WorldWideScience

Sample records for hominidae

  1. The nasal and paranasal architecture of the Middle Miocene ape Pierolapithecus catalaunicus (primates: Hominidae): phylogenetic implications.

    Science.gov (United States)

    Pérez de Los Ríos, Miriam; Moyà-Solà, Salvador; Alba, David M

    2012-09-01

    The internal (nasal and paranasal) cranial anatomy of the Middle Miocene (11.9 Ma [millions of years ago]) great ape Pierolapithecus catalaunicus (Hominidae: Dryopithecini) is described on the basis of computed-tomography scans of the holotype specimen (IPS21350), with particular emphasis on its phylogenetic implications. Pierolapithecus displays the following characters: an anteriorly-restricted maxillary sinus that posteriorly spreads towards the ethmoidal area (thus resembling the pongine condition), although being situated well above the molar roots (as in kenyapithecins, other dryopithecins and pongines); lack of frontal sinus (a synapomorphy of derived pongines, independently acquired by both cercopithecoids and hylobatids); posteriorly-situated turbinals (as in Pongo); anteriorly-projecting nasolacrimal canal (as in Pongo); and probably stepped nasal floor with non-overlapping premaxillary-maxillary contact (as in dryopithecines and stem hominoids, although it cannot be conclusively shown due to bone damage). Overall, Pierolapithecus displays a mosaic of primitive hominid and derived pongine features that are inconsistent with this taxon being a hominine (as previously suggested). Two alternative phylogenetic interpretations are possible: Pierolapithecus may be a stem member of the Hominidae as previously suggested in its original description, or alternatively this taxon may be a stem member of the Ponginae s.l. (with the European dryopithecines being the sister taxon to the Asian pongines). Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. The hominins: a very conservative tribe? Last common ancestors, plasticity and ecomorphology in Hominidae. Or, What's in a name?

    Science.gov (United States)

    Crompton, Robin Huw

    2016-04-01

    In the early 20th century the dominant paradigm for the ecological context of the origins of human bipedalism was arboreal suspension. In the 1960s, however, with recognition of the close genetic relationship of humans, chimpanzees and bonobos, and with the first field studies of mountain gorillas and common chimpanzees, it was assumed that locomotion similar to that of common chimpanzees and mountain gorillas, which appeared to be dominated by terrestrial knuckle-walking, must have given rise to human bipedality. This paradigm has been popular, if not universally dominant, until very recently. However, evidence that neither the knuckle-walking or vertical climbing of these apes is mechanically similar to human bipedalism, as well as the hand-assisted bipedality and orthograde clambering of orang-utans, has cast doubt on this paradigm. It now appears that the dominance of terrestrial knuckle-walking in mountain gorillas is an artefact seen only in the extremes of their range, and that both mountain and lowland gorillas have a generalized orthogrady similar to that seen in orang-utans. These data, together with evidence for continued arboreal competence in humans, mesh well with an increasing weight of fossil evidence suggesting that a mix of orang-utan and gorilla-like arboreal locomotion and upright terrestrial bipedalism characterized most australopiths. The late split date of the panins, corresponding to dates for separation of Homo and Australopithecus, leads to the speculation that competition with chimpanzees, as appears to exist today with gorillas, may have driven ecological changes in hominins and perhaps cladogenesis. However, selection for ecological plasticity and morphological conservatism is a core characteristic of Hominidae as a whole, including Hominini. © 2015 Anatomical Society.

  3. Knuckle-walking anteater: a convergence test of adaptation for purported knuckle-walking features of African Hominidae.

    Science.gov (United States)

    Orr, Caley M

    2005-11-01

    Appeals to synapomorphic features of the wrist and hand in African apes, early hominins, and modern humans as evidence of knuckle-walking ancestry for the hominin lineage rely on accurate interpretations of those features as adaptations to knuckle-walking locomotion. Because Gorilla, Pan, and Homo share a relatively close common ancestor, the interpretation of such features is confounded somewhat by phylogeny. The study presented here examines the evolution of a similar locomotor regime in New World anteaters (order Xenarthra, family Myrmecophagidae) and uses the terrestrial giant anteater (Myrmecophaga tridactyla) as a convergence test of adaptation for purported knuckle-walking features of the Hominidae. During the stance phase of locomotion, Myrmecophaga transmits loads through flexed digits and a vertical manus, with hyperextension occurring at the metacarpophalangeal joints of the weight-bearing rays. This differs from the locomotion of smaller, arboreal anteaters of outgroup genera Tamandua and Cyclopes that employ extended wrist postures during above-branch quadrupedality. A number of features shared by Myrmecophaga and Pan and Gorilla facilitate load transmission or limit extension, thereby stabilizing the wrist and hand during knuckle-walking, and distinguish these taxa from their respective outgroups. These traits are a distally extended dorsal ridge of the distal radius, proximal expansion of the nonarticular surface of the dorsal capitate, a pronounced articular ridge on the dorsal aspects of the load-bearing metacarpal heads, and metacarpal heads that are wider dorsally than volarly. Only the proximal expansion of the nonarticular area of the dorsal capitate distinguishes knuckle-walkers from digitigrade cercopithecids, but features shared with digitigrade primates might be adaptive to the use of a vertical manus of some sort in the stance phase of terrestrial locomotion. The appearance of capitate nonarticular expansion and the dorsal ridge of the

  4. Evolution of life history and behavior in Hominidae: towards phylogenetic reconstruction of the chimpanzee-human last common ancestor.

    Science.gov (United States)

    Duda, Pavel; Zrzavý, Jan

    2013-10-01

    The origin of the fundamental behavioral differences between humans and our closest living relatives is one of the central issues of evolutionary anthropology. The prominent, chimpanzee-based referential model of early hominin behavior has recently been challenged on the basis of broad multispecies comparisons and newly discovered fossil evidence. Here, we argue that while behavioral data on extant great apes are extremely relevant for reconstruction of ancestral behaviors, these behaviors should be reconstructed trait by trait using formal phylogenetic methods. Using the widely accepted hominoid phylogenetic tree, we perform a series of character optimization analyses using 65 selected life-history and behavioral characters for all extant hominid species. This analysis allows us to reconstruct the character states of the last common ancestors of Hominoidea, Hominidae, and the chimpanzee-human last common ancestor. Our analyses demonstrate that many fundamental behavioral and life-history attributes of hominids (including humans) are evidently ancient and likely inherited from the common ancestor of all hominids. However, numerous behaviors present in extant great apes represent their own terminal autapomorphies (both uniquely derived and homoplastic). Any evolutionary model that uses a single extant species to explain behavioral evolution of early hominins is therefore of limited use. In contrast, phylogenetic reconstruction of ancestral states is able to provide a detailed suite of behavioral, ecological and life-history characters for each hypothetical ancestor. The living great apes therefore play an important role for the confident identification of the traits found in the chimpanzee-human last common ancestor, some of which are likely to represent behaviors of the fossil hominins. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. A new nematode, Pongobius hugoti gen. et sp. n. from the orangutan Pongo abelii (Primates: Hominidae)

    Czech Academy of Sciences Publication Activity Database

    Baruš, Vlastimil; Foitová, I.; Koubková, B.; Hodová, I.; Šimková, A.; Nurcahyo, W.

    2007-01-01

    Roč. 44, č. 4 (2007), s. 162-169 ISSN 0440-6605 Institutional research plan: CEZ:AV0Z60220518 Keywords : Pongobius hugoti * Nematoda * Pongo abelii * orangutan * Sumatra * morphometric and molecular analyses Subject RIV: EG - Zoology Impact factor: 0.373, year: 2007

  6. Subspecies identification of Chimpanzees Pan troglodytes (Primates: Hominidae from the National Zoo of the Metropolitan Park of Santiago, Chile, using mitochondrial DNA sequences

    Directory of Open Access Journals (Sweden)

    J.A. Vega

    2014-05-01

    Full Text Available Natural populations of Chimpanzees Pan troglodytes are declining because of hunting and illegal live animal trafficking. Four subspecies of Chimpanzee have been reported: Pan troglodytes troglodytes, P.t. schweinfurthii, P.t. verus and P.t. ellioti, which have remained geographically separated by natural barriers such as the rivers Niger, Sanaga and Ubangi in central Africa. Sequence analysis of mitochondrial DNA (mtDNA has been used for the determination of these subspecies, which indirectly can also suggest their geographic origin. It was decided to identify the subspecies and the geographic origin of three captive chimpanzees of the National Zoo of the Metropolitan Park of Santiago (Chile, by analyzing their mitochondrial DNA. DNA was extracted from the saliva of three adult chimpanzees (two males and one female. After the analysis of sequences of the mitochondrial hypervariable region (HVI, a phylogenetic tree was constructed using mitochondrial sequences of known Pan troglodytes subspecies. Molecular phylogeny analysis revealed that the chimpanzees are likely to belong to three different subspecies: P.t. schweinfurthii, P.t. verus and P.t. troglodytes. Identification of subspecies of the three chimpanzees of the National Zoo of the Metropolitan Park of Santiago (Chile was possible due to mtDNA analysis. Future identification of chimpanzees will allow the development of a studbook for the chimpanzee subspecies in other Latin American zoos.

  7. The Bonobo Pan paniscus (Mammalia: Primates: Hominidae nesting patterns and forest canopy layers in the Lake Tumba forests and Salonga National Park, Democratic Republic of Congo

    Directory of Open Access Journals (Sweden)

    Bila-Isia Inogwabini

    2015-10-01

    Full Text Available The description and differentiation of habitat types is a major concern in ecology.  This study examined relationships between Bonobo Pan paniscus nesting patterns and forest structure in the Lake Tumba Swampy Forests. Data on presence of fresh Bonobo nests, canopy cover, canopy structure, tree densities and tree basal areas were collected systematically along 134 transects at 400m and 800m intervals, and the leaf-covered area (LCA was calculated for each of seven forest types. I observed a significant correlation between bonobo nests and mixed mature forest/closed understory forest type (r=-0.730, df = 21, p <0.05, but not mixed mature forest/open understory, old secondary forest and young secondary forest.  Basal areas of non-nesting trees along transects did not differ significantly from those in sites where bonobos nested.  Higher LCA (55% and 55% occurred in nesting sites when compared with non-nesting sites (39% and 42% at elevations 4–8 m and 8–16 m above the soil.  There was greater leaf cover in the understorey at sites where bonobos did not nest, while there was greater leaf cover in the mid-storey at sites where bonobos did nest.  

  8. Emergence of Darwinian theories on evolution of Homo sapiens (Catarrhini: Hominidae and their relevance for social sciences Origen de las teorías darwinianas de la evolución de Homo sapiens (Catarrhini: Hominidae y su importancia para las ciencias sociales

    Directory of Open Access Journals (Sweden)

    GERMÁN MANRÍQUEZ

    2010-12-01

    Full Text Available Despite the great impact that the Darwinian theories on organic evolution have had in the development and consolidation of biology as an autonomous scientific discipline, their relevance in social sciences, and particularly in archaeology and anthropology still remain ambiguous. This ambiguity is reflected in the classical interpretation of Darwin's work pervading Social Sciences during more than one century, according to which the same ideas that contributed to the understanding of natural processes from a scientific perspective would be at the basis of a misleading interpretation of the evolution of human societies due to the application of the principie of natural selection to the social processes. Here we show how the works of T.H. Huxley and A.R. Wallace positively stimulated Darwin to answer to the question about the origin of human populations considering culture from an evolutionary perspective as a factor opposed to the negative action of natural selection on human societies, thus refuting the classical interpretation of Darwin's work made by Social Sciences. The role played by the biocultural approach in understanding human evolution as well as in promoting the integrative thinking in Social Sciences is also discussed.A pesar del enorme impacto que las teorías de Darwin sobre la evolución orgánica han tenido en el desarrollo y la consolidación de la biología como disciplina científica autónoma, su pertinencia en ciencias sociales, y particularmente en arqueología y antropología sigue siendo ambigua. Esta ambigüedad se refleja en la interpretación clásica de la obra de Darwin que ha permanecido en las ciencias sociales durante más de un siglo, según la cual las mismas ideas que contribuyeron a la comprension de los procesos naturales desde una perspectiva científica estarían en la base de una interpretación errónea de la evolución de las sociedades humanas debido a la aplicación del principio de la selección natural a los procesos sociales. Se muestra cómo la obra de T.H. Huxley y AR. Wallace estimularon positivamente a Darwin para responder a la pregunta sobre el origen de las poblaciones humanas. Esta respuesta consideró a la cultura desde una perspectiva evolutiva y como un factor opuesto a la acción negativa de la selección natural en las sociedades humanas, rechazándose así la interpretación clásica de la obra de Darwin formulada desde las ciencias sociales. Se discute el rol que juega el enfoque biocultural en la comprension de la evolución humana así como en promover el pensamiento integrativo en las ciencias sociales.

  9. Phytochemical investigation and TLC screening for antioxidant activity of 24 plant species consumed by the Eastern Lowland Gorillas (Gorilla beringei ssp. graueri: Hominidae, Primates) endemic to Democratic Republic of the Congo

    OpenAIRE

    Koto-te-Nyiwa Ngbolua

    2014-01-01

    Humans and great apes (bonobos, chimpanzees, gorillas, and orangutans) share a common gut anatomy. Although, some diseases that cause countless deaths in humans are ineffective or have minor non disturbing effects in apes. Because of their phylogenetic closeness and common neural pathways of chemosensory perception, humans and great apes, when displaying symptoms of illness could alter their foraging to ingest non-nutritive chemical as diet (pharmacophagy). The aim of the present study was to...

  10. Cognitive cladistics and cultural override in Hominid spatial cognition

    NARCIS (Netherlands)

    Haun, D.B.M.; Rapold, C.J.; Call, J.; Janzen, G.; Levinson, S.C.

    2006-01-01

    Current approaches to human cognition often take a strong nativist stance based on Western adult performance, backed up where possible by neonate and infant research and almost never by comparative research across the Hominidae. Recent research suggests considerable cross-cultural differences in

  11. 78 FR 40762 - Endangered Species; Marine Mammals; Receipt of Applications for Permit

    Science.gov (United States)

    2013-07-08

    ..., Division of Management Authority, U.S. Fish and Wildlife Service, 4401 North Fairfax Drive, Room 212... Felidae (does not include jaguar, margay and ocelot) Hominidae Hylobatidae Lemuridae Species Bali starling... renewal of their captive-bred wildlife registration under 50 CFR 17.21(g) for the family Gruidae and Bali...

  12. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

    Science.gov (United States)

    Thybert, David; Roller, Maša; Navarro, Fábio C P; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C; Laukaitis, Christina M; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M; Odom, Duncan T; Flicek, Paul

    2018-04-01

    Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli , which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. © 2018 Thybert et al.; Published by Cold Spring Harbor Laboratory Press.

  13. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

    Science.gov (United States)

    Thybert, David; Roller, Maša; Navarro, Fábio C.P.; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C.; Laukaitis, Christina M.; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A.; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J.; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M.; Odom, Duncan T.; Flicek, Paul

    2018-01-01

    Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. PMID:29563166

  14. Homo sapiens natriuretic peptide precursor type C (NPPC) mRNA,partial cds and 3' UTR.

    OpenAIRE

    Landi, Stefano; Melaiu, Ombretta; Cabiati, Manuela; Landi, Debora; Caselli, Chiara; Prescimone, Tommaso; Giannessi, Daniela; Gemignani, Federica; Del Ry, Silvia

    2010-01-01

    LOCUS HQ419060 318 bp mRNA linear PRI 24-NOV-2010 DEFINITION Homo sapiens natriuretic peptide precursor type C (NPPC) mRNA, partial cds and 3' UTR. ACCESSION HQ419060 VERSION HQ419060.1 GI:312261407 KEYWORDS . SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 318) AUTHORS Landi,S., Melaiu,O., Cabiati,M., Landi,D., C...

  15. Cognitive cladistics and cultural override in Hominid spatial cognition

    OpenAIRE

    Haun, D.; Rapold, C.; Call, J.; Janzen, G.; Levinson, S.

    2006-01-01

    Current approaches to human cognition often take a strong nativist stance based on Western adult performance, backed up where possible by neonate and infant research and almost never by comparative research across the Hominidae. Recent research suggests considerable cross-cultural differences in cognitive strategies, including relational thinking, a domain where infant research is impossible because of lack of cognitive maturation. Here, we apply the same paradigm across children and adults o...

  16. The Genus Ixodes (Acari: Ixodidae) in Mexico: Adult Identification Keys, Diagnoses, Hosts, and Distribution (El genero Ixodes (Acari: Ixodidae) en Mexico: claves de identificacion para adultos, diagnosis, huespedes y distribucion)

    Science.gov (United States)

    2010-01-01

    also from Estado de México (Hoffmann, 1969). Hosts in Mexico. Cricetidae and Hominidae ( Homo sapiens Linnaeus, 1758) (Mammalia) (Hoffmann, 1969...distribution El género Ixodes (Acari: Ixodidae) en México: claves de identifi cación para adultos, diagnosis, huéspedes y distribución Carmen Guzmán...postdoctoral scholarship under the Programa de Formación e Incorporación de Profesores de Carrera en Facultades y Escuelas para el Fortalecimiento de la

  17. The Genus Ixodes (Acari: Ixodidae) in Mexico: Adult Identification Keys, Diagnoses, Hosts, and Distribution

    Science.gov (United States)

    2010-01-01

    Cricetidae and Hominidae ( Homo sapiens Linnaeus, 1758) (Mammalia) (Hoffmann, 1969). Note. The tick from Valle de Bravo, Estado de México, was...distribution El género Ixodes (Acari: Ixodidae) en México: claves de identifi cación para adultos, diagnosis, huéspedes y distribución Carmen Guzmán...Incorporación de Profesores de Carrera en Facultades y Escuelas para el Fortalecimiento de la Investigación (PROFIP). Tila María Pérez, Curator of CNAC

  18. Natural Selection in the Great Apes.

    Science.gov (United States)

    Cagan, Alexander; Theunert, Christoph; Laayouni, Hafid; Santpere, Gabriel; Pybus, Marc; Casals, Ferran; Prüfer, Kay; Navarro, Arcadi; Marques-Bonet, Tomas; Bertranpetit, Jaume; Andrés, Aida M

    2016-12-01

    Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size. Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments. Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species. We also identify loci with evidence of positive selection across several lineages. Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes. Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context. The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurl.com/nf8qmzh. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Symbolic complexity for nucleotide sequences: a sign of the genome structure

    International Nuclear Information System (INIS)

    Salgado-García, R; Ugalde, E

    2016-01-01

    We introduce a method for estimating the complexity function (which counts the number of observable words of a given length) of a finite symbolic sequence, which we use to estimate the complexity function of coding DNA sequences for several species of the Hominidae family. In all cases, the obtained symbolic complexities show the same characteristic behavior: exponential growth for small word lengths, followed by linear growth for larger word lengths. The symbolic complexities of the species we consider exhibit a systematic trend in correspondence with the phylogenetic tree. Using our method, we estimate the complexity function of sequences obtained by some known evolution models, and in some cases we observe the characteristic exponential-linear growth of the Hominidae coding DNA complexity. Analysis of the symbolic complexity of sequences obtained from a specific evolution model points to the following conclusion: linear growth arises from the random duplication of large segments during the evolution of the genome, while the decrease in the overall complexity from one species to another is due to a difference in the speed of accumulation of point mutations. (paper)

  20. Ectocranial suture fusion in primates: pattern and phylogeny.

    Science.gov (United States)

    Cray, James; Cooper, Gregory M; Mooney, Mark P; Siegel, Michael I

    2014-03-01

    Patterns of ectocranial suture fusion among Primates are subject to species-specific variation. In this study, we used Guttman Scaling to compare modal progression of ectocranial suture fusion among Hominidae (Homo, Pan, Gorilla, and Pongo), Hylobates, and Cercopithecidae (Macaca and Papio) groups. Our hypothesis is that suture fusion patterns should reflect their evolutionary relationship. For the lateral-anterior suture sites there appear to be three major patterns of fusion, one shared by Homo-Pan-Gorilla, anterior to posterior; one shared by Pongo and Hylobates, superior to inferior; and one shared by Cercopithecidae, posterior to anterior. For the vault suture pattern, the Hominidae groups reflect the known phylogeny. The data for Hylobates and Cercopithecidae groups is less clear. The vault suture site termination pattern of Papio is similar to that reported for Gorilla and Pongo. Thus, it may be that some suture sites are under larger genetic influence for patterns of fusion, while others are influenced by environmental/biomechanic influences. Copyright © 2013 Wiley Periodicals, Inc.

  1. Tempo and mode in human evolution.

    Science.gov (United States)

    McHenry, H M

    1994-01-01

    The quickening pace of paleontological discovery is matched by rapid developments in geochronology. These new data show that the pattern of morphological change in the hominid lineage was mosaic. Adaptations essential to bipedalism appeared early, but some locomotor features changed much later. Relative to the highly derived postcrania of the earliest hominids, the craniodental complex was quite primitive (i.e., like the reconstructed last common ancestor with the African great apes). The pattern of craniodental change among successively younger species of Hominidae implies extensive parallel evolution between at least two lineages in features related to mastication. Relative brain size increased slightly among successively younger species of Australopithecus, expanded significantly with the appearance of Homo, but within early Homo remained at about half the size of Homo sapiens for almost a million years. Many apparent trends in human evolution may actually be due to the accumulation of relatively rapid shifts in successive species. PMID:8041697

  2. Heterochronical patterns of evolution in the transitional stages of vertebrate classes.

    Science.gov (United States)

    Schad, W

    1993-12-01

    Transitional forms of the recent classes of vertebrates are only known in paleontology. The well described examples are: Eusthenopteron foordi (Crossopterygii), Ichthyostega and Acanthostega (Labyrinthodontia) between Osteichthyes and Amphibia, Seymouria baylorensis (Amphibiosaria) between Amphibia and Reptilia, Archaeopteryx lithographica (Archaeornithes) between Reptilia and Aves, and the mammal-like reptiles Pelycosauria, Therapsida and Cynodontia between Reptilia and Aves, and the description of their phylogenetical heterochronies in terms of peramorphosis and paedomorphosis shows the progressive role of the motorial, especially the locomotorial organ systems and their functions in comparison with the retarded evolution of the axial system, especially the skull and central nervous system. The evolution of the Hominidae shows the same rule. The evaluation of these transitional forms in their fossil context reveals them as inhabitants of biotopes situated in the border areas of coastal and shore landscapes of marine, brackish or fresh water. These biotopes have obviously favoured the innovations on the high taxonimic level of macro-evolutionary characteristics.

  3. Regularity dimension of sequences and its application to phylogenetic tree reconstruction

    International Nuclear Information System (INIS)

    Pham, Tuan D.

    2012-01-01

    The concept of dimension is a central development of chaos theory for studying nonlinear dynamical systems. Different types of dimensions have been derived to interpret different geometrical or physical observations. Approximate entropy and its modified methods have been introduced for studying regularity and complexity of time-series data in physiology and biology. Here, the concept of power laws and entropy measure are adopted to develop the regularity dimension of sequences to model a mathematical relationship between the frequency with which information about signal regularity changes in various scales. The proposed regularity dimension is applied to reconstruct phylogenetic trees using mitochondrial DNA (mtDNA) sequences for the family Hominidae, which can be validated according to the hypothesized evolutionary relationships between organisms.

  4. Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Kepp, Kasper Planeta

    2017-01-01

    Positive (adaptive) selection has recently been implied in human superoxide dismutase 1 (SOD1), a highly abundant antioxidant protein with energy signaling and antiaging functions, one of very few examples of direct selection on a human protein product (exon); the molecular drivers...... and SOD1 aggregates and triggered by aging. Our study thus marks an example of direct selection for a particular chemical phenotype (high net charge and stability) in a single human protein with possible implications for the evolution of aging....... of this selection are unknown. We mapped 30 extant SOD1 sequences to the recently established mammalian species tree and inferred ancestors, key substitutions, and signatures of selection during the protein's evolution. We detected elevated substitution rates leading to great apes (Hominidae) at ~1 per 2 million...

  5. Long-sightedness in old wild bonobos during grooming.

    Science.gov (United States)

    Ryu, Heungjin; Graham, Kirsty E; Sakamaki, Tetsuya; Furuichi, Takeshi

    2016-11-07

    Some scientists have suggested that, among Hominidae, prolonged postmenopausal longevity evolved uniquely in humans [1], while others disagree [2]. There have, however, been few empirical studies on how physiological aging and somatic durability in humans compare to our closest relatives - chimpanzees and bonobos [3]. If prolonged lifespan is selected for in humans, physiological aging, including reproductive and somatic senescence, might be different for Pan and Homo. But it seems that the parameters of reproductive senescence, such as the age of having their final offspring and the number of years between generations, are not very different between chimpanzee and human females [4]. Here, we report evidence for five cases of long-sightedness (presbyopia) in old wild bonobos, exhibited during grooming. Our results suggest that senescence of the eye has not changed much since the divergence of Pan and Homo from their common ancestor. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.

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    Kim, Soonok; Cho, Yun Sung; Kim, Hak-Min; Chung, Oksung; Kim, Hyunho; Jho, Sungwoong; Seomun, Hong; Kim, Jeongho; Bang, Woo Young; Kim, Changmu; An, Junghwa; Bae, Chang Hwan; Bhak, Youngjune; Jeon, Sungwon; Yoon, Hyejun; Kim, Yumi; Jun, JeHoon; Lee, HyeJin; Cho, Suan; Uphyrkina, Olga; Kostyria, Aleksey; Goodrich, John; Miquelle, Dale; Roelke, Melody; Lewis, John; Yurchenko, Andrey; Bankevich, Anton; Cho, Juok; Lee, Semin; Edwards, Jeremy S; Weber, Jessica A; Cook, Jo; Kim, Sangsoo; Lee, Hang; Manica, Andrea; Lee, Ilbeum; O'Brien, Stephen J; Bhak, Jong; Yeo, Joo-Hong

    2016-10-11

    There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.

  7. Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers

    Directory of Open Access Journals (Sweden)

    Walker Jerilyn A

    2012-04-01

    Full Text Available Abstract Background Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. Results Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes, but absent from Hylobatidae (gibbon and siamang. We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla, this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion. Conclusions This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.

  8. Milk composition of captive vervet monkey (Chlorocebus pygerythrus) and rhesus macaque (Macaca mulatta) with observations on gorilla (Gorilla gorilla gorilla) and white handed gibbon (Hylobates lar).

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    Osthoff, G; Hugo, A; de Wit, M; Nguyen, T P M; Seier, J

    2009-04-01

    The nutrient content and fatty acid composition of vervet monkey milk has been determined and is compared with rhesus macaque, and two hominoid apes, the white handed gibbon and gorilla. With 15.7+/-4.1 g protein, 33.1+/-9.4 g fat, and 85.1+/-7.5 g lactose per kg milk, vervet monkey milk does not differ from that of rhesus macaque, and is within the range of other primates. Small amounts (>1 g kg(-1)) of oligosaccharides, glucose, galactose and fucose were noted. In comparison, gorilla milk has a low fat content of 13.8 g kg(-1), but contains high levels of oligosaccharides at 7.0 g kg(-1) milk. The hominoid partner, the white handed gibbon, contains no oligosaccharides and a milk fat content similar to other hominoid species. Differences between vervet monkey and rhesus macaque milks were observed in the electrophoretic pattern of the milk proteins, mainly amongst the kappa- and gamma-caseins, which also differ from that of the hominids. The fatty acid contents of these milks differ from studies where a natural diet of leafy material was available in that a low content of alpha-linolenic acid (18:3n-3) was noted. A phylogenetic effect is observed for the content of 8:0, 10:0 fatty acids between the Cercopithecidae and Hominoidea, and a further phylogenetic effect suggested between the Hylobatidae and Hominidae.

  9. Updated chronology for the Miocene hominoid radiation in Western Eurasia

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    Casanovas-Vilar, Isaac; Alba, David M.; Garcés, Miguel; Robles, Josep M.; Moyà-Solà, Salvador

    2011-01-01

    Extant apes (Primates: Hominoidea) are the relics of a group that was much more diverse in the past. They originated in Africa around the Oligocene/Miocene boundary, but by the beginning of the Middle Miocene they expanded their range into Eurasia, where they experienced a far-reaching evolutionary radiation. A Eurasian origin of the great ape and human clade (Hominidae) has been favored by several authors, but the assessment of this hypothesis has been hampered by the lack of accurate datings for many Western Eurasian hominoids. Here we provide an updated chronology that incorporates recently discovered Iberian taxa and further reevaluates the age of many previously known sites on the basis of local biostratigraphic scales and magnetostratigraphic data. Our results show that identifiable Eurasian kenyapithecins (Griphopithecus and Kenyapithecus) are much younger than previously thought (ca. 14 Ma instead of 16 Ma), which casts serious doubts on the attribution of the hominoid tooth from Engelswies (16.3–16.5 Ma) to cf. Griphopithecus. This evidence is further consistent with an alternative scenario, according to which the Eurasian pongines and African hominines might have independently evolved in their respective continents from similar kenyapithecin ancestors, resulting from an early Middle Miocene intercontinental range extension followed by vicariance. This hypothesis, which would imply an independent origin of orthogrady in pongines and hominines, deserves further testing by accurately inferring the phylogenetic position of European dryopithecins, which might be stem pongines rather than stem hominines. PMID:21436034

  10. Comparative morphometric analysis of the proximal femur of African hominids and felids

    Directory of Open Access Journals (Sweden)

    Andrew Gallagher

    2015-09-01

    Full Text Available Size and shape of the mammalian proximal femur and taxon-specific distinctions in the relative proportions of the proximal articulation, the femoral neck and the proximal femoral diaphysis, are critical determinants in its adaptation to differential biomechanical stresses and observed locomotor habitus in different taxa. The morphometrics of the proximal femur are considered equally critical in the assessment of locomotor habitus of extinct fossil mammals, particularly extinct Miocene anthropoids and Plio-Pleistocene hominins. Analyses of size and shape of k=10 dimensions of the proximal femur were undertaken for a large sample series of two extant mammal families the Felidae and Hominidae using conventional multivariate statistical procedures, commonly used size-correction methods, and post-hoc tests of significance. While significant differences in form do exist, there are equally striking convergences in the functional morphology of extant hominid and felid taxa. Multivariate and bivariate allometric analyses confirm that the proximal femur of these two mammalian families share a common underlying structure manifest in a shared first common principal component. Nevertheless, while considerable convergences in general form of the proximal femur of African hominids and large-bodied felids are apparent, there exist equally discreet distinctions which are consistent with the differential structural demands imposed by their distinct locomotor and behavioural habitus.

  11. Np9, a cellular protein of retroviral ancestry restricted to human, chimpanzee and gorilla, binds and regulates ubiquitin ligase MDM2

    Science.gov (United States)

    Heyne, Kristina; Kölsch, Kathrin; Bruand, Marine; Kremmer, Elisabeth; Grässer, Friedrich A; Mayer, Jens; Roemer, Klaus

    2015-01-01

    Humans and primates are long-lived animals with long reproductive phases. One factor that appears to contribute to longevity and fertility in humans, as well as to cancer-free survival, is the transcription factor and tumor suppressor p53, controlled by its main negative regulator MDM2. However, p53 and MDM2 homologs are found throughout the metazoan kingdom from Trichoplacidae to Hominidae. Therefore the question arises, if p53/MDM2 contributes to the shaping of primate features, then through which mechanisms. Previous findings have indicated that the appearances of novel p53-regulated genes and wild-type p53 variants during primate evolution are important in this context. Here, we report on another mechanism of potential relevance. Human endogenous retrovirus K subgroup HML-2 (HERV-K(HML-2)) type 1 proviral sequences were formed in the genomes of the predecessors of contemporary Hominoidea and can be identified in the genomes of Nomascus leucogenys (gibbon) up to Homo sapiens. We previously reported on an alternative splicing event in HERV-K(HML-2) type 1 proviruses that can give rise to nuclear protein of 9 kDa (Np9). We document here the evolution of Np9-coding capacity in human, chimpanzee and gorilla, and show that the C-terminal half of Np9 binds directly to MDM2, through a domain of MDM2 that is known to be contacted by various cellular proteins in response to stress. Np9 can inhibit the MDM2 ubiquitin ligase activity toward p53 in the cell nucleus, and can support the transactivation of genes by p53. Our findings point to the possibility that endogenous retrovirus protein Np9 contributes to the regulation of the p53-MDM2 pathway specifically in humans, chimpanzees and gorillas. PMID:26103464

  12. Placental invasion, preeclampsia risk and adaptive molecular evolution at the origin of the great apes: evidence from genome-wide analyses.

    Science.gov (United States)

    Crosley, E J; Elliot, M G; Christians, J K; Crespi, B J

    2013-02-01

    Recent evidence from chimpanzees and gorillas has raised doubts that preeclampsia is a uniquely human disease. The deep extravillous trophoblast (EVT) invasion and spiral artery remodeling that characterizes our placenta (and is abnormal in preeclampsia) is shared within great apes, setting Homininae apart from Hylobatidae and Old World Monkeys, which show much shallower trophoblast invasion and limited spiral artery remodeling. We hypothesize that the evolution of a more invasive placenta in the lineage ancestral to the great apes involved positive selection on genes crucial to EVT invasion and spiral artery remodeling. Furthermore, identification of placentally-expressed genes under selection in this lineage may identify novel genes involved in placental development. We tested for positive selection in approximately 18,000 genes using the ratio of non-synonymous to synonymous amino acid substitution for protein-coding DNA. DAVID Bioinformatics Resources identified biological processes enriched in positively selected genes, including processes related to EVT invasion and spiral artery remodeling. Analyses revealed 295 and 264 genes under significant positive selection on the branches ancestral to Hominidae (Human, Chimp, Gorilla, Orangutan) and Homininae (Human, Chimp, Gorilla), respectively. Gene ontology analysis of these gene sets demonstrated significant enrichments for several functional gene clusters relevant to preeclampsia risk, and sets of placentally-expressed genes that have been linked with preeclampsia and/or trophoblast invasion in other studies. Our study represents a novel approach to the identification of candidate genes and amino acid residues involved in placental pathologies by implicating them in the evolution of highly-invasive placenta. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Patterns of dental development in Homo, Australopithecus, Pan, and Gorilla.

    Science.gov (United States)

    Smith, B H

    1994-07-01

    Smith ([1986] Nature 323:327-330) distinguished patterns of development of teeth of juvenile fossil hominids as being "more like humans" or "more like apes" based on statistical similarity to group standards. Here, this central tendency discrimination (CTD) is tested for its ability to recognize ape and human patterns of dental development in 789 subadult hominoids. Tooth development of a modern human sample (665 black southern Africans) was scored entirely by an outside investigator; pongid and fossil hominid samples (59 Pan, 50 Gorilla, and 14 fossil hominids) were scored by the author. The claim of Lampl et al. ([1993] Am. J. Phys. Anthropol. 90:113-127) that Smith's 1986 method succeeds in only 8% of human cases was not sustained. Figures for overall success of classification (87% humans, 68% apes) mask important effects of teeth sampled and age class. For humans, the power of CTD varied between 53% and 92% depending on the number and kind of teeth available--nearly that of a coin toss when data described only two nearby teeth, but quite successful with more teeth or distant teeth. For apes, only age class affected accuracy: "Infant" apes (M1 development or = root 1/4), however, were correctly discriminated in 87% of cases. Overall, CTD can be considered reliable (accuracy of 92% for humans and 88% for apes) when data contrast development of distant dental fields and subjects are juveniles (not infants). Restricting analysis of fossils to specimens satisfying these criteria, patterns of dental development of gracile australopithecines and Homo habilis remain classified with African apes. Those of Homo erectus and Neanderthals are classified with humans, suggesting that patterns of growth evolved substantially in the Hominidae. To standardize future research, the computer program that operationalizes CTD is now available.

  14. Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes.

    Science.gov (United States)

    Ari, Eszter; Ittzés, Péter; Podani, János; Thi, Quynh Chi Le; Jakó, Eena

    2012-04-01

    Boolean analysis (or BOOL-AN; Jakó et al., 2009. BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. Evol. 52, 887-97.), a recently developed method for sequence comparison uses the Iterative Canonical Form of Boolean functions. It considers sequence information in a way entirely different from standard phylogenetic methods (i.e. Maximum Parsimony, Maximum-Likelihood, Neighbor-Joining, and Bayesian analysis). The performance and reliability of Boolean analysis were tested and compared with the standard phylogenetic methods, using artificially evolved - simulated - nucleotide sequences and the 22 mitochondrial tRNA genes of the great apes. At the outset, we assumed that the phylogeny of Hominidae is generally well established, and the guide tree of artificial sequence evolution can also be used as a benchmark. These offer a possibility to compare and test the performance of different phylogenetic methods. Trees were reconstructed by each method from 2500 simulated sequences and 22 mitochondrial tRNA sequences. We also introduced a special re-sampling method for Boolean analysis on permuted sequence sites, the P-BOOL-AN procedure. Considering the reliability values (branch support values of consensus trees and Robinson-Foulds distances) we used for simulated sequence trees produced by different phylogenetic methods, BOOL-AN appeared as the most reliable method. Although the mitochondrial tRNA sequences of great apes are relatively short (59-75 bases long) and the ratio of their constant characters is about 75%, BOOL-AN, P-BOOL-AN and the Bayesian approach produced the same tree-topology as the established phylogeny, while the outcomes of Maximum Parsimony, Maximum-Likelihood and Neighbor-Joining methods were equivocal. We conclude that Boolean analysis is a promising alternative to existing methods of sequence comparison for phylogenetic reconstruction and congruence analysis. Copyright © 2012 Elsevier Inc. All