduced, defined as information processing mechanisms evolved to solve recurrent problems faced by ancestral populations that are expressed in a probabilistic fashion in each individual in a generation and are based on the continuous and bidirectional interaction over time at all levels of organization, from the genetic through the cultural. Early perceptual/cognitive biases result in behavior that, when occurring in a species-typical environment, produce continuous adaptive changes in behavior (and cognition, yielding adaptive outcomes. Examples from social learning and tool use are provided, illustrating the development of adaptations via evolved probabilistic cognitive mechanisms. The integration of developmental concepts into mainstream evolutionary psychology (and evolutionary concepts into mainstream developmental psychology will provide a clearer picture of what it means to be human.
Chela-Flores, Julian [Instituto de Estudios Avanzados, Caracas (Venezuela); [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)
A major objective in solar system exploration is the insertion of appropriate biology-oriented experiments in future missions. We discuss various reasons for suggesting that this type of research be considered a high priority for feasibility studies and, subsequently, for technological development of appropriate melters and submersibles. Based on numerous examples, we argue in favour of the assumption that Darwin's theory is valid for the evolution of life anywhere in the universe. We have suggested how to obtain preliminary insights into the question of the distribution of life in the universe. Universal evolution of intelligent behaviour is at the end of an evolutionary pathway, in which evolution of ion channels in the membrane of microorganisms occurs in its early stages. Further, we have argued that a preliminary test of this conjecture is feasible with experiments on the Europan surface or ocean, involving evolutionary biosignatures (ion channels). This aspect of the exploration for life in the solar system should be viewed as a complement to the astronomical approach for the search of evidence of the later stages of the evolutionary pathways towards intelligent behaviour. (author)
Dennehy, John J
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. © 2016 New York Academy of Sciences.
Miyazaki, Jun-Ichi; de Oliveira Martins, Leonardo; Fujita, Yuko; Matsumoto, Hiroto; Fujiwara, Yoshihiro
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. 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. 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 symbiosis in that nutritional adaptation to the deep sea proceeded from extracellular
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
Full Text Available What kind mechanisms one deems central for the evolutionary process deeply influences one’s understanding of the nature of organisms, including cognition. Reversely, adopting a certain approach to the nature of life and cognition and the relationship between them or between the organism and its environment should affect one’s view of evolutionary theory. This paper explores this reciprocal relationship in more detail. In particular it argues that the view of living and cognitive systems, especially humans, as deeply integrated beings embedded in and transformed by their genetic, epigenetic (molecular and cellular, behavioral, ecological, socio-cultural and cognitive-symbolic legacies calls for an extended evolutionary synthesis that goes beyond either a theory of genes juxtaposed against a theory of cultural evolution and or even more sophisticated theories of gene-culture coevolution and niche construction. Environments, particularly in the form of developmental environments, do not just select for variation, they also create new variation by influencing development through the reliable transmission of non-genetic but heritable information. This paper stresses particularly views of embodied, embedded, enacted and extended cognition, and their relationship to those aspects of extended inheritance that lie between genetic and cultural inheritance, the still grey area of epigenetic and behavioral inheritance systems that play a role in parental effect. These are the processes that can be regarded as transgenerational developmental plasticity and that I think can most fruitfully contribute to, and be investigated by, developmental psychology.
What kind mechanisms one deems central for the evolutionary process deeply influences one's understanding of the nature of organisms, including cognition. Reversely, adopting a certain approach to the nature of life and cognition and the relationship between them or between the organism and its environment should affect one's view of evolutionary theory. This paper explores this reciprocal relationship in more detail. In particular it argues that the view of living and cognitive systems, especially humans, as deeply integrated beings embedded in and transformed by their genetic, epigenetic (molecular and cellular), behavioral, ecological, socio-cultural and cognitive-symbolic legacies calls for an extended evolutionary synthesis that goes beyond either a theory of genes juxtaposed against a theory of cultural evolution and or even more sophisticated theories of gene-culture coevolution and niche construction. Environments, particularly in the form of developmental environments, do not just select for variation, they also create new variation by influencing development through the reliable transmission of non-genetic but heritable information. This paper stresses particularly views of embodied, embedded, enacted and extended cognition, and their relationship to those aspects of extended inheritance that lie between genetic and cultural inheritance, the still gray area of epigenetic and behavioral inheritance systems that play a role in parental effect. These are the processes that can be regarded as transgenerational developmental plasticity and that I think can most fruitfully contribute to, and be investigated by, developmental psychology.
Lei, Yutian; Anders, Hans-Joachim
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.
Orive, Maria E; Barfield, Michael; Fernandez, Carlos; Holt, Robert D
Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a population's rate of evolution and evolutionary lag is unknown. Effects of clonal reproduction on mean phenotype partition into two portions: one that is phenotype dependent, and another that is genotype dependent. This partitioning is governed by the association between the nonadditive genetic plus random environmental component of phenotype of clonal offspring and their parents. While clonality slows phenotypic evolution toward an optimum, it can dramatically increase population survival after a sudden step change in optimal phenotype. Increased adult survival slows phenotypic evolution but facilitates population survival after a step change; this positive effect can, however, be lost given survival-fecundity trade-offs. Simulations indicate that the benefits of increased clonality under environmental change greatly depend on the nature of that change: increasing population persistence under a step change while decreasing population persistence under a continuous linear change requiring de novo variation. The impact of clonality on the probability of persistence for species in a changing world is thus inexorably linked to the temporal texture of the change they experience.
K.D. Klepzig; A.S. Adams; J. Handelsman; K.F. Raffa
Symbiosis is receiving increased attention among all aspects of biology because of the unifying themes it helps construct across ecological,evolutionary, developmental, semiochemical, and pest management theory. Insects show a vast array of symbiotic relationships with a wide diversity of microorganisms. These relationships may confer a variety of benefits to the host...
Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.
Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.
Krześlak, Michał; Świerniak, Andrzej
The goal of this paper is to study the classical hawk-dove model using mixed spatial evolutionary games (MSEG). In these games, played on a lattice, an additional spatial layer is introduced for dependence on more complex parameters and simulation of changes in the environment. Furthermore, diverse polymorphic equilibrium points dependent on cell reproduction, model parameters, and their simulation are discussed. Our analysis demonstrates the sensitivity properties of MSEGs and possibilities for further development. We discuss applications of MSEGs, particularly algorithms for modelling cell interactions during the development of tumours. Copyright © 2015 Elsevier Ltd. All rights reserved.
This Section of Australian Feminist Studies is the product of an event that took place at King’s College London in January 2015, hosted as part of the UK-based ‘Critical Sexology’ seminar series. Participants at this event – feminist scholars working across the fields of lin- guistics, cultural studies, sociology, and psychology – were invited to reflect on their encounters with evolutionary psychology (EP). As the event organiser, I was interested to prompt a discussion about how EP shapes t...
Clancy, Thomas R
As systems evolve over time, their natural tendency is to become increasingly more complex. Studies on complex systems have generated new perspectives on management in social organizations such as hospitals. Much of this research appears as a natural extension of the cross-disciplinary field of systems theory. This is the 18th in a series of articles applying complex systems science to the traditional management concepts of planning, organizing, directing, coordinating, and controlling. In this article, I discuss methods to optimize complex healthcare processes through learning, adaptation, and evolutionary planning.
Masters, Roger D
Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological
Laland, Kevin N; Odling-Smee, John; Feldman, Marcus W; Kendal, Jeremy
In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, "niche construction". This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.
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...
Szabó, György; Borsos, István
Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.
Szabó, György, E-mail: email@example.com; Borsos, István, E-mail: firstname.lastname@example.org
Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.
Full Text Available Mechanisms of self-destruction are difficult to reconcile with evolution’s first rule of thumb: survive and reproduce. However, evolutionary success ultimately depends on inclusive fitness. The altruistic suicide hypothesis posits that the presence of low reproductive potential and burdensomeness toward kin can increase the inclusive fitness payoff of self-removal. The bargaining hypothesis assumes that suicide attempts could function as an honest signal of need. The payoff may be positive if the suicidal person has a low reproductive potential. The parasite manipulation hypothesis is founded on the rodent—Toxoplasma gondii host-parasite model, in which the parasite induces a “suicidal” feline attraction that allows the parasite to complete its life cycle. Interestingly, latent infection by T. gondii has been shown to cause behavioral alterations in humans, including increased suicide attempts. Finally, we discuss how suicide risk factors can be understood as nonadaptive byproducts of evolved mechanisms that malfunction. Although most of the mechanisms proposed in this article are largely speculative, the hypotheses that we raise accept self-destructive behavior within the framework of evolutionary theory.
Szabó, György; Borsos, István
Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the "equilibrium state" by adding non-potential components representing games of cyclic dominance.
Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando; Welker, Frido; Pedersen, Mikkel Winther; Allentoft, Morten E; de Barros Damgaard, Peter; Gutenbrunner, Petra; Dunne, Julie; Hammann, Simon; Roffet-Salque, Mélanie; Ilardo, Melissa; Moreno-Mayar, J Víctor; Wang, Yucheng; Sikora, Martin; Vinner, Lasse; Cox, Jürgen; Evershed, Richard P; Willerslev, Eske
Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
The concept of evolutionary development of structures constituted a real revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of such systems has shown that indeed, systems under a flux of energy or matter can self-organize into complex patterns, think for instance to Rayleigh-Bernard convection, Liesegang rings, patterns formed by granular systems under shear. Following this line, one could characterize life as a state of matter, characterized by the slow, continuous process that we call evolution. In this paper we try to identify the organizational level of life, that spans several orders of magnitude from the elementary constituents to whole ecosystems. Although similar structures can be found in other contexts like ideas (memes) in neural systems and self-replicating elements (computer viruses, worms, etc.) in computer systems, we shall concentrate on biological evolutionary structure, and try to put into evidence the role and the emergence of network structure in such systems.
Zu, Jian; Yuan, Bo; Du, Jianqiang
We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator׳s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.
Van Vugt, Mark
Responds to comments made by George B. Graen and Stephen J. Guastello on the current author's article Leadership, followership, and evolution: Some lessons from the past by Van Vugt, Hogan, and Kaiser. In the original article my co-authors and I proposed a new way of thinking about leadership, informed by evolutionary (neo-Darwinian) theory. In the first commentary, Graen noted that we ignored a number of recently developed psychological theories of leadership that take into account the leader-follower relationship, most notably LMX theory. LMX theory asserts that leadership effectiveness and team performance are affected by the quality of working relationships between superior and subordinates. Because the original article primarily dealt with questions about the origins of leadership--the phylogenetic and evolutionary causes--we had to be concise in our review of proximate psychological theories of leadership. In the second commentary, Guastello concurred with the importance of an evolutionary game analysis for studying leadership but disagreed with certain details of our analysis. (PsycINFO Database Record (c) 2009 APA, all rights reserved).
The key idea of this model is that firms are the result of an evolutionary process. Based on demand and supply considerations the evolutionary model presented here derives explicitly Gibrat's law of proportionate effects as the result of the competition between products. Applying a preferential attachment mechanism for firms, the theory allows to establish the size distribution of products and firms. Also established are the growth rate and price distribution of consumer goods. Taking into account the characteristic property of human activities to occur in bursts, the model allows also an explanation of the size-variance relationship of the growth rate distribution of products and firms. Further the product life cycle, the learning (experience) curve and the market size in terms of the mean number of firms that can survive in a market are derived. The model also suggests the existence of an invariant of a market as the ratio of total profit to total revenue. The relationship between a neo-classic and an evolutionary view of a market is discussed. The comparison with empirical investigations suggests that the theory is able to describe the main stylized facts concerning the size and growth of firms.
Goldie, Xavier; Gillman, Len; Crisp, Mike; Wright, Shane
The covariation of biodiversity with climate is a fundamental pattern in nature. However, despite the ubiquity of this relationship, a consensus on the ultimate cause remains elusive. The evolutionary speed hypothesis posits direct mechanistic links between ambient temperature, the tempo of micro-evolution and, ultimately, species richness. Previous research has demonstrated faster rates of molecular evolution in warmer climates for a broad range of poikilothermic and homeothermic organisms, in both terrestrial and aquatic environments. In terrestrial systems, species richness increases with both temperature and water availability and the interaction of those terms: productivity. However, the influence of water availability as an independent variable on micro-evolutionary processes has not been examined previously. Here, using methodology that limits the potentially confounding role of cladogenetic and demographic processes, we report, to our knowledge, the first evidence that woody plants living in the arid Australian Outback are evolving more slowly than related species growing at similar latitudes in moist habitats on the mesic continental margins. These results support a modified evolutionary speed explanation for the relationship between the water-energy balance and plant diversity patterns.
P Cooke; M G Uranga; G Etxebarria
The authors develop the concept of regional systems of innovation and relate it to preexisting research on national systems of innovation. They argue that work conducted in the 'new regional science' field is complementary to systems of innovation approaches. They seek to link new regional work to evolutionary economics, and argue for the development of evolutionary regional science. Common elements of interest to evolutionary innovation research and new regional science are important in unde...
.... NSS Acquisition Policy 03-01 provided some space-oriented customization and, similarly to the original DOD directives, also positioned Evolutionary Acquisition and Spiral Development as preferred...
Mills, E. N. C.; Madsen, Charlotte Bernhard; Shewry, P. R.
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...
site-encoding disease-resistance gene analogues in sweet potato. (Ipomoea batatas Lam.) ... terminal domain of the protein, this class of R-genes can be subdivided into TIR ... from young leaflets using the modified 2.0% (w/v) cetyl trimethyl ...
@@ With 230 species throughout tropical and subtropical Asia, Alpinia is the largest, most widespread and most taxonomically complex genus in the ginger family (Zingiberaceae). Species of Alpinia often predominate in the understory of forests, and some of them are important ornamentals and medicinals. By using DNA-sequence-based methods, Prof. Li Qingjun from the CASXishuangbanna Tropical Botanical Garden and his collaborators from the US National Museum of Natural History and UK Royal Botanic Garden have set up the monophyly of the genus. Their work is highlighted on the cover of the first issue of American Journal of Botany in 2005.
llozymes in bud tissue and monoterpene contents in xylem oleoresin of slash pine (Pinus elliottii) were analyzed from populations across the natural distribution, as well as those from other species in the AUSTRALES pines. Allozyme diversity measures of slash pine were similar to those found in other southern pines.
Mills, E.N.C.; Madsen, C.; Shewry, P.R.; Wichers, H.J.
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
Jensen, Jens Ledet
This paper is about stochastic models for the evolution of DNA. For a set of aligned DNA sequences, connected in a phylogenetic tree, the models should be able to explain - in probabilistic terms - the differences seen in the sequences. From the estimates of the parameters in the model one can...... start to make biologically interpretations and conclusions concerning the evolutionary forces at work. In parallel with the increase in computing power, models have become more complex. Starting with Markov processes on a space with 4 states, and extended to Markov processes with 64 states, we are today...... studying models on spaces with 4n (or 64n) number of states with n well above one hundred, say. For such models it is no longer possible to calculate the transition probability analytically, and often Markov chain Monte Carlo is used in connection with likelihood analysis. This is also the approach taken...
Torday, J S
Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.
Ottino-Loffler, Bertrand; Scott, Jacob G; Strogatz, Steven H
The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.
Hansen, Pelle Guldborg
-defined metaphors of individual learning and social imitation processes, from which a revised theory of convention may be erected (see Sugden 2004, Binmore 1993 and Young 1998). This paper makes a general argument in support of the evolutionary turn in the theory of convention by a progressive exposition of its...... in Aumann (1976) and which, together with the assumptions of perfect rationality, came to be defining of classical game theory. However, classical game theory is currently undergoing severe crisis as a tool for exploring social phenomena; a crisis emerging from the problem of equilibrium selection around......Some thirty years ago Lewis published his Convention: A Philosophical Study (Lewis, 2002). This laid the foundation for a game-theoretic approach to social conventions, but became more famously known for its seminal analysis of common knowledge; the concept receiving its canonical analysis...
Doolittle, Russell F.; York, Amanda L.
According to the conventional wisdom, the existence of a cytoskeleton in eukaryotes and its absence in prokaryotes constitute a fundamental divide between the two domains of life. An integral part of the dogma is that a cytoskeleton enabled an early eukaryote to feed upon prokaryotes, a consequence of which was the occasional endosymbiosis and the eventual evolution of organelles. Two recent papers present compelling evidence that actin, one of the principal components of a cytoskeleton, has a homolog in Bacteria that behaves in many ways like eukaryotic actin. Sequence comparisons reveml that eukaryotic actin and the bacterial homolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories.
Münch, Philipp C.; Stecher, Bärbel; McHardy, Alice C.
Abstract Summary Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses. Availability and implementation EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden. Contact email@example.com Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637301
Luca, F; Perry, G H; Di Rienzo, A
Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.
If thermodynamics is to physics as logic is to philosophy, recent theoretical advancements lend new coherence to the marvel and dynamism of life on Earth. Enzo Tiezzi's "Steps Towards an Evolutionary Physics" is a primer and guide, to those who would to stand on the shoulders of giants to attain this view: Heisenberg, Planck, Bateson, Varela, and Prigogine as well as notable contemporary scientists. The adventure of such a free and enquiring spirit thrives not so much on answers as on new questions. The book offers a new gestalt on the uncertainty principle and concept of probability. A wide range of examples, enigmas, and paradoxes lead one's imagination on an exquisite dance. Among the applications are: songs and shapes of nature, oscillatory reactions, orientors, goal functions and configurations of processes, and "dissipative structures and the city". Ecodynamics is a new science, which proposes a cross-fertilization between Charles Darwin and Ilya Prigogine. As an enigma in thermodynamics, Entropy forms ...
Trujillo, Leonardo; Legrand, Pierrick; Maldonado, Yazmin
This volume comprises a selection of works presented at the Numerical and Evolutionary Optimization (NEO) workshop held in September 2015 in Tijuana, Mexico. The development of powerful search and optimization techniques is of great importance in today’s world that requires researchers and practitioners to tackle a growing number of challenging real-world problems. In particular, there are two well-established and widely known fields that are commonly applied in this area: (i) traditional numerical optimization techniques and (ii) comparatively recent bio-inspired heuristics. Both paradigms have their unique strengths and weaknesses, allowing them to solve some challenging problems while still failing in others. The goal of the NEO workshop series is to bring together people from these and related fields to discuss, compare and merge their complimentary perspectives in order to develop fast and reliable hybrid methods that maximize the strengths and minimize the weaknesses of the underlying paradigms. Throu...
Markov networks and other probabilistic graphical modes have recently received an upsurge in attention from Evolutionary computation community, particularly in the area of Estimation of distribution algorithms (EDAs). EDAs have arisen as one of the most successful experiences in the application of machine learning methods in optimization, mainly due to their efficiency to solve complex real-world optimization problems and their suitability for theoretical analysis. This book focuses on the different steps involved in the conception, implementation and application of EDAs that use Markov networks, and undirected models in general. It can serve as a general introduction to EDAs but covers also an important current void in the study of these algorithms by explaining the specificities and benefits of modeling optimization problems by means of undirected probabilistic models. All major developments to date in the progressive introduction of Markov networks based EDAs are reviewed in the book. Hot current researc...
Wolf Yuri I
Full Text Available Abstract Background The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria and eukaryotic mitochondria and chloroplasts and V-type (found in archaea, some bacteria, and eukaryotic vacuoles ATPases can translocate either protons or sodium ions. The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments. Results We combine structural and phylogenetic analyses to clarify the evolutionary relation between the proton- and sodium-translocating ATPases. A comparison of the structures of the membrane-embedded oligomeric proteolipid rings of sodium-dependent F- and V-ATPases reveals nearly identical sets of amino acids involved in sodium binding. We show that the sodium-dependent ATPases are scattered among proton-dependent ATPases in both the F- and the V-branches of the phylogenetic tree. Conclusion Barring convergent emergence of the same set of ligands in several lineages, these findings indicate that the use of sodium gradient for ATP synthesis is the ancestral modality of membrane bioenergetics. Thus, a primitive, sodium-impermeable but proton-permeable cell membrane that harboured a set of sodium-transporting enzymes appears to have been the evolutionary predecessor of the more structurally demanding proton-tight membranes. The use of proton as the coupling ion appears to be a later innovation that emerged on several independent occasions. Reviewers This article was reviewed by J. Peter Gogarten, Martijn A. Huynen, and Igor B. Zhulin. For the full reviews, please go to the Reviewers' comments section.
Sun, Wei; Yu, Hongsong; Shen, Yihong; Banno, Yutaka; Xiang, Zhonghuai; Zhang, Ze
The silkworm, Bombyx mori, played an important role in the old Silk Road that connected ancient Asia and Europe. However, to date, there have been few studies of the origins and domestication of this species using molecular methods. In this study, DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives. All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm. Domestication was estimated to have occurred about 4100 years ago (ya), and the radiation of the different geographic strains of B. mori about 2000 ya. The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya. These estimates are in good agreement with the fossil evidence and historical records. In addition, we show that the domesticated silkworm experienced a population expansion around 1000 ya. The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics, in the genetic analysis of domestic animals, and for understanding the spread of human civilizations.
N. Onur Sönmez
Full Text Available In its parallel pursuit of an increased competitivity for design offices and more pleasurable and easier workflows for designers, artificial design intelligence is a technical, intellectual, and political challenge. While human-machine cooperation has become commonplace through Computer Aided Design (CAD tools, a more improved collaboration and better support appear possible only through an endeavor into a kind of artificial design intelligence, which is more sensitive to the human perception of affairs. Considered as part of the broader Computational Design studies, the research program of this quest can be called Artificial / Autonomous / Automated Design (AD. The current available level of Artificial Intelligence (AI for design is limited and a viable aim for current AD would be to develop design assistants that are capable of producing drafts for various design tasks. Thus, the overall aim of this thesis is the development of approaches, techniques, and tools towards artificial design assistants that offer a capability for generating drafts for sub-tasks within design processes. The main technology explored for this aim is Evolutionary Computation (EC, and the target design domain is architecture. The two connected research questions of the study concern, first, the investigation of the ways to develop an architectural design assistant, and secondly, the utilization of EC for the development of such assistants. While developing approaches, techniques, and computational tools for such an assistant, the study also carries out a broad theoretical investigation into the main problems, challenges, and requirements towards such assistants on a rather overall level. Therefore, the research is shaped as a parallel investigation of three main threads interwoven along several levels, moving from a more general level to specific applications. The three research threads comprise, first, theoretical discussions and speculations with regard to both
The material collected in this volume discusses the present as well as expected future directions of development of the field with particular emphasis on applications. The seven survey articles present different topics in Evolutionary PDE's, written by leading experts.- Review of new results in the area- Continuation of previous volumes in the handbook series covering Evolutionary PDEs- Written by leading experts
Evolutionary games have considerable unrealized potential for modeling substantive economic issues. They promise richer predictions than orthodox game models but often require more extensive specifications. This paper exposits the specification of evolutionary game models and classifies the possible asymptotic behavior for one and two dimensional models.
Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P
Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.
In this article, I argue that distinguishing 'evolutionary' from 'Darwinian' medicine will help us assess the variety of roles that evolutionary explanations can play in a number of medical contexts. Because the boundaries of evolutionary and Darwinian medicine overlap to some extent, however, they are best described as distinct 'research traditions' rather than as competing paradigms. But while evolutionary medicine does not stand out as a new scientific field of its own, Darwinian medicine is united by a number of distinctive theoretical and methodological claims. For example, evolutionary medicine and Darwinian medicine can be distinguished with respect to the styles of evolutionary explanations they employ. While the former primarily involves 'forward looking' explanations, the latter depends mostly on 'backward looking' explanations. A forward looking explanation tries to predict the effects of ongoing evolutionary processes on human health and disease in contemporary environments (e.g., hospitals). In contrast, a backward looking explanation typically applies evolutionary principles from the vantage point of humans' distant biological past in order to assess present states of health and disease. Both approaches, however, are concerned with the prevention and control of human diseases. In conclusion, I raise some concerns about the claim that 'nothing in medicine makes sense except in the light of evolution'.
We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.
Dunn, Robert Roberdeau; Beasley, DeAnna E.
The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This ...
Cai, Y.; Zhang, M.; Cai, H.
A hybrid chaotic quantum evolutionary algorithm is proposed to reduce amount of computation, speed up convergence and restrain premature phenomena of quantum evolutionary algorithm. The proposed algorithm adopts the chaotic initialization method to generate initial population which will form a pe...... tests. The presented algorithm is applied to urban traffic signal timing optimization and the effect is satisfied....
This paper investigates whether 'tough' bargaining behavior, which gives rise to inefficiency, can be evolutionary stable. We show that in a two-stage Nash Demand Game tough behavior survives. Indeed, almost all the surplus may be wasted. We also study the Ultimatum Game. Here evolutionary select...
Cruickshank, Mark N; Fenwick, Emily; Karimi, Mahdad; Abraham, Lawrence J; Ulgiati, Daniela
Stringent developmental transcription requires multiple transcription factor (TF) binding sites, cell-specific expression of signaling molecules, TFs and co-regulators and appropriate chromatin structure. During B-lymphopoiesis, human Complement receptor 2 (CR2/CD21) is detected on immature and mature B cells but not on B cell precursors and plasma cells. We examined cell- and stage-specific human CR2 gene regulation using cell lines modeling B-lymphopoiesis. Chromatin accessibility assays revealed a region between -409 and -262 with enhanced accessibility in mature B cells and pre-B cells, compared to either non-lymphoid or plasma cell-types, however, accessibility near the transcription start site (TSS) was elevated only in CR2-expressing B cells. A correlation between histone acetylation and CR2 expression was observed, while histone H3K4 dimethylation was enriched near the TSS in both CR2-expressing B cells and non-expressing pre-B cells. Candidate sites within the CR2 promoter were identified which could regulate chromatin, including a matrix attachment region associated with CDP, SATB1/BRIGHT and CEBP-beta sites as well as two CBF1 sites. ChIP assays verified that both CBF1 and C/EBP-beta bind the CR2 promoter in B cells raising the possibility that these factors facilitate or respond to alterations in chromatin structure to control the timing and/or level of CR2 transcription.
In the context of the upcoming implementation of the environmental tax policy, there is a need for a focus on the relationship between government regulation and corporate emissions. To achieve the real effect of environmental tax policy, government need to regulate the illegal emissions of enterprises. Based on the hypothesis of bounded rationality, this paper analyses the strategic set of government regulators and polluting enterprises in the implementation of environmental tax policy. By using the evolutionary game model, the utility function and payoff matrix of the both sides are constructed, and the evolutionary analysis and strategy adjustment of the environmental governance target and the actual profit of the stakeholders are carried out. Thus, the wrong behaviours could be corrected so that the equilibrium of the evolutionary system can be achieved gradually, which could also get the evolutionary stable strategies of the government and the polluting enterprises in the implementation of environmental tax policy.
Charles G Nathanson
Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.
Full Text Available From an evolutionary perspective, environmental threats relevant for survival constantly challenged human beings. Current research suggests the evolution of a fear processing module in the brain to cope with these threats. Recently, humans increasingly encountered modern threats (e.g., guns or car accidents in addition to evolutionary threats (e.g., snakes or predators which presumably required an adaptation of perception and behavior. However, the neural processes underlying the perception of these different threats remain to be elucidated. We investigated the effect of image content (i.e., evolutionary vs. modern threats on the activation of neural networks of emotion processing. During functional magnetic resonance imaging (fMRI 41 participants watched affective pictures displaying evolutionary-threatening, modern-threatening, evolutionary-neutral and modern-neutral content. Evolutionary-threatening stimuli evoked stronger activations than modern-threatening stimuli in left inferior frontal gyrus and thalamus, right middle frontal gyrus and parietal regions as well as bilaterally in parietal regions, fusiform gyrus and bilateral amygdala. We observed the opposite effect, i.e., higher activity for modern-threatening than for evolutionary-threatening stimuli, bilaterally in the posterior cingulate and the parahippocampal gyrus. We found no differences in subjective arousal ratings between the two threatening conditions. On the valence scale though, subjects rated modern-threatening pictures significantly more negative than evolutionary-threatening pictures, indicating a higher level of perceived threat. The majority of previous studies show a positive relationship between arousal rating and amygdala activity. However, comparing fMRI results with behavioral findings we provide evidence that neural activity in fear processing areas is not only driven by arousal or valence, but presumably also by the evolutionary content of the stimulus. This has
failure probability. Multiobjective Evolutionary Computation algorithms (MOEAs) are well-suited for Multiobjective task scheduling on heterogeneous environment. The two Multi-Objective Evolutionary Algorithms such as Multiobjective Genetic. Algorithm (MOGA) and Multiobjective Evolutionary Programming (MOEP) with.
Brady, Steven P.; Richardson, Jonathan L.; Kunz, Bethany K.
Ecotoxicological studies have provided extensive insights into the lethal and sublethal effects of environmental contaminants. These insights are critical for environmental regulatory frameworks, which rely on knowledge of toxicity for developing policies to manage contaminants. While varied approaches have been applied to ecotoxicological questions, perspectives related to the evolutionary history of focal species or populations have received little consideration. Here, we evaluate chloride toxicity from the perspectives of both macroevolution and contemporary evolution. First, by mapping chloride toxicity values derived from the literature onto a phylogeny of macroinvertebrates, fish, and amphibians, we tested whether macroevolutionary relationships across species and taxa are predictive of chloride tolerance. Next, we conducted chloride exposure tests for two amphibian species to assess whether potential contemporary evolutionary change associated with environmental chloride contamination influences chloride tolerance across local populations. We show that explicitly evaluating both macroevolution and contemporary evolution can provide important and even qualitatively different insights from those obtained via traditional ecotoxicological studies. While macroevolutionary perspectives can help forecast toxicological end points for species with untested sensitivities, contemporary evolutionary perspectives demonstrate the need to consider the environmental context of exposed populations when measuring toxicity. Accounting for divergence among populations of interest can provide more accurate and relevant information related to the sensitivity of populations that may be evolving in response to selection from contaminant exposure. Our data show that approaches accounting for and specifically examining variation among natural populations should become standard practice in ecotoxicology.
Sikosek, Tobias; Chan, Hue Sun
The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599
Criscuolo, Alexis; Michel, Christian J
We develop a new approach to estimate a matrix of pairwise evolutionary distances from a codon-based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance matrices are weighted according to an estimate of the global evolutionary rate of each codon position and averaged into a unique distance matrix. Using a large set of both real and simulated codon-based alignments of nucleotide sequences, we show that this approach leads to distance matrices that have a significantly better treelikeness compared to those obtained by standard nucleotide evolutionary distances. We also propose an alternative weighting to eliminate the part of the noise often associated with some codon positions, particularly the third position, which is known to induce a fast evolutionary rate. Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate as, if not better, than those inferred by maximum likelihood. Finally, a well-known multigene dataset composed of eight yeast species and 106 codon-based alignments is reanalyzed and shows that our codon evolutionary distances allow building a phylogenetic tree which is similar to those obtained by non-distance-based methods (e.g., maximum parsimony and maximum likelihood) and also significantly improved compared to standard nucleotide evolutionary distance estimates.
Csibra, Gergely; Gergely, György
We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of 'natural pedagogy' in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species.
Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff
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.
Su, Qi; Li, Aming; Wang, Long
As evidenced by many cases in human societies, individuals often make different behavior decisions in different interactions, and adaptively adjust their behavior in changeable interactive scenarios. However, up to now, how such diverse interactive behavior affects cooperation dynamics has still remained unknown. Here we develop a general framework of interactive diversity, which models individuals’ separated behavior against distinct opponents and their adaptive adjustment in response to opponents’ strategies, to explore the evolution of cooperation. We find that interactive diversity enables individuals to reciprocate every single opponent, and thus sustains large-scale reciprocal interactions. Our work witnesses an impressive boost of cooperation for a notably extensive range of parameters and for all pairwise games. These results are robust against well-mixed and various networked populations, and against degree-normalized and cumulative payoff patterns. From the perspective of network dynamics, distinguished from individuals competing for nodes in most previous work, in this paper, the system evolves in the form of behavior disseminating along edges. We propose a theoretical method based on evolution of edges, which predicts well both the frequency of cooperation and the compact cooperation clusters. Our thorough investigation clarifies the positive role of interactive diversity in resolving social dilemmas and highlights the significance of understanding evolutionary dynamics from the viewpoint of edge dynamics.
Huizinga, Joost; Clune, Jeff
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. PMID:27280881
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.
Gokhale, Chaitanya S; Traulsen, Arne
Evolutionary game dynamics of two players with two strategies has been studied in great detail. These games have been used to model many biologically relevant scenarios, ranging from social dilemmas in mammals to microbial diversity. Some of these games may, in fact, take place between a number of individuals and not just between two. Here we address one-shot games with multiple players. As long as we have only two strategies, many results from two-player games can be generalized to multiple players. For games with multiple players and more than two strategies, we show that statements derived for pairwise interactions no longer hold. For two-player games with any number of strategies there can be at most one isolated internal equilibrium. For any number of players with any number of strategies , there can be at most isolated internal equilibria. Multiplayer games show a great dynamical complexity that cannot be captured based on pairwise interactions. Our results hold for any game and can easily be applied to specific cases, such as public goods games or multiplayer stag hunts.
Szolnoki, Attila; Perc, Matjaž
Our well-being depends on both our personal success and the success of our society. The realization of this fact makes cooperation an essential trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remains elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. Ranging from indirect territorial battle to the spontaneous emergence and destruction of coexistence, phase diagrams and the underlying spatial patterns reveal fascinatingly rich social dynamics that explain why this costly behavior has evolved and persevered. Comparisons with adaptive punishment, however, uncover an Achilles heel of adaptive rewarding, coming from over-aggression, which in turn hinders optimal utilization of network reciprocity. This may explain why, despite its success, rewarding is not as firmly embedded into our societal organization as punishment. (paper)
Csibra, Gergely; Gergely, György
We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of ‘natural pedagogy’ in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species. PMID:21357237
Young, J; Persell, R
Some of the controversy surrounding evolutionary explanations of human behavior may be due to cognitive information-processing patterns that are themselves the result of evolutionary processes. Two such patterns are (1) the tendency to oversimplify information so as to reduce demand on cognitive resources and (2) our strong desire to generate predictability and stability from perceptions of the external world. For example, research on social stereotyping has found that people tend to focus automatically on simplified social-categorical information, to use such information when deciding how to behave, and to rely on such information even in the face of contradictory evidence. Similarly, an undying debate over nature vs. nurture is shaped by various data-reduction strategies that frequently oversimplify, and thus distort, the intent of the supporting arguments. This debate is also often marked by an assumption that either the nature or the nurture domain may be justifiably excluded at an explanatory level because one domain appears to operate in a sufficiently stable and predictable way for a particular argument. As a result, critiques in-veighed against evolutionary explanations of behavior often incorporate simplified--and erroneous--assumptions about either the mechanics of how evolution operates or the inevitable implications of evolution for understanding human behavior. The influences of these tendencies are applied to a discussion of the heritability of behavioral characteristics. It is suggested that the common view that Mendelian genetics can explain the heritability of complex behaviors, with a one-gene-one-trait process, is misguided. Complex behaviors are undoubtedly a product of a more complex interaction between genes and environment, ensuring that both nature and nurture must be accommodated in a yet-to-be-developed post-Mendelian model of genetic influence. As a result, current public perceptions of evolutionary explanations of behavior are
Grodal, Torben Kragh
that great work of art are also automatically fitness-enhancing in the present day environment, at that there are simple correllations between whether a work of art has a high aesthetic value and whether it is fitness-enhancing or not. Keywords : Evolutionary aesthetics, film theory, literary theory......The article is an invited response to a target article by Joseph Carroll entitled "An evolutionary paradigm for literary study". It argues that the target article misuse the fact that works of art are based on adaptations that were fitness-enhancing in the era of evolutionary adaptations to claim...
Full Text Available AbstractMany advances in our understanding of the genetic basis of species differences have arisen from transformation experiments, which allow us to study the effect of genes from one species (the donor when placed in the genetic background of another species (the recipient. Such interspecies transformation experiments are usually focused on candidate genes – genes that, based on work in model systems, are suspected to be responsible for certain phenotypic differences between the donor and recipient species. We suggest that the high efficiency of transformation in a few plant species, most notably Arabidopsis thaliana, combined with the small size of typical plant genes and their cis-regulatory regions allow implementation of a screening strategy that does not depend upon a priori candidate gene identification. This approach, transgenomics, entails moving many large genomic inserts of a donor species into the wild type background of a recipient species and then screening for dominant phenotypic effects. As a proof of concept, we recently conducted a transgenomic screen that analyzed more than 1100 random, large genomic inserts of the Alabama gladecress Leavenworthia alabamica for dominant phenotypic effects in the A. thaliana background. This screen identified one insert that shortens fruit and decreases A. thaliana fertility. In this paper we discuss the principles of transgenomic screens and suggest methods to help minimize the frequencies of false positive and false negative results. We argue that, because transgenomics avoids committing in advance to candidate genes it has the potential to help us identify truly novel genes or cryptic functions of known genes. Given the valuable knowledge that is likely to be gained, we believe the time is ripe for the plant evolutionary community to invest in transgenomic screens, at least in the mustard family Brassicaceae Burnett where many species are amenable to efficient transformation.
Jackson, Russell E; Calvillo, Dusti P
Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.
Russell E. Jackson
Full Text Available Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.
Dorronsoro, Bernabé; Danoy, Grégoire; Pigné, Yoann; Bouvry, Pascal
Describes how evolutionary algorithms (EAs) can be used to identify, model, and minimize day-to-day problems that arise for researchers in optimization and mobile networking. Mobile ad hoc networks (MANETs), vehicular networks (VANETs), sensor networks (SNs), and hybrid networks—each of these require a designer’s keen sense and knowledge of evolutionary algorithms in order to help with the common issues that plague professionals involved in optimization and mobile networking. This book introduces readers to both mobile ad hoc networks and evolutionary algorithms, presenting basic concepts as well as detailed descriptions of each. It demonstrates how metaheuristics and evolutionary algorithms (EAs) can be used to help provide low-cost operations in the optimization process—allowing designers to put some “intelligence” or sophistication into the design. It also offers efficient and accurate information on dissemination algorithms topology management, and mobility models to address challenges in the ...
Stearns, Stephen C
This review is aimed at readers seeking an introductory overview, teaching courses and interested in visionary ideas. It first describes the range of topics covered by evolutionary medicine, which include human genetic variation, mismatches to modernity, reproductive medicine, degenerative disease, host-pathogen interactions and insights from comparisons with other species. It then discusses priorities for translational research, basic research and health management. Its conclusions are that evolutionary thinking should not displace other approaches to medical science, such as molecular medicine and cell and developmental biology, but that evolutionary insights can combine with and complement established approaches to reduce suffering and save lives. Because we are on the cusp of so much new research and innovative insights, it is hard to estimate how much impact evolutionary thinking will have on medicine, but it is already clear that its potential is enormous.
The exploitation of linkage learning is enhancing the performance of evolutionary algorithms. This monograph examines recent progress in linkage learning, with a series of focused technical chapters that cover developments and trends in the field.
Full Text Available Evolutionary robotics applies the selection, variation, and heredity principles of natural evolution to the design of robots with embodied intelligence. It can be considered as a subfield of robotics that aims to create more robust and adaptive robots. A pivotal feature of the evolutionary approach is that it considers the whole robot at once, and enables the exploitation of robot features in a holistic manner. Evolutionary robotics can also be seen as an innovative approach to the study of evolution based on a new kind of experimentalism. The use of robots as a substrate can help address questions that are difficult, if not impossible, to investigate through computer simulations or biological studies. In this paper we consider the main achievements of evolutionary robotics, focusing particularly on its contributions to both engineering and biology. We briefly elaborate on methodological issues, review some of the most interesting findings, and discuss important open issues and promising avenues for future work.
Nałecz-Jawecki, Paweł; Miekisz, Jacek
The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1 /3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.
There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt...
This year marks a hundred and fifty years since the formal enunciation of the ... publication of R. A. Fisher's landmark paper reconciling the statistical results of the ... applications of evolutionary thinking that has emerged over the past fifteen.
Hendry, A. P.; Kinnison, M. T.; Heino, M.
Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles...... are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design...... of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently...
The ABC protein superfamily-also called traffic ATPases-are energy-dependent ubiquitous proteins, representing one of the crucial and the largest family in the fungal genomes. The ATP-binding cassette endows a characteristic 200-250 amino acids and is omnipresent in all organisms ranging from prokaryotes to eukaryotes. Unlike in bacteria with nutrient import functions, ABC transporters in fungal entomopathogens serve as effective efflux pumps that are largely involved in the shuttle of metabolites across the biological membranes. Thus, the search for ABC proteins may prove of immense importance in elucidating the functional and molecular mechanism at the host-pathogen (insect-fungus) interface. Their sequence homology, domain topology, and functional traits led to the actual identification of nine different families in fungal entomopathogens. Evolutionary relationships within the ABC superfamily are discussed, concentrating on computational approaches for comparative identification of ABC transporters in insect-pathogenic fungi (entomopathogens) with those of animals, plants, and their bacterial orthologs. Ancestors of some fungal candidates have duplicated extensively in some phyla, while others were lost in one lineage or the other, and predictions for the cause of their duplications and/or loss in some phyla are made. ABC transporters of fungal insect-pathogens serve both defensive and offensive functions effective against land-dwelling and ground foraging voracious insects. This study may help to unravel the molecular cascades of ABC proteins to illuminate the means through which insects cope with fungal infection and fungal-related diseases. Copyright © 2017 Elsevier Inc. All rights reserved.
Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A
Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.
Ocampo, Denise; Booth, Mark
Current interventions against malaria have significantly reduced the number of people infected and the number of deaths. Concerns about emerging resistance of both mosquitoes and parasites to intervention have been raised, and questions remain about how best to generate wider knowledge of the underlying evolutionary processes. The pedagogical and research principles of evolutionary medicine may provide an answer to this problem. Eight programme managers and five academic researchers were interviewed by telephone or videoconference to elicit their first-hand views and experiences of malaria control given that evolution is a constant threat to sustainable control. Interviewees were asked about their views on the relationship between practit groups and academics and for their thoughts on whether or not evolutionary medicine may provide a solution to reported tensions. There was broad agreement that evolution of both parasites and vectors presents an obstacle to sustainable control. It was also widely agreed that through more efficient monitoring, evolution could be widely monitored. Interviewees also expressed the view that even well planned interventions may fail if the evolutionary biology of the disease is not considered, potentially making current tools redundant. This scoping study suggests that it is important to make research, including evolutionary principles, available and easily applicable for programme managers and key decision-makers, including donors and politicians. The main conclusion is that sharing knowledge through the educational and research processes embedded within evolutionary medicine has potential to relieve tensions and facilitate sustainable control of malaria and other parasitic infections.
Ainsworth, Shaaron; Saffer, Jessica
Representations of the "tree of life" such as cladograms show the history of lineages and their relationships. They are increasingly found in formal and informal learning settings. Unfortunately, there is evidence that these representations can be challenging to interpret correctly. This study explored the question of whether children…
Wu, Amy; Liao, David; Sturm, James; Austin, Robert
Evolutionary game theory applied to two interacting cell populations can yield quantitative prediction of the future densities of the two cell populations based on the initial interaction terms. We will discuss how in a complex ecology that evolutionary game theory successfully predicts the future densities of strains of stromal and cancer cells (multiple myeloma), and discuss the possible clinical use of such analysis for predicting cancer progression. Supported by the National Science Foundation and the National Cancer Institute.
Louis-Philippe Rochon; Sergio Rossi
The purpose of this paper is to shed light on the endogenous nature of money. Contrary to the established post-Keynesian, or evolutionary, view, this paper argues that money has always been endogenous, irrespective of the historical period. Instead of the evolutionary theory of money and banking that can be traced back to Chick (1986), this paper puts forward a revolutionary definition of endogenous money consistent with many aspects of post-Keynesian economics as well as with the monetary ci...
the top of a flight of stairs selects for climbing ; suspending the robot and the target object above the ground and creating rungs between the two will...REPORT Avoiding Local Optimawith Interactive Evolutionary Robotics 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The main bottleneck in evolutionary... robotics has traditionally been the time required to evolve robot controllers. However with the continued acceleration in computational resources, the
Applied Evolutionary Economics and Economic Geography aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and sociologists, all of whom share an interest in explaining the uneven distribution of economic activities in space and the historical processes that have produced these patterns.
Mess, Andrea; Carter, Anthony M.
in traditional systematics. In the present study, we attempted a reconstruction of the evolution of characters associated with placentation, the fetal membranes and the female reproductive tract. The evolutionary history of 21 characters has been traced, based on a current hypothesis of eutherian relationships...
van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel
Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. ...
Belkum, Alex; Struelens, M.; Visser, Arjan; Verbrugh, Henri; Tibayrench, M.
textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiologi...
Hughes, William O H; Pagliarini, Roberta; Madsen, Henning Bang
of the reservoir did not relate with the evolutionary transition from lower to higher attines and correlated at most only slightly with colony size. The results thus suggest that the relationship between leaf-cutting ants and their parasites is distinctly different from that for other attine ants, in accord...
Where host-parasite associations are rigid and unique, the host preference(s) of parasites and the evolutionary relationships between their hosts may offer insights into the parasites' evolu–tionary history. Where such associations are less rigid, however, the assumption that current host preferences are useful in formulating ...
Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley
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.
Boone, Randall B
Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species' niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate.
Qin, Jun; Yi, Yunfei; Wu, Hongrun; Liu, Yuhang; Tong, Xiaonian; Zheng, Bojin
The force of the ethnic separatism, essentially originating from the negative effect of ethnic identity, is damaging the stability and harmony of multiethnic countries. In order to eliminate the foundation of the ethnic separatism and set up a harmonious ethnic relationship, some scholars have proposed a viewpoint: ethnic harmony could be promoted by popularizing civic identity. However, this viewpoint is discussed only from a philosophical prospective and still lacks support of scientific evidences. Because ethnic group and ethnic identity are products of evolution and ethnic identity is the parochialism strategy under the perspective of game theory, this paper proposes an evolutionary game simulation model to study the relationship between civic identity and ethnic conflict based on evolutionary game theory. The simulation results indicate that: (1) the ratio of individuals with civic identity has a negative association with the frequency of ethnic conflicts; (2) ethnic conflict will not die out by killing all ethnic members once for all, and it also cannot be reduced by a forcible pressure, i.e., increasing the ratio of individuals with civic identity; (3) the average frequencies of conflicts can stay in a low level by promoting civic identity periodically and persistently.
To report a simultaneous and evolutionary analysis of the concepts of joy and long-term happiness. Joy and happiness are underrepresented in the nursing literature, though negative concepts are well represented. When mentioned in the literature, neither joy nor happiness is adequately defined, explained, or clearly understood. To promote further investigation of these concepts in nursing and to explore their relationship with health and healing, conceptual clarity is an essential first step. Concept analysis. The following databases were searched, without time restrictions, for articles in English: Academic Search Complete, Anthropology Plus; ATLA Religious Database with ATLASerials; Cumulative Index of Nursing and Allied Health Literature (CINAHL); Education Research Complete; Humanities International Complete; Psych EXTRA; and SocINDEX with Full Text. The final sample size consists of 61 articles and one book, published between 1978-2014. An adapted combination of Rodgers' Evolutionary Model and Haase et al.'s Simultaneous Concept Analysis (SCA) method. Though both are positive concepts, joy and happiness have significant differences. Attributes of joy describe a spontaneous, sudden and transient concept associated with connection, awareness, and freedom. Attributes of happiness describe a pursued, long-lasting, stable mental state associated with virtue and self-control. Further exploration of joy and happiness is necessary to ascertain their relationship with health and their value to nursing practice and theory development. Nurses are encouraged to consider the value of positive concepts to all areas of nursing. © 2016 John Wiley & Sons Ltd.
An analytic model is presented that considers the evolution of a market of durable goods. The model suggests that after introduction goods spread always according to a Bass diffusion. However, this phase will be followed by a diffusion process for durable consumer goods governed by a variation-selection-reproduction mechanism and the growth dynamics can be described by a replicator equation. The theory suggests that products play the role of species in biological evolutionary models. It implies that the evolution of man-made products can be arranged into an evolutionary tree. The model suggests that each product can be characterized by its product fitness. The fitness space contains elements of both sites of the market, supply and demand. The unit sales of products with a higher product fitness compared to the mean fitness increase. Durables with a constant fitness advantage replace other goods according to a logistic law. The model predicts in particular that the mean price exhibits an exponential decrease over a long time period for durable goods. The evolutionary diffusion process is directly related to this price decline and is governed by Gompertz equation. Therefore it is denoted as Gompertz diffusion. Describing the aggregate sales as the sum of first, multiple and replacement purchase the product life cycle can be derived. Replacement purchase causes periodic variations of the sales determined by the finite lifetime of the good (Juglar cycles). The model suggests that both, Bass- and Gompertz diffusion may contribute to the product life cycle of a consumer durable. The theory contains the standard equilibrium view of a market as a special case. It depends on the time scale, whether an equilibrium or evolutionary description is more appropriate. The evolutionary framework is used to derive also the size, growth rate and price distribution of manufacturing business units. It predicts that the size distribution of the business units (products) is lognormal
Kriegs, Jan Ole; Churakov, Gennady; Jurka, Jerzy; Brosius, Jürgen; Schmitz, Jürgen
The evolutionary relationships of 7SL RNA-derived SINEs such as the primate Alu or the rodent B1 elements have hitherto been obscure. We established an unambiguous phylogenetic tree for Supraprimates, and derived intraordinal relationships of the 7SL RNA-derived SINEs. As well as new elements in Tupaia and primates, we also found that the purported ancestral fossil Alu monomer was restricted to Primates, and provide here the first description of a potential chimeric promoter box region in SINEs.
Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D
Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.
Shackelford, Todd K; Liddle, James R
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.
Wells, Jonathan C K; Nesse, Randolph M; Sear, Rebecca; Johnstone, Rufus A; Stearns, Stephen C
The emerging discipline of evolutionary medicine is breaking new ground in understanding why people become ill. However, the value of evolutionary analyses of human physiology and behaviour is only beginning to be recognised in the field of public health. Core principles come from life history theory, which analyses the allocation of finite amounts of energy between four competing functions-maintenance, growth, reproduction, and defence. A central tenet of evolutionary theory is that organisms are selected to allocate energy and time to maximise reproductive success, rather than health or longevity. Ecological interactions that influence mortality risk, nutrient availability, and pathogen burden shape energy allocation strategies throughout the life course, thereby affecting diverse health outcomes. Public health interventions could improve their own effectiveness by incorporating an evolutionary perspective. In particular, evolutionary approaches offer new opportunities to address the complex challenges of global health, in which populations are differentially exposed to the metabolic consequences of poverty, high fertility, infectious diseases, and rapid changes in nutrition and lifestyle. The effect of specific interventions is predicted to depend on broader factors shaping life expectancy. Among the important tools in this approach are mathematical models, which can explore probable benefits and limitations of interventions in silico, before their implementation in human populations. Copyright © 2017 Elsevier Ltd. All rights reserved.
When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as "evolutionary mismatch," or "evolutionary novelty." The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander's sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.
Gupta, Abhishek; Ong, Yew-Soon; Feng, Liang; Tan, Kay Chen
In recent decades, the field of multiobjective optimization has attracted considerable interest among evolutionary computation researchers. One of the main features that makes evolutionary methods particularly appealing for multiobjective problems is the implicit parallelism offered by a population, which enables simultaneous convergence toward the entire Pareto front. While a plethora of related algorithms have been proposed till date, a common attribute among them is that they focus on efficiently solving only a single optimization problem at a time. Despite the known power of implicit parallelism, seldom has an attempt been made to multitask, i.e., to solve multiple optimization problems simultaneously. It is contended that the notion of evolutionary multitasking leads to the possibility of automated transfer of information across different optimization exercises that may share underlying similarities, thereby facilitating improved convergence characteristics. In particular, the potential for automated transfer is deemed invaluable from the standpoint of engineering design exercises where manual knowledge adaptation and reuse are routine. Accordingly, in this paper, we present a realization of the evolutionary multitasking paradigm within the domain of multiobjective optimization. The efficacy of the associated evolutionary algorithm is demonstrated on some benchmark test functions as well as on a real-world manufacturing process design problem from the composites industry.
By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.
ZURINA BT MOHAIDIN
Full Text Available Human behaviour can be explained not only through experience and environments but also by incorporating evolutionary explanation. Consumer behaviour could not be understood accurately without infusing Darwinian evolutionary theory which has contributed in the knowledge of human nature. Evolutionary psychology revolves around the human’s evolved mental and the impact on human’s traits and behaviour where the influence of the environment to our genes would determine our individual behaviour and traits, resulting in variation among us. Foraging which is a part of behavioural ecology involves many sequences or repetitions of animals’ activities and decision making which is useful to relate these patterns of activities to the decisions made in human consumption. The aim of this research is to investigate the similarities of human consumption and ecological behaviour by employing interpretative and comparative approach. It is hoped that by applying the evolutionary theory in explaining consumer choice, this study is able to contribute to the development of behavioural ecology in human consumption. The analysis of the data is done aggregately for 200 consumers and individually for 20 consumers, who have purchased four product categories over a year. This study concludes that the theories of evolutionary psychology can fit to the consumers’ buying behaviour implicating its usefulness in explaining the consumers’ choice.
Brown, Gillian R.; Dickins, Thomas E.; Sear, Rebecca; Laland, Kevin N.
Human beings persist in an extraordinary range of ecological settings, in the process exhibiting enormous behavioural diversity, both within and between populations. People vary in their social, mating and parental behaviour and have diverse and elaborate beliefs, traditions, norms and institutions. The aim of this theme issue is to ask whether, and how, evolutionary theory can help us to understand this diversity. In this introductory article, we provide a background to the debate surrounding how best to understand behavioural diversity using evolutionary models of human behaviour. In particular, we examine how diversity has been viewed by the main subdisciplines within the human evolutionary behavioural sciences, focusing in particular on the human behavioural ecology, evolutionary psychology and cultural evolution approaches. In addition to differences in focus and methodology, these subdisciplines have traditionally varied in the emphasis placed on human universals, ecological factors and socially learned behaviour, and on how they have addressed the issue of genetic variation. We reaffirm that evolutionary theory provides an essential framework for understanding behavioural diversity within and between human populations, but argue that greater integration between the subfields is critical to developing a satisfactory understanding of diversity. PMID:21199836
Zheng, Xiu-Deng; Li, Cong; Lessard, Sabin; Tao, Yi
Over the past 30 years, evolutionary game theory and the concept of an evolutionarily stable strategy have been not only extensively developed and successfully applied to explain the evolution of animal behaviors, but also widely used in economics and social sciences. Nonetheless, the stochastic dynamical properties of evolutionary games in randomly fluctuating environments are still unclear. In this study, we investigate conditions for stochastic local stability of fixation states and constant interior equilibria in a two-phenotype model with random payoffs following pairwise interactions. Based on this model, we develop the concepts of stochastic evolutionary stability (SES) and stochastic convergence stability (SCS). We show that the condition for a pure strategy to be SES and SCS is more stringent than in a constant environment, while the condition for a constant mixed strategy to be SES is less stringent than the condition to be SCS, which is less stringent than the condition in a constant environment.
The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.
Stein, Dan J; Hermesh, Haggai; Eilam, David; Segalas, Cosi; Zohar, Joseph; Menchon, Jose; Nesse, Randolph M
Full Text Available This article focuses on the interdisciplinary research involving Computer Music and Generative Visual Art. We describe the implementation of two interactive artistic systems based on principles of Gestural Data (WILSON, 2002 retrieval and self-organization (MORONI, 2003, to control an Evolutionary Sound Synthesis method (ESSynth. The first implementation uses, as gestural data, image mapping of handmade drawings. The second one uses gestural data from dynamic body movements of dance. The resulting computer output is generated by an interactive system implemented in Pure Data (PD. This system uses principles of Evolutionary Computation (EC, which yields the generation of a synthetic adaptive population of sound objects. Considering that music could be seen as “organized sound” the contribution of our study is to develop a system that aims to generate "self-organized sound" – a method that uses evolutionary computation to bridge between gesture, sound and music.
Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio
To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.
The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin's days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.
Corns, Steven; Long, Suzanna K.; Shoberg, Thomas G.
This paper presents an evolutionary algorithm to address restoration issues for supply chain interdependent critical infrastructure. Rapid restoration of infrastructure after a large-scale disaster is necessary to sustaining a nation's economy and security, but such long-term restoration has not been investigated as thoroughly as initial rescue and recovery efforts. A model of the Greater Saint Louis Missouri area was created and a disaster scenario simulated. An evolutionary algorithm is used to determine the order in which the bridges should be repaired based on indirect costs. Solutions were evaluated based on the reduction of indirect costs and the restoration of transportation capacity. When compared to a greedy algorithm, the evolutionary algorithm solution reduced indirect costs by approximately 12.4% by restoring automotive travel routes for workers and re-establishing the flow of commodities across the three rivers in the Saint Louis area.
Full Text Available Abstract Background The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans, an insect (Drosophila melanogaster, and a vertebrate (Homo sapiens. Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes. Results We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes. Conclusion We conclude that insects (arthropods are genetically and evolutionarily closer to humans than to nematode worms.
Few topics generate such controversy and emotional reactivity as the nature of human mating behavior. Unfortunately, and potentially to the detriment of good patient care, sexual medicine practitioners have largely avoided this matter. An understanding of the scientific literature can empower practitioners to more effectively confront the inevitable monogamy and nonmonogamy challenges present in research and clinical practice. To review and summarize relevant scientific literature as a context to evaluate the more common myths and misunderstanding relating to the practice of monogamy and nonmonogamy in humans. This review also is intended to promote a discussion of the ways human mating strategies may impact sexual function and dysfunction for the individual and couple. A review of English written peer-reviewed evolutionary, anthropological, neuropsychiatric, zoological research, and other scholarly texts was conducted. Work published between 2000 and 2016 concentrating on evolutionary theory, long- and short-term mating strategies in primates and most specifically in humans, and consensual nonmonogamy was highlighted. Main outcomes included a brief explanation of evolutionary theory and a review of relevant literature regarding long- and short-term mating behaviors and consensual nonmonogamy. Serial sexual and social monogamy is the norm for humans. Across time and cultures, humans have adapted both long- and short-term mating strategies that are used flexibly, and sometimes simultaneously, based on unique personal, social, and environmental circumstances. Human mating behavior is individualistic, the result of numerous biopsychosocial influences. The clinician cannot assume that an individual presenting as a patient maintains a monogamy-valued view of his or her intimate relationship. Patients may experience conflict between the cultural monogamous ideal and their actual sexual behaviors. This conflict may be critical in understanding a patient's sexual
Murray, B G
Scientists observe nature, search for generalizations, and provide explanations for why the world is as it is. Generalizations are of two kinds. The first are descriptive and inductive, such as Boyle's Law. They are derived from observations and therefore refer to observables (in this case, pressure and volume). The second are often imaginative and form the axioms of a deductive theory, such as Newton's Laws of Motion. They often refer to unobservables (e.g. inertia and gravitation). Biology has many inductive generalizations (e.g. Bergmann's Rule and 'all cells arise from preexisting cells') but few, if any, recognized universal laws and virtually no deductive theory. Many biologists and philosophers of biology have agreed that predictive theory is inappropriate in biology, which is said to be more complex than physics, and that one can have nonpredictive explanations, such as the neo-Darwinian Theory of Evolution by Natural Selection. Other philosophers dismiss nonpredictive, explanatory theories, including evolutionary 'theory', as metaphysics. Most biologists do not think of themselves as philosophers or give much thought to the philosophical basis of their research. Nevertheless, their philosophy shows in the way they do research. The plethora of ad hoc (i.e. not universal) hypotheses indicates that biologists are reluctant inductivists in that the search for generalization does not have a high priority. Biologists test their hypotheses by verification. Theoretical physicists, in contrast, are deductive unifiers and test their explanatory hypotheses by falsification. I argue that theoretical biology (concerned with unobservables, such as fitness and natural selection) is not scientific because it lacks universal laws and predictive theory. In order to make this argument, I review the differences between verificationism and falsificationism, induction and deduction, and descriptive and explanatory laws. I show how these differ with a specific example of a
Full Text Available Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance was investigated for signatures of selection (comparing QST-FST using clustering of individuals by climate of origin (temperature and precipitation. 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages across the P. trichocarpa sampling range as population groupings. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation; 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes were associated with adaptive traits (based on significant QST. Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show
Lombardi, C.G.; Mazzini, R.A.
The reader is urged to consider the material in ''The Evolutionary Theory of Cost Management'' carefully before proceeding with the material in this paper. The recommendations in this paper flow from the revised line of thinking generated by the evolutionary approach. The suggestions will be difficult to accept in the absence of an understanding of the underlying theory. Although the authors briefly discuss some of the theory, it is nevertheless recommended that the reader develop a fuller understanding of the concepts by studying the prior paper
Karyotis, Vasileios; Papavassiliou, Symeon
Until recently, most network design techniques employed a bottom-up approach with lower protocol layer mechanisms affecting the development of higher ones. This approach, however, has not yielded fascinating results in the case of wireless distributed networks. Addressing the emerging aspects of modern network analysis and design, Evolutionary Dynamics of Complex Communications Networks introduces and develops a top-bottom approach where elements of the higher layer can be exploited in modifying the lowest physical topology-closing the network design loop in an evolutionary fashion similar to
Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter
We present an evolutionary optimisation technique for stochastic production processes, which is able to find improved production materials workflow processes with respect to arbitrary combinations of numerical quantities associated with the production process. Working from a core fragment...... of the BPMN language, we employ an evolutionary algorithm where stochastic model checking is used as a fitness function to determine the degree of improvement of candidate processes derived from the original process through mutation and cross-over operations. We illustrate this technique using a case study...
Full Text Available Wide usage of biometric information for person identity verification purposes, terrorist acts prevention measures and authenticationprocess simplification in computer systems has raised significant attention to reliability and efficiency of biometricsystems. Modern biometric systems still face many reliability and efficiency related issues such as reference databasesearch speed, errors while recognizing of biometric information or automating biometric feature extraction. Current scientificinvestigations show that application of evolutionary algorithms may significantly improve biometric systems. In thisarticle we provide a comprehensive review of main scientific research done in sphere of evolutionary algorithm applicationfor biometric system parameter improvement.
Belvin, W. Keith; Elliott, Kenny B.; Horta, Lucas G.; Bailey, Jim P.; Bruner, Anne M.; Sulla, Jeffrey L.; Won, John; Ugoletti, Roberto M.
A testbed for the development of Controls Structures Interaction (CSI) technology to improve space science platform pointing is described. The evolutionary nature of the testbed will permit the study of global line-of-sight pointing in phases 0 and 1, whereas, multipayload pointing systems will be studied beginning with phase 2. The design, capabilities, and typical dynamic behavior of the phase 0 version of the CSI evolutionary model (CEM) is documented for investigator both internal and external to NASA. The model description includes line-of-sight pointing measurement, testbed structure, actuators, sensors, and real time computers, as well as finite element and state space models of major components.
Nie, Pu-Yan; Zhang, Pei-Ai
Evolutionary graph theory was recently proposed by Lieberman et al. in 2005. In the previous papers about evolutionary graphs (EGs), the fitness of the residents in the EGs is in general assumed to be unity, and the fitness of a mutant is assumed to be a constant r. We aim to extend EG to general cases in this paper, namely, the fitness of a mutant is heavily dependent upon frequency. The corresponding properties for these new EGs are analyzed, and the fixation probability is obtained for large population.
With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.
Meredith J. Martin
Full Text Available Navigating the ubiquitous conflict, competition, and complex group dynamics of the peer group is a pivotal developmental task of childhood. Difficulty negotiating these challenges represents a substantial source of risk for psychopathology. Evolutionary developmental psychology offers a unique perspective with the potential to reorganize the way we think about the role of peer relationships in shaping how children cope with the everyday challenges of establishing a social niche. To address this gap, we utilize the ethological reformulation of the emotional security theory as a guide to developing an evolutionary framework for advancing an understanding of the defense strategies children use to manage antagonistic peer relationships and protect themselves from interpersonal threat (Davies and Sturge-Apple, 2007. In this way, we hope to illustrate the value of an evolutionary developmental lens in generating unique theoretical insight and novel research directions into the role of peer relationships in the development of psychopathology.
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.
ABSTRACT: BACKGROUND: The evolution of high throughput technologies that measure gene expression levels has created a data base for inferring GRNs (a process also known as reverse engineering of GRNs). However, the nature of these data has made this process very difficult. At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. RESULTS: This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. The aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. CONCLUSIONS: Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. Promising methods are identified and a platform for development of appropriate model formalisms is established.
Orlando, Ludovic; Metcalf, Jessica L; Alberdi, Maria T; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L; Salas-Gismondi, Rodolfo; Shockey, Bruce J; Wrinn, Patrick J; Vasil'ev, Sergei K; Ovodov, Nikolai D; Cherry, Michael I; Hopwood, Blair; Male, Dean; Austin, Jeremy J; Hänni, Catherine; Cooper, Alan
The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.
Poliseno, Angelo; Feregrino, Christian; Sartoretto, Stéphane; Aurelle, Didier; Wörheide, Gert; McFadden, Catherine S; Vargas, Sergio
Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms. Copyright © 2017 Elsevier Inc. All rights reserved.
Fedyk, Mark; Kushnir, Tamar
Our conscious abilities are learned in environments that have evolved to support them. This insight provides an alternative way of framing Huang & Bargh's (H&B's) provocative hypothesis. To understand the conflict between unconscious goals and consciousness, we can study the emergence of conscious thought and control in childhood. These developmental processes are also central to the best available current evolutionary theories.
Húsek, Dušan; Snášel, Václav; Neruda, Roman; Owais, S.S.J.; Krömer, P.
Roč. 3, č. 1 (2006), s. 15-20 ISSN 1790-0832 R&D Projects: GA AV ČR 1ET100300414 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary algorithms * genetic algorithms * information retrieval * Boolean query Subject RIV: BA - General Mathematics
Pasold, Anke; Foged, Isak Worre
As the title ‘Function Follows Performance in Evolutionary Computational Processing’ suggests, this paper explores the potentials of employing multiple design and evaluation criteria within one processing model in order to account for a number of performative parameters desired within varied...
The study of evolutionary patterns of cognitive convergence would be greatly helped by a clear demarcation of cognition. Cognition is often used as an equivalent of mind, making it difficult to pin down empirically or to apply it confidently beyond the human condition. Recent developments in
Stoops, John L.
As is becoming increasingly clear, the human species evolvedin the East African savannah. Details of the precise evolutionary chainremain unresolved however it appears that the process lasted severalmillion years, culminating with the emergence of modern Homo sapiensroughly 200,000 years ago. Following that final evolutionary developmentmodern Homo sapiens relatively quickly populated the entire world.Clearly modern Homo sapiens is a successful, resourceful and adaptablespecies. In the developed societies, modern humans live an existence farremoved from our evolutionary ancestors. As we have learned over the lastcentury, this "new" lifestyle can often result in unintendedconsequences. Clearly, our modern access to food, shelter, transportationand healthcare has resulted in greatly expanded expected lifespan butthis new lifestyle can also result in the emergence of different kinds ofdiseases and health problems. The environment in modern buildings haslittle resemblance to the environment of the savannah. We strive tocreate environments with little temperature, air movement and lightvariation. Building occupants often express great dissatisfaction withthese modern created environments and a significant fraction even developsomething akin to allergies to specific buildings (sick buildingsyndrome). Are the indoor environments we are creating fundamentallyunhealthy -- when examined from an evolutionary perspective?
Joosten, Reinoud A.M.G.; Roorda, Berend
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
Carson, Hampton L.
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…
Douglas L. Brutlag Nancy Ryan Gray
This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.
Liao Zeyang; Qin Gan; Hu Lingzhi; Li Songjian; Xu Nanyang [Hefei National Laboratory for Physical Science at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Du Jiangfeng [Hefei National Laboratory for Physical Science at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Fachbereich Physik, Universitaet Dortmund, 44221 Dortmund (Germany)], E-mail: firstname.lastname@example.org
We apply the continuous-variable quantization scheme to quantize public goods game and find that new pure strategy Nash equilibria emerge in the static case. Furthermore, in the evolutionary public goods game, entanglement can also contribute to the persistence of cooperation under various population structures without altruism, voluntary participation, and punishment.
Redaktionen af et temanummer i Journal for the Cognitive Science of Religion 4 (1) 2016: 1-90 med en række bidrag som respons til en targetartikel skrevet af Jonathan H. Turner med titlen "Using Neurosociology and Evolutionary Sociology to Explain the Origin and Evolution of Religions". Der er ko...
Nicholson, Michael; Xiao, Sarah Hong
This article locates consumer behavior analysis within the modern neo-Darwinian synthesis, seeking to establish an interface between the ultimate-level theorizing of human evolutionary psychology and the proximate level of inquiry typically favored by operant learning theorists. Following an initial overview of the central tenets of neo-Darwinism,…
Andersen, Esben Sloth
Schumpeter’s unique type of evolutionary analysis can hardly be understood unless we recognise that he developed it in relation to a study of the strength and weaknesses of the Walrasian form of neoclassical economics. The paper demonstrates that Schumpeter’s major steps were already performed in...
Evolutionary algorithms are widely used in single and multi-objective optimization. They are easy to use and provide solution(s) in one simulation run. They are used in food processing industries for decision making. Food processing presents constrained and unconstrained optimization problems. This paper reviews the ...
Drummond Alexei J
Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
Bergh, van den Jeroen C.J.M.; Gowdy, John M.
We consider the microfoundations controversy from the perspective ofeconomic evolution and show that the debate can benefit from lessons learned in evolutionary biology. Although the analogy between biology and economics has been noted before, it has rarely focused on clarifying the micro-macro
Fan, Zhun; Wang, Jiachuan; Achiche, Sofiane
In this paper, we discuss the hierarchy that is involved in a typical MEMS design and how evolutionary approaches can be used to automate the hierarchical synthesis process for MEMS. The paper first introduces the flow of a structured MEMS design process and emphasizes that system-level lumped...
Zhang, Hua; Liu, Duanduan; Poel, Mannes; Nijholt, Antinus; Zha, H.; Taniguchi, R.-I.; Maybank, S.
In this paper, we present a face alignment approach using granular features, boosting, and an evolutionary search algorithm. Active Appearance Models (AAM) integrate a shape-texture-combined morphable face model into an efficient fitting strategy, then Boosting Appearance Models (BAM) consider the
Boschma, R.A.; Frenken, K.
Following last decade’s programmatic papers on Evolutionary Economic Geography, we report on recent empirical advances and how this empirical work can be positioned vis-a`-vis other strands of research in economic geography. First, we review studies on the path dependent nature of clustering, and
Boschma, R.A.; Frenken, K.
Following last decade’s programmatic papers on Evolutionary Economic Geography, we report on recent empirical advances and how this empirical work can be positioned vis-à-vis other strands of research in economic geography. First, we review studies on the path dependent nature of clustering, and how
Boschma, R.A.; Frenken, K.
Following last decade’s programmatic papers on Evolutionary Economic Geography, we report on recent empirical advances and how this empirical work can be positioned vis-a`-vis other strands of research in economic geography. First, we review studies on the path dependent nature of clustering, and
Rusch, Hannes; Störmer, C.
Humans are one of the most cooperative and altruistic species on the planet. At the same time, humans have a long history of violent and deadly intergroup conflicts or wars. Recently, contemporary evolutionary theorists have revived Charles Darwin’s idea that human in-group altruism and out-group
Souza, De Fernanda Coelho; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J.W.; Chave, Jerome; Galbraith, David R.; Gonzalez, Gabriela Lopez; Mendoza, Abel Monteagudo; Toby Pennington, R.; Poorter, Lourens; Arets, E.J.M.M.; Boot, Rene G.A.; Meer, van der Peter J.
Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of
Thomsen, Rene; Fogel, Gary B.; Krink, Thimo
Multiple sequence alignment (MSA) is a crucial task in bioinformatics. In this paper we extended previous work with evolutionary algorithms (EA) by using MSA solutions obtained from the wellknown Clustal V algorithm as a candidate solution seed of the initial EA population. Our results clearly show...
In the introduction and chapter 2 the incentives and way of reasoning are given for the description of an evolutionary basis of pollination ecology. Starting from the until recently rather anecdotical character of the study of pollination ecology as a whole, and in the absence of large-scale
Full Text Available Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. The spliced-leader RNA is attached to all mRNAs. It contains an unusual hypermethylated cap-4 structure in its 5 end. The cap-binding complex, eIF4F, has gone through evolutionary changes in accordance with the requirement to bind cap-4. The eIF4F components in trypanosomatids are highly diverged from their orthologs in higher eukaryotes, and their potential functions are discussed. The cap-binding activity in all eukaryotes is a target for regulation and plays a similar role in trypanosomatids. Recent studies revealed a novel eIF4E-interacting protein, involved in directing stage-specific and stress-induced translation pathways. Translation regulation during stress also follows unusual regulatory cues, as the increased translation of Hsp83 following heat stress is driven by a defined element in the 3 UTR, unlike higher eukaryotes. Overall, the environmental switches experienced by trypanosomatids during their life cycle seem to affect their translational machinery in unique ways.
Oyola Morales, José R.; Vital-García, Cuauhcihuatl; Hews, Diana K.; Martins, Emília P.
Many evolutionary forces can shape the evolution of communicative signals, and the long-term impact of each force may depend on relative timing and magnitude. We use a phylogenetic analysis to infer the history of blue belly patches of Sceloporus lizards, and a detailed spectrophotometric analysis of four species to explore the specific forces shaping evolutionary change. We find that the ancestor of Sceloporus had blue patches. We then focus on four species; the first evolutionary shift (captured by comparison of S. merriami and S. siniferus) represents an ancient loss of the belly patch by S. siniferus, and the second evolutionary shift, bounded by S. undulatus and S. virgatus, represents a more recent loss of blue belly patch by S. virgatus. Conspicuousness measurements suggest that the species with the recent loss (S. virgatus) is the least conspicuous. Results for two other species (S. siniferus and S. merriami) suggest that over longer periods of evolutionary time, new signal colours have arisen which minimize absolute contrast with the habitat while maximizing conspicuousness to a lizard receiver. Specifically, males of the species representing an ancient loss of blue patch (S. siniferus) are more conspicuous than are females in the UV, whereas S. merriami males have evolved a green element that makes their belly patches highly sexually dimorphic but no more conspicuous than the white bellies of S. merriami females. Thus, our results suggest that natural selection may act more immediately to reduce conspicuousness, whereas sexual selection may have a more complex impact on communicative signals through the introduction of new colours. PMID:28018661
Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun
Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.
Boschma, R.A.; Frenken, K.
The paper explains the commonalities and differences between neoclassical, institutional and evolutionary approaches that have been influential in economic geography during the last couple of decades. By separating the three approaches in terms of theoretical content and research methodology, wecan
Lockard, Meghan A; Ebert, Margaret S; Bargmann, Cornelia I
The molecular and functional conservation of oxytocin-related neuropeptides in behavior is striking. In animals separated by at least 600 million years of evolution, from roundworms to humans, oxytocin homologs play critical roles in the modulation of reproductive behavior and other biological functions. Here, we review the roles of oxytocin in invertebrate behavior from an evolutionary perspective. We begin by tracing the evolution of oxytocin through the invertebrate animal lineages, and then describe common themes in invertebrate behaviors that are mediated by oxytocin-related peptides, including reproductive behavior, learning and memory, food arousal, and predator/prey relationships. Finally, we discuss interesting future directions that have recently become experimentally tractable. Studying oxytocin in invertebrates offers precise insights into the activity of neuropeptides on well-defined neural circuits; the principles that emerge may also be represented in the more complex vertebrate brain. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 128-142, 2017. © 2016 Wiley Periodicals, Inc.
Balliet, Daniel; Tybur, Joshua M; Van Lange, Paul A M
Social interactions are characterized by distinct forms of interdependence, each of which has unique effects on how behavior unfolds within the interaction. Despite this, little is known about the psychological mechanisms that allow people to detect and respond to the nature of interdependence in any given interaction. We propose that interdependence theory provides clues regarding the structure of interdependence in the human ancestral past. In turn, evolutionary psychology offers a framework for understanding the types of information processing mechanisms that could have been shaped under these recurring conditions. We synthesize and extend these two perspectives to introduce a new theory: functional interdependence theory (FIT). FIT can generate testable hypotheses about the function and structure of the psychological mechanisms for inferring interdependence. This new perspective offers insight into how people initiate and maintain cooperative relationships, select social partners and allies, and identify opportunities to signal social motives.
Schwenk, K.; Spaak, P.
The evolutionary process of interspecific hybridization in cladocerans is reviewed based on ecological and population genetic data. The evolutionary consequences of hybridization, biogeographic patterns and fitness comparisons are analyzed within the conceptual framework of theories on
Bartley, W W
This collection of essays in support of the theory of evolutionary epistemology includes articles by Karl Popper, Peter Munz and Gerhard Vollmer. This volume attempts to show how an evolutionary and non-justificational approach affects the sociology of knowledge.
Silberman Jeffrey D
Full Text Available Abstract Background Glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. The glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. However, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. We have conducted an expressed sequence tag (EST survey of the anaerobic flagellate Trimastix pyriformis to investigate the nature of the evolutionary origins of the glycolytic enzymes in this relatively unstudied organism. Results We have found genes in the Trimastix EST data that encode enzymes potentially catalyzing nine of the ten steps of the glycolytic conversion of glucose to pyruvate. Furthermore, we have found two different enzymes that in principle could catalyze the conversion of phosphoenol pyruvate (PEP to pyruvate (or the reverse reaction as part of the last step in glycolysis. Our phylogenetic analyses of all of these enzymes revealed at least four cases where the relationship of the Trimastix genes to homologs from other species is at odds with accepted organismal relationships. Although lateral gene transfer events likely account for these anomalies, with the data at hand we were not able to establish with confidence the bacterial donor lineage that gave rise to the respective Trimastix enzymes. Conclusion A number of the glycolytic enzymes of Trimastix have been transferred laterally from bacteria instead of being inherited from the last common eukaryotic ancestor. Thus, despite widespread conservation of the glycolytic biochemical pathway across eukaryote diversity, in a number of protist lineages the enzymatic components of the pathway have been replaced by lateral gene transfer from disparate evolutionary sources. It remains unclear if these replacements result from selectively advantageous properties of the introduced enzymes or if they are neutral
Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito
Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.
Full Text Available Abstract Background Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution. Results A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution, which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions. Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the
Yue, Jia-Xing; Li, Jinpeng; Wang, Dan; Araki, Hitoshi; Tian, Dacheng; Yang, Sihai
associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the mechanism determining the molecular evolutionary rate at the genomic level.
Numerous psychological, biological, and evolutionary theories have been proposed to explain sexual orientation. For a theory to be valid it must account for the evolutionary or Darwinian paradox of how homosexual behavior seemingly blocking evolutionary fitness could have evolved. Typically it is only evolutionary based theories that attempt to address this issue. All theories proposed to date have limitations, a major one being that they tend to be specific for male or female sexual orientat...
Full Text Available effects have the potential to be influential agents of natural selection (25). Imbalances of expec- tation and reward may therefore have broad effects on health and physiology in humans and may represent a powerful evolutionary force in nature. References... considerable effort to the identification of universal relationships to de- scribe the structure and function of biomes (16). However, it has not been clear whether such re- lationships exist. Any such relationships may be confounded by the unique evolutionary...
Full Text Available Evolutionary theory study of processes that transform economy for firms, institutions, industries, employment, production, trade and growth within, through the actions of diverse agents from experience and interactions, using evolutionary methodology. Evolutionary theory analyses the unleashing of a process of technological and institutional innovation by generating and testing a diversity of ideas which discover and accumulate more survival value for the costs incurred than competing alternatives.This paper presents study the behavior of the firms on the market used the evolutionary theory.The paper is to present in full the developments that have led to the re-assessment of theories of firms starting from the criticism on Coase's theory based on the lack of testable hypotheses and on non-operative definition of transaction costs. In the literature in the field studies on firms were allotted a secondary place for a long period of time, to date the new theories of the firm hold a dominant place in the firms’ economic analysis. In an article, published in 1937, Ronald H. Coase identified the main sources of the cost of using the market mechanism. The firms theory represent a issue intensively studied in the literature in the field, regarding the survival, competitiveness and innovation of firm on the market. The research of Nelson and Winter, “An Evolutionary Theory of Economic Change” (1982 is the starting point for a modern literature in the field which considers the approach of the theory of the firm from an evolutionary perspective. Nelson and Winter have shown that the “orthodox” theory, is objectionable primarily by the fact that the hypothesis regarding profit maximization has a normative character and is not valid in any situation. Nelson and Winter reconsidered their microeconomic analysis showing that excessive attention should not be paid to market equilibrium but rather to dynamic processes resulting from irreversible
This new book focuses on how evolutionary computing techniques benefit engineering research and development tasks by converting practical problems of growing complexities into simple formulations, thus largely reducing development efforts. This book begins with an overview of the optimization the...... theory and modern evolutionary computing techniques, and goes on to cover specific applications of evolutionary computing to power system optimization and control problems....
Kong, Yi; Anderson, Trevor; Pelaez, Nancy
Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly…
Hopcroft, Rosemary L.
In this article I argue that evolutionary theorizing can help sociologists and feminists better understand gender inequality. Evolutionary theory explains why control of the sexuality of young women is a priority across most human societies both past and present. Evolutionary psychology has extended our understanding of male violence against…
Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E
Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.
Skowronski, John J.; Sedikides, Constantine
Section I: Philosophical issues 1. Evolutionary pyschology in the round , Robin Dunbar & Louise Barrett 2. The power of culture , Henry Plotkin 3. Evolution and psychology in philosophical perspective , Matteo Mameli 4. Niche construction, human behavioural ecology and evolutionary psychology , Kevin N Laland 5. Group level evolutionary processes , David Sloan Wilson Section II: The comparative Approach 6. Homologizing the mind , Drew Rendall, Hugh Nottman & John ...
This paper introduces evolutionary algorithms with its applications in multi-objective optimization. Here elitist and non-elitist multiobjective evolutionary algorithms are discussed with their advantages and disadvantages. We also discuss constrained multiobjective evolutionary algorithms and their applications in various areas.
Eugene V. Koonin
Full Text Available When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain ‘ribosomal Tree of Life’ that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: i pervasive horizontal gene transfer (HGT, in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment of the Tree of Life concept, ii Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and iii evolution of evolvability, i.e. dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary
Full Text Available Abstract Background Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes. Results We assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, Mus musculus, and Drosophila melanogaster. It is even more remarkable that the differences between codon usages in different age groups exhibit similar and consistent behavior in various organisms. While we find that GC content and gene length are also associated with the evolutionary age of genes, they can provide only a partial explanation for the observed codon usage. Conclusion While factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan genomes.
Ivanchenko Hennadii F.
Full Text Available The aim of the article is developing information tools for the economic and mathematical modeling of the dynamics of evolutionary processes concerning trophic relationships of populations of enterprises, which allowed to conduct the phase and bifurcation analysis of possible dynamic regimes of the populations’ evolution, determine the mechanisms of influence of the external environment and the internal structure of the system, identify patterns and limits of stability of M&A processes. In the work the main provisions of the evolutionary concept concerning development of the population of enterprises as an economic system are analyzed, the provisions of the evolutionary concept of population systems’ development are considered, the basis of evolutionary modeling methods allowing to analyze the functioning of populations of enterprises in terms of individual strategies of each enterprise’s behavior is studied. The basic principles of synergy of the life cycle evolution for populations of enterprises are determined. An evolutionary approach to the evaluation of a synergistic effect of M & A is proposed. The evolutionary modeling of the scenario for self-organization of populations of dairy industry enterprises through a combination of statistical and expert data is applied. There also created a model of the population of firms reflecting behavioral and resource and technological characteristics of the studied in the work real population of industrial enterprises, which form the input flows of matter, energy and information to the dairy industry, which allows to combine the reflection of main possible options in terms of the external conditions of the population functioning and its internal structure.
Klug, Hope; Bonsall, Michael B; Alonzo, Suzanne H
Evolutionary transitions among maternal, paternal, and bi-parental care have been common in many animal groups. We use a mathematical model to examine the effect of male and female life-history characteristics (stage-specific maturation and mortality) on evolutionary transitions among maternal, paternal, and bi-parental care. When males and females are relatively similar - that is, when females initially invest relatively little into eggs and both sexes have similar mortality and maturation - transitions among different patterns of care are unlikely to be strongly favored. As males and females become more different, transitions are more likely. If females initially invest heavily into eggs and this reduces their expected future reproductive success, transitions to increased maternal care (paternal → maternal, paternal → bi-parental, bi-parental → maternal) are favored. This effect of anisogamy (i.e., the fact that females initially invest more into each individual zygote than males) might help explain the predominance of maternal care in nature and differs from previous work that found no effect of anisogamy on the origin of different sex-specific patterns of care from an ancestral state of no care. When male mortality is high or male egg maturation rate is low, males have reduced future reproductive potential and transitions to increased paternal care (maternal → paternal, bi-parental → paternal, maternal → bi-parental) are favored. Offspring need (i.e., low offspring survival in the absence of care) also plays a role in transitions to paternal care. In general, basic life-history differences between the sexes can drive evolutionary transitions among different sex-specific patterns of care. The finding that simple life-history differences can alone lead to transitions among maternal and paternal care suggests that the effect of inter-sexual life-history differences should be considered as a baseline scenario when attempting to understand how other
Cuevas, Erik; Oliva, Diego
This book compares the performance of various evolutionary computation (EC) techniques when they are faced with complex optimization problems extracted from different engineering domains. Particularly focusing on recently developed algorithms, it is designed so that each chapter can be read independently. Several comparisons among EC techniques have been reported in the literature, however, they all suffer from one limitation: their conclusions are based on the performance of popular evolutionary approaches over a set of synthetic functions with exact solutions and well-known behaviors, without considering the application context or including recent developments. In each chapter, a complex engineering optimization problem is posed, and then a particular EC technique is presented as the best choice, according to its search characteristics. Lastly, a set of experiments is conducted in order to compare its performance to other popular EC methods.
Practical optimization problems are often hard to solve, in particular when they are black boxes and no further information about the problem is available except via function evaluations. This work introduces a collection of heuristics and algorithms for black box optimization with evolutionary algorithms in continuous solution spaces. The book gives an introduction to evolution strategies and parameter control. Heuristic extensions are presented that allow optimization in constrained, multimodal, and multi-objective solution spaces. An adaptive penalty function is introduced for constrained optimization. Meta-models reduce the number of fitness and constraint function calls in expensive optimization problems. The hybridization of evolution strategies with local search allows fast optimization in solution spaces with many local optima. A selection operator based on reference lines in objective space is introduced to optimize multiple conflictive objectives. Evolutionary search is employed for learning kernel ...
JONES,JAKE S.; DAVIDSON,GEORGE S.
In the last decade there has been interest and research in the area of designing circuits with genetic algorithms, evolutionary algorithms, and genetic programming. However, the ability to design circuits of the size and complexity required by modern engineering design problems, simply by specifying required outputs for given inputs has as yet eluded researchers. This paper describes current research in the area of designing logic circuits using an evolutionary algorithm. The goal of the research is to improve the effectiveness of this method and make it a practical aid for design engineers. A novel method of implementing the algorithm is introduced, and results are presented for various multiprocessing systems. In addition to evolving standard arithmetic circuits, work in the area of evolving circuits that perform digital signal processing tasks is described.
Yakushkina, Tatiana; Saakian, David B.; Bratus, Alexander; Hu, Chin-Kun
Evolutionary games are used in various fields stretching from economics to biology. In most of these games a constant payoff matrix is assumed, although some works also consider dynamic payoff matrices. In this article we assume a possibility of switching the system between two regimes with different sets of payoff matrices. Potentially such a model can qualitatively describe the development of bacterial or cancer cells with a mutator gene present. A finite population evolutionary game is studied. The model describes the simplest version of annealed disorder in the payoff matrix and is exactly solvable at the large population limit. We analyze the dynamics of the model, and derive the equations for both the maximum and the variance of the distribution using the Hamilton-Jacobi equation formalism.
Lieberman, Daniel E
An evolutionary perspective helps evaluate the extent to which exercise is medicine and to explain the exercise paradox: why people tend to avoid exercise despite its benefits. Many lines of evidence indicate that humans evolved to be adapted for regular, moderate amounts of endurance physical activity into late age. However, because energy from food was limited, humans also were selected to avoid unnecessary exertion, and most anatomical and physiological systems evolved to require stimuli from physical activity to adjust capacity to demand. Consequently, selection never operated to cope with the long-term effects of chronic inactivity. However, because all adaptations involve trade-offs, there is no evolutionary-determined dose or type of physical activity that will optimize health. Furthermore, because humans evolved to be active for play or necessity, efforts to promote exercise will require altering environments in ways that nudge or even compel people to be active and to make exercise fun.
Carroll, Scott P.; Jørgensen, Peter Søgaard; Kinnison, Michael T.; Bergstrom, Carl T.; Denison, R. Ford; Gluckman, Peter; Smith, Thomas B.; Strauss, Sharon Y.; Tabashnik, Bruce E.
Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development. PMID:25213376
Financial history is not conventionally thought of in evolutionary terms, but it should be. Traditional ways of thinking about finance, dating back to Hilferding, emphasize the importance of concentration and economies of scale. But these approaches overlook the rich "biodiversity" that characterizes the financial world. They also overlook the role of natural selection. To be sure, natural selection in the financial world is not exactly analogous to the processes first described by Darwin and elaborated on by modern biologists. There is conscious adaptation as well as random mutation. Moreover, there is something resembling "intelligent design" in finance, whereby regulators and legislators act in a quasidivine capacity, putting dinosaurs on life support. The danger is that such interventions in the natural processes of the market may ultimately distort the evolutionary process, by getting in the way of Schumpeter's "creative destruction."
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
Full Text Available Asia's population, wealth, cognitive capital, and scientific influence are growing quickly. Reasonable demographic, economic, and psychometric projections suggest that by the mid-21st century, most of the world's psychology will be done in Asia, by Asians. Even if evolutionary psychology wins the battles for academic respectability in the United States and European Union, if it ignores the rise of Asian psychology, it will fail to have any serious, long-term, global influence in the behavioral sciences after the current generations of researchers are dead. I outline a ‘marketing strategy’ for promoting evolutionary psychology in the current Asian powers (Japan, South Korea, Taiwan, Hong Kong, Singapore, the new Asian mega-powers (China, India, and other developing Asia countries (e.g. Vietnam, Thailand, Malaysia, in a way that takes advantage of Asia's relative secularism, freedom from political correctness, sex-positive social attitudes, and intellectual traditions of Hinduism, Buddhism, and Confucianism.
Ploeger, A.; van der Maas, H.L.J.; Raijmakers, M.E.J.
Evolutionary psychology has been proposed as a metatheoretical framework for psychology. We argue that evolutionary psychology should be expanded if it is to offer new insights regarding the major issues in psychology. Evolutionary developmental biology can provide valuable new insights into issues
Evolutionary algorithms (EAs) are metaheuristics that learn from natural collective behavior and are applied to solve optimization problems in domains such as scheduling, engineering, bioinformatics, and finance. Such applications demand acceptable solutions with high-speed execution using finite computational resources. Therefore, there have been many attempts to develop platforms for running parallel EAs using multicore machines, massively parallel cluster machines, or grid computing environments. Recent advances in general-purpose computing on graphics processing units (GPGPU) have opened u
Herold, Florian; Netzer, Nick
The economic concept of the second-best involves the idea that multiple simultaneous deviations from a hypothetical first-best optimum may be optimal once the first-best itself can no longer be achieved, since one distortion may partially compensate for another. Within an evolutionary framework, we translate this concept to behavior under uncertainty. We argue that the two main components of prospect theory, the value function and the probability weighting function, are complements in the sec...
Miikkulainen, Risto; Iscoe, Neil; Shagrin, Aaron; Cordell, Ron; Nazari, Sam; Schoolland, Cory; Brundage, Myles; Epstein, Jonathan; Dean, Randy; Lamba, Gurmeet
Conversion optimization means designing a web interface so that as many users as possible take a desired action on it, such as register or purchase. Such design is usually done by hand, testing one change at a time through A/B testing, or a limited number of combinations through multivariate testing, making it possible to evaluate only a small fraction of designs in a vast design space. This paper describes Sentient Ascend, an automatic conversion optimization system that uses evolutionary op...
Oechssler, Jörg; Riedel, Frank
The study of evolutionary dynamics was so far mainly restricted to finite strategy spaces. In this paper we show that this unsatisfying restriction is unnecessary. We specify a simple condition under which the continuous time replicator dynamics are well defined for the case of infinite strategy spaces. Furthermore, we provide new conditions for the stability of rest points and show that even strict equilibria may be unstable. Finally, we apply this general theory to a number of applications ...
Ramachandran, Vilayanur S.; Jalal, Baland
The old dogma has always been that the most complex aspects of human emotions are driven by culture; Germans and English are thought to be straight-laced whereas Italians and Indians are effusive. Yet in the last two decades there has been a growing realization that even though culture plays a major role in the final expression of human nature, there must be a basic scaffolding specified by genes. While this is recognized to be true for simple emotions like anger, fear, and joy, the relevance of evolutionary arguments for more complex nuances of emotion have been inadequately explored. In this paper, we consider envy or jealousy as an example; the feeling evoked when someone is better off than you. Our approach is broadly consistent with traditional evolutionary psychology (EP) approaches, but takes it further by exploring the complexity and functional logic of the emotion – and the precise social triggers that elicit them – by using deliberately farfetched, and contrived “thought experiments” that the subject is asked to participate in. When common sense (e.g., we should be jealous of Bill Gates – not of our slightly richer neighbor) appears to contradict observed behavior (i.e., we are more envious of our neighbor) the paradox can often be resolved by evolutionary considerations which h predict the latter. Many – but not all – EP approaches fail because evolution and common sense do not make contradictory predictions. Finally, we briefly raise the possibility that gaining deeper insight into the evolutionary origins of certain undesirable emotions or behaviors can help shake them off, and may therefore have therapeutic utility. Such an approach would complement current therapies (such as cognitive behavior therapies, psychoanalysis, psychopharmacologies, and hypnotherapy), rather than negate them. PMID:28970815
This thesis has examined how evolutionary economics can contribute to modelling the micromechanisms that underlie transitions towards sustainable development. In general, transitions are fundamental or structural system changes. They involve, or even require, escaping lock-in of dominant, environmentally unsustainable technologies, introducing major technical or social innovations, and changing prevailing social practices and structures. Due to the complexity of socioeconomic interactions, it is not always possible to identify, and thus target with appropriate policy instruments, causes of specific unsustainable patterns of behaviour. Formal modelling exercises can help improve our understanding of the interaction of various transition mechanisms which are otherwise difficult to grasp intuitively. They allow exploring effects of policy interventions in complex systems. However, existing models of transitions focus on social phenomena and seldom address economic problems. As opposed, mainstream (neoclassical) economic models of technological change do not account for social interactions, and changing heterogeneity of users and their perspectives - even though all of these can influence the direction of innovations and patterns of socio-technological development. Evolutionary economics offers an approach that goes beyond neoclassical economics - in the sense of employing more realistic assumptions regarding the behaviour and heterogeneity of consumers, firms and investors. It can complement current transition models by providing them with a better understanding of associated economic dynamics. In this thesis, formal models were proposed to illustrate the usefulness of a range of evolutionary-economic techniques for modelling transitions. Modelling exercises aimed to explain the core properties of socio-economic systems, such as lock-in, path-dependence, coevolution, group selection and recombinant innovation. The studies collected in this dissertation illustrate that
Kružík, Martin; Zimmer, J.
Roč. 16, č. 1 (2010), s. 1-22 ISSN 1262-3377 R&D Projects: GA AV ČR IAA1075402 Institutional research plan: CEZ:AV0Z10750506 Keywords : concentrations * energetic solution * energies with linear growth * oscillations * relaxation Subject RIV: BA - General Mathematics Impact factor: 1.084, year: 2009 http://library.utia.cas.cz/separaty/2008/MTR/kruzik-evolutionary problems in non-reflexive spaces.pdf
Goetz, Jennifer L.; Keltner, Dacher; Simon-Thomas, Emiliana
What is compassion? And how did it evolve? In this review, we integrate three evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct appraisal processes attuned to undeserved suffering, distinct signaling behavior related to caregiving patterns of touch, posture, and vocalization...
Sofge, Donald A.
This effort examines the intersection of the emerging field of quantum computing and the more established field of evolutionary computation. The goal is to understand what benefits quantum computing might offer to computational intelligence and how computational intelligence paradigms might be implemented as quantum programs to be run on a future quantum computer. We critically examine proposed algorithms and methods for implementing computational intelligence paradigms, primarily focused on ...
Davis, Edward V., Jr.
Approved for public release; distribution unlimited. Rapid prototyping is emerging as a promising software development paradigm. It provides a systematic and automatable means of developing a software system under circumstances where initial requirements are not well known or where requirements change frequently during development. To provide high software quality assurance requires sufficient software testing. The unique nature of evolutionary iterative prototyping is not well-suited for ...
Parousis-Orthodoxou, K J; Vlachos, D S
The following work uses the dynamic capabilities of an evolutionary algorithm in order to obtain an optimal immunization strategy in a user specified network. The produced algorithm uses a basic genetic algorithm with crossover and mutation techniques, in order to locate certain nodes in the inputted network. These nodes will be immunized in an SIR epidemic spreading process, and the performance of each immunization scheme, will be evaluated by the level of containment that provides for the spreading of the disease
Vilayanur S. Ramachandran
Full Text Available The old dogma has always been that the most complex aspects of human emotions are driven by culture; Germans and English are thought to be straight-laced whereas Italians and Indians are effusive. Yet in the last two decades there has been a growing realization that even though culture plays a major role in the final expression of human nature, there must be a basic scaffolding specified by genes. While this is recognized to be true for simple emotions like anger, fear, and joy, the relevance of evolutionary arguments for more complex nuances of emotion have been inadequately explored. In this paper, we consider envy or jealousy as an example; the feeling evoked when someone is better off than you. Our approach is broadly consistent with traditional evolutionary psychology (EP approaches, but takes it further by exploring the complexity and functional logic of the emotion – and the precise social triggers that elicit them – by using deliberately farfetched, and contrived “thought experiments” that the subject is asked to participate in. When common sense (e.g., we should be jealous of Bill Gates – not of our slightly richer neighbor appears to contradict observed behavior (i.e., we are more envious of our neighbor the paradox can often be resolved by evolutionary considerations which h predict the latter. Many – but not all – EP approaches fail because evolution and common sense do not make contradictory predictions. Finally, we briefly raise the possibility that gaining deeper insight into the evolutionary origins of certain undesirable emotions or behaviors can help shake them off, and may therefore have therapeutic utility. Such an approach would complement current therapies (such as cognitive behavior therapies, psychoanalysis, psychopharmacologies, and hypnotherapy, rather than negate them.