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Cited by 1,414Evolution and Paleontology StudiesGenomics and Phylogenetic StudiesPrimate Behavior and Ecology

A molecular phylogeny of living primates

Open access
Perelman, Polina, Johnson, Warren E., Roos, Christian, Seuánez, Hector N., Horvath, Julie E., Moreira, Miguel A. M., Kessing, Bailey, Pontius, Joan +6 more·2011·PLoS Genetics
DOI 10.1371/journal.pgen.1001342PMC PMC3060065
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Abstract

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

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Written from the paper’s full text.

TL;DR

This study presents a highly resolved molecular phylogeny of living primates based on new genomic sequence from 186 primates representing 61 genera, using 34,927 bp from 54 nuclear genes. It clarifies primate taxonomic relationships, divergence dates, and patterns of genome evolution including rate heterogeneity and insertion/deletion variation.

Key findings

  • The phylogeny includes 191 taxa (186 primates representing 61 genera, about 90% of described genera) plus outgroups from Dermoptera, Scandentia, and Lagomorpha; 166 of 189 nodes (88%) have bootstrap values of 90–100% and Bayesian posterior probabilities of 0.9–1.0, with only 3 of 189 nodes collapsed into polytomies in bootstrap analyses.
  • Strepsirrhini split from Haplorrhini approximately 87 MYA (node 185); tarsiers are supported as sister to Simiiformes (BS = 85 MP; 98 ML; 0.99 PP) to form Haplorrhini, and Dermoptera is affirmed as the closest mammalian order to Primates, followed by Scandentia.
  • Platyrrhini diverged from Catarrhini roughly 43.5 MYA; within Cebidae, Cebus and Saimiri emerged about 20 MYA, followed by a lineage splitting to Callitrichinae and Aotus, with Aotus showing 15 synapomorphic indels, the most observed in Simiiformes, and Callitrichinae branching mirroring decreasing body size.
  • Cercopithecoidea shows low divergence, especially Papionini; Cercopithecini divergence is nearly twice that of Papionini (mean branch length = 13.1 vs. 7.43, p<0.005), Homo-Pan genetic distance ranges from 6.92 to 7.90×10−3 substitutions/site, and the global nucleotide substitution rate is 6.163×10−4 substitutions/site/MY.

Methods

  • New genomic sequence (~8 Mb) was generated from 186 primates representing 61 genera, with outgroups from Dermoptera, Scandentia, and Lagomorpha; 54 nuclear genes yielded a final 34,927 bp after correction for ambiguous sites from an original 43,493 bp per OTU.
  • DNA was extracted from blood, buffy coat, hair, buccal swabs, tissues, or cell cultures, PCR-amplified, Sanger-sequenced, aligned with MAFFT, and edited with GBLOCK; partitions included X, Y, autosome, intron, exon, and UTR segments.
  • Phylogenetic reconstruction used maximum likelihood and maximum parsimony in PAUP* and GARLI with bootstrap support (1000 MP, 100 ML), plus Bayesian BEAST analyses with an uncorrelated lognormal relaxed clock and nine fossil calibration points; indels were identified with FASTGAP and analyzed by regression and ANOVA.

Limitations

  • The paper states that only 3 of 189 nodes are polytomies in bootstrap analyses (nodes 28, 38, 158), that Lemuriformes node 158 collapses into an unresolved trichotomy, that the origin of primates remains unresolved, and that computational constraints limited BEAST analyses to five different species sets.
  • The text notes that approximately half of the 261–377 described primate species and 90% of genera are included, that the Y-chromosome tree is based on 127 males as a subset of 191 total taxa, and that some indels were in regions not amplified across all species.
  • Evident from the text: despite overall high resolution, some nodes have low support (e.g., node 158; node 187 posterior probability 0.54), and several taxonomic controversies remain, including within Galago, Cercopithecus, and Asian Colobinae.

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Integrity signals

Registry

Crossref · 10.1371/journal.pgen.1001342

Cites

86 of 86 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 55 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Strepsirrhines split with Haplorrhini approximately 87 MYA (node 185).

    “Here we provide strong evidence that strepsirrhines split with suborder Haplorrhini approximately 87 MYA (node 185).”
    Quote in the paperSubstantial claim
  • Findingown data

    Separate phylogenetic analyses of the data partitions are generally concordant.

    “Separate phylogenetic analyses of these data partitions are generally concordant.”
    Quote in the paperSubstantial claim
  • Findingown data

    Greater frequency of phylogenetic inconsistencies or unresolved nodes occur in subset trees compared with the entire concatenated data set.

    “However, greater frequency of phylogenetic inconsistencies or unresolved nodes occur in these subset trees (Figures S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13), compared with the entire concatenated data set (Figure 2, Figure S1).”
    Quote in the paperSubstantial claim
  • Findingown data

    Only 3 of 189 nodes (nodes 28, 38, 158) are polytomies in the bootstrap analyses.

    “Further, only 3 of 189 nodes (nodes 28, 38, 158) are polytomies in the bootstrap analyses (Table 1 and Table 3; Figure 2, Figure S1).”
    Quote in the paperSubstantial claim
  • Findingown data

    The greatest proportion of phylogenetically informative sites occurred in Y-linked genes (56%) compared with regions sequenced from the X-chromosome (40%) and autosomes (42%).

    “The greatest proportion of phylogenetically informative sites occurred in Y-linked genes (56%) compared with regions sequenced from the X-chromosome (40%) and autosomes (42%) (Table 4, Table S4), a finding also observed in carnivores [6], [7].”
    Quote in the paperNot a substantial claim
  • May combine two claims. 60
  • Classified as probably not a substantial claim. 21

  • May combine two claims.

    Findingcitation

    Dermoptera is the closest mammalian order relative to Primates, followed by Scandentia.

    “Rooted by Lagomorpha, the phylogeny affirms Dermoptera as the closest mammalian order relative to Primates, followed by Scandentia [16], [17].”
    • Also stated in: § Conclusions · plain
      “Dermoptera is the closest mammalian order to Primates;”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [16] JE Janecka, 2007, Molecular and genomic data identify the closest living relative of primates., Science source

      Not checked in the free run.

    • cites [17] JO Kriegs, 2007, Evolutionary history of 7SL RNA-derived SINEs in supraprimates., Trends in Genetics source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The study provides new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and includes outgroup species from Dermoptera, Scandentia, and Lagomorpha.

    “Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The ancient lineage is monophyletic and defined by a long branch and eight shared insertions/deletions (indels) (node 144).

    “The ancient lineage is monophyletic and defined by a long branch and eight shared insertions/deletions (indels) (node 144).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The phylogeny is highly resolved, with bootstrap values of 90-100% and Bayesian posterior probabilities of 0.9-1.0 at 166 of the 189 nodes (88%).

    “The phylogeny is highly resolved, with bootstrap values of 90–100% and Bayesian posterior probabilities of 0.9–1.0 at 166 of the 189 nodes (88%)(Table 1, Table 2, Table 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Daubentonia is a single relict genus defined by a long branch with high indel frequency (N = 14).

    “and today consists of a single relict genus Daubentonia defined by a long branch with high indel frequency (N = 14) (Figure 2, Figure S1, Table S7).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    The Cebidae radiation initiated with the emergence of sister taxa Cebus (Cebinae) and Saimiri (Saimirinae) approximately 20 MYA (node 113), in agreement with other molecular studies.

    “The Cebidae radiation initiated with the emergence of sister taxa Cebus (Cebinae) and Saimiri (Saimirinae) approximately 20 MYA (node 113), in agreement with other molecular studies [27]-[30].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [27]-[30]

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Within Lorisidae, the four extant genera split into the African subfamily Perodicticinae (Arctocebus, Perodictus) and the Asian subfamily Lorisinae (Nycticebus, Loris) and are the most divergent within all of primates.

    “Within Lorisidae, the four extant genera split into the African subfamily Perodicticinae (Arctocebus, Perodictus) and the Asian subfamily Lorisinae (Nycticebus, Loris) and are the most divergent within all of primates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Next to radiate are the Atelidae (node 126), with the most basal lineage leading to Alouatta, followed by the divergence of Ateles from a South American lineage comprised of sister genera Lagothrix and Brachyteles.

    “Next to radiate are the Atelidae (node 126), with the most basal lineage leading to Alouatta (howler monkeys), currently widely distributed from Mexico to northern Argentina, followed by the divergence of Ateles (spider monkeys) from South American lineage comprised of sister genera (node 121) of Lagothrix (woolly monkeys) and Brachyteles (muriquis).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A few indels define alternate evolutionary topologies, such as tarsiers aligned with Strepsirrhini (1 indel, ZFX) or Scandentia (1 indel, DCTN2), compared with those that support an ancestral grouping of Tarsiiformes + Strepsirrhini + Dermoptera + Scandentia (2 indels, PLCB4, POLA1).

    “A few indels (Table S5) define alternate evolutionary topologies, such as tarsiers aligned with Strepsirrhini (1 indel, ZFX) or Scandentia (1 indel, DCTN2), compared with those that support an ancestral grouping of Tarsiiformes +Strepsirrhini +Dermoptera +Scandentia (2 indels, PLCB4, POLA1).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Our data affirm the ancient split of Strepsirrhini, approximately 68.7 MYA (node 144), into the progenitors of Lemuriformes/Chiromyiformes (origin 58.6 MYA, node 174) and Lorisiformes (origin 40.3 MYA, node 184).

    “Our data affirm the ancient split of Strepsirrhini, approximately 68.7 MYA (node 144), into the progenitors of Lemuriformes/Chiromyiformes (origin 58.6 MYA, node 174) and Lorisiformes (origin 40.3 MYA, node 184).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    This branching pattern among Lemuriformes families agrees with earlier nuclear gene segment findings and differs from studies using mtDNA sequence and Alu insertion variation.

    “This branching pattern among families agrees with earlier nuclear gene segment findings [20] that differ from studies using mtDNA sequence and Alu insertion variation which were unable to resolve these hierarchical associations [19].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [20] JE Horvath, 2007, Primate comparative genomics: lemur biology and evolution., Trends in Genetics source

      Not checked in the free run.

    • cites [19] C Roos, 2004, Primate jumping genes elucidate strepsirrhine phylogeny., Proceedings of the National Academy of Sciences of the United States of America source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Lorisiformes evolution includes the radiation of Lorisidae (37 MYA, node 179) and Galagidae (19.9 MYA, node 183) species.

    “Lorisiformes evolution includes the radiation of Lorisidae (pottos and lorises, 37 MYA, node 179) and Galagidae (19.9 MYA, node 183) species.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The evolution of the four Lemuriformes families began 38.6 MYA (node 173) with the emergence of Lemuridae, followed by Indriidae and a monophyletic lineage that split 32.9 MYA (node 152) to form the sister lineages of Lepilemuridae and Cheirogaleidae.

    “The evolution of the four Lemuriformes families began 38.6 MYA (node 173) with the emergence of Lemuridae, followed by Indriidae and a monophyletic lineage that split 32.9 MYA (node 152) to form the sister lineages of Lepilemuridae and Cheirogaleidae.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    The hierarchical branching order among the remaining Callitrichinae of Leontopithecus, Callimico, Callithrix and Mico mirrors decreasing body size and culminates with the smallest platyrrhine species, Cebuella pygmaea, as most derived.

    “The hierarchical branching order among the remaining Callitrichinae of Leontopithecus, Callimico, Callithrix and Mico mirrors decreasing body size and culminates with the smallest platyrrhine species, Cebuella pygmaea, as most derived.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Asian (tribe Presbytini) and African (tribe Colobini) genera are monophyletic (nodes 53 and 61, respectively), supporting earlier genetic findings over morphology-based taxonomy.

    “Asian (tribe Presbytini) and African (tribe Colobini) genera are monophyletic (nodes 53 and 61, respectively), supporting earlier genetic findings [4], [40] over morphology-based taxonomy [2], [45].”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [4] HJ Chatterjee, 2009, Estimating the phylogeny and divergence times of primates using a supermatrix approach., BMC Evolutionary Biology source

      Not checked in the free run.

    • cites [40] N Ting, 2008, Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys., Molecular Phylogenetics and Evolution source

      Not checked in the free run.

    • cites [2] CP Groves, 2001, Primate taxonomy.

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The Presbytis lineage, distinguished by 3 indel events (node 56), diverged first within Asian Colobinae, followed by the odd-nosed group (Rhinopithecus, Nasalis, Pygathrix), Trachypithecus and Semnopithecus.

    “Here, the Presbytis lineage, distinguished by 3 indel events (node 56), diverged first within Asian Colobinae, followed by the odd-nosed group (Rhinopithecus, Nasalis, Pygathrix), Trachypithecus and Semnopithecus.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    Colobinae radiation started approximately 12 MYA (node 42) with species adapted to an arboreal, leaf-eating existence.

    “Colobinae radiation started approximately 12 MYA (node 42) with species adapted to an arboreal, leaf-eating existence.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    In Callitrichinae, Saguinus is the first to diverge with S. fuscicollis currently distributed south of the Amazon River.

    “In Callitrichinae, Saguinus is the first to diverge with S. fuscicollis currently distributed south of the Amazon River.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Aotus species divide into sister lineages, with the "grey-necked" species (A. trivirgatus + A. lemurinus griseimembra) distributed north of the Amazon River, and "red-necked" species A. nancymaae, A. azarae species and associated subspecies located most to the south (nodes 98, 101, 102).

    “Aotus species divide into sister lineages, with the “grey-necked” species (A. trivirgatus + A. lemurinus griseimembra) distributed north of the Amazon River, and “red-necked” species A. nancymaae, A. azarae species and associated subspecies located most to the south (nodes 98, 101, 102).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    Cercopithecidae includes two subfamilies, Colobinae and Cercopithecinae, which diverged 18 MYA (node 62).

    “Cercopithecidae includes two subfamilies, Colobinae and Cercopithecinae, which diverged 18 MYA (node 62)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The Aotus lineage (node 98) radiated with unusually high numbers of synapomorphic indels (N = 15), the most observed in Simiiformes.

    “The Aotus lineage (node 98) radiated with unusually high numbers of synapomorphic indels (N = 15), the most observed in Simiiformes (Table 2 and Table 3)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    The genus diversified into northern (S. bicolor, S. midas, S. martinsi, S. geoffroyi, S. oedipus) and south Amazonian species (S. imperator, S. mystax, S. labiatus); a trend generally similar to findings based on mtDNA and single nuclear genes.

    “Subsequently, the genus diversified into northern (S. bicolor, S. midas, S. martinsi, S. geoffroyi, S. oedipus) and south Amazonian species (S. imperator, S. mystax, S. labiatus); a trend generally similar to findings based on mtDNA [33] and single nuclear genes [34].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [33] SJ Cropp, 1999, Historical biogeography of tamarins, genus Saguinus: The molecular phylogenetic evidence., American Journal of Physical Anthropology source

      Not checked in the free run.

    • cites [34] FC Canavez, 1999, Phylogenetic relationships of the callitrichinae (Platyrrhini, Primates) based on beta(2)-microglobulin DNA sequences., American Journal of Primatology source

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    Differences in behavior, morphology, karyology, and genetic data between the two island populations support the taxonomic designation as two separate species of Bornean (P. pygmaeus) and Sumatran orangutans (P. abelii), and these designations are upheld by the data presented here.

    “Differences in behavior, morphology, karyology, and genetic data between the two island populations [2] support the taxonomic designation as two separate species of Bornean (P. pygmaeus) and Sumatran orangutans (P. abelii), and these designations are upheld by the data presented here.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [2] CP Groves, 2001, Primate taxonomy.

      Not checked in the free run.

  • May combine two claims.

    Findingnone given

    Generally arboreal, Miopithecus and Allenopithecus are early offshoots with respect to the two Cercopithecini subclades formed approximately 7 MYA.

    “Generally arboreal, Miopithecus and Allenopithecus are early offshoots with respect to the two Cercopithecini subclades formed approximately 7 MYA.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Cercopithecini include lineages rooted by divergent monotypic genera followed by more recent speciation, characterized by transition from an arboreal to a terrestrial lifestyle.

    “Cercopithecini (guenons, patas monkey, talapoin, green monkeys) include lineages rooted by divergent monotypic genera followed by more recent speciation, characterized by transition from an arboreal to a terrestrial lifestyle.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Based on 54 gene regions, Homo-Pan genetic distance range from 6.92 to 7.90×10−3 substitutions/site (P. paniscus and P. troglodytes, respectively), which is less than previous estimates based on large scale sequencing of specific regions such as chromosome 7.

    “Based on 54 gene regions, Homo-Pan genetic distance range from 6.92 to 7.90×10−3 substitutions/site (P. paniscus and P. troglodytes, respectively), which is less than previous estimates based on large scale sequencing of specific regions such as chromosome 7 [50].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [50] N Elango, 2006, Variable molecular clocks in hominoids., Proceedings of the National Academy of Sciences of the United States of America source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The branch forming the Homo and Pan lineage apart from Gorilla is relatively short (node 73, 27 steps MP, 0 indels) compared with that of the Pan genus (node 72, 91 steps MP, 2 indels).

    “The branch forming the Homo and Pan lineage apart from Gorilla is relatively short (node 73, 27 steps MP, 0 indels) compared with that of the Pan genus (node 72, 91 steps MP, 2 indels)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The global rate of nucleotide substitution across the entire primate phylogeny is 6.163×10−4 substitutions/site/MY, but exhibits significant heterogeneity across lineages and among branches.

    “The global rate of nucleotide substitution across the entire primate phylogeny is 6.163×10−4 substitutions/ site/ MY, but exhibits significant heterogeneity across lineages (Figure 3) and among branches (Table 1, Table 2, Table 3; Tables S6, S7, S8).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    The Cercopithecus lineage (node 34) radiated after Miopithecus and retained an arboreal lifestyle.

    “The Cercopithecus lineage (node 34) radiated after Miopithecus and retained an arboreal lifestyle.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Nomascus species appear more recent than Symphalangus and Hylobates, with node divergence dates estimated at less than 1 MY.

    “Moreover, Nomascus species appear more recent than Symphalangus and Hylobates, with node divergence dates estimated at less than 1 MY (Table 3, Table S9, Figure 2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The phylogeny affirms Groves proposal that Lophocebus and Theropithecus are distinct clades apart from Papio (nodes 18, 19), although the average nucleotide divergence among these three genera are generally less than between other recognized Papionin genera (Macaca, Mandrillus, Cercocebus).

    “Moreover, the phylogeny affirms Groves [2] proposal that Lophocebus and Theropithecus are distinct clades apart from Papio (nodes 18, 19), although the average nucleotide divergence among these three genera are generally less than between other recognized Papionin genera (Macaca, Mandrillus, Cercocebus) (Figure 2, Figure S1, Table 3, Table S9).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [2] CP Groves, 2001, Primate taxonomy.

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    Macaca diverged 5.1 MYA and today is represented by an African lineage comprised of a single species M. sylvanus, and an Asian lineage consisting of well-defined species groups (fascicularis, sinica, mulatta, nemestrina, Sulawesi) inhabiting India and Asia, SE Asia and Sundaland.

    “One of the more familiar genera within Cercopithecoidea, Macaca (macaques) diverged 5.1 MYA and today is represented by an African lineage comprised of a single species M. sylvanus, and an Asian lineage consisting of well-defined species groups (fascicularis, sinica, mulatta, nemestrina, Sulawesi) inhabiting India and Asia, SE Asia and Sundaland [49].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [49] T Ziegler, 2007, Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the M. silenus group., Molecular Phylogenetics and Evolution source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The eight species included in this study form three clades that coincide with genus designation (absent is Hoolock; nodes 64-69) that diverged rapidly 8.9 MYA.

    “The eight species included in this study form three clades that coincide with genus designation (absent is Hoolock; nodes 64–69) that diverged rapidly 8.9 MYA.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Genome divergence varies across primate lineages, with the least inter-specific differences observed in Cercopithecidae lineages and the most in Lorisidae.

    “Genome divergence varies across primate lineages, with the least inter-specific differences observed in Cercopithecidae lineages and the most in Lorisidae”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The second Cercopithecini subclade, rooted by Allenopithecus, forms a terrestrial clade of Erythrocebus patas and Chlorocebus species, with Cercopithecus l'hoesti separated from the other Cercopithecus.

    “The second, rooted by Allenopithecus, forms a terrestrial clade of Erythrocebus patas and Chlorocebus species, with Cercopithecus l'hoesti separated the other Cercopithecus.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The highly endangered orangutan forms the single genus Pongo in subfamily Ponginae (nodes 75-76), the sister lineage to Homininae.

    “The highly endangered orangutan forms the single genus Pongo in subfamily Ponginae (nodes 75–76), the sister lineage to Homininae.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    With the exception of the fascicularis group, which is split in this study whereby M. arctoides [fascicularis] is more closely aligned with M. thibetana [sinica] rather than M. fascicularis as expected, our data otherwise strongly support these macaque species groups (nodes 6, 11).

    “With the exception of the fascicularis group, which is split in this study whereby M. arctoides [fascicularis] is more closely aligned with M. thibetana [sinica] rather than M. fascicularis as expected, our data otherwise strongly support these macaque species groups (nodes 6, 11).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    In the New World, the phylogenetic placement of the unique, nocturnal Aotinae is unambiguously resolved, diverging rapidly after the sister lineage of Cebinae+Saimirinae and prior to the Callitrichinae within the family Cebidae.

    “In the New World, the phylogenetic placement of the unique, nocturnal Aotinae is unambiguously resolved, diverging rapidly after the sister lineage of Cebinae+Saimirinae and prior to the Callitrichinae within the family Cebidae.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Excluding the infraorders Tarsiiformes (25 indels) and Chiromyiformes (14 indels) due to statistically inadequate sampling, the indel frequency per branch varies by a factor of 20 with the greatest accumulation within Lorisidae (particularly Arctocebus calabarensis) and the least in Cercopithecidae.

    “Excluding the infraorders Tarsiiformes (25 indels) and Chiromyiformes (14 indels) due to statistically inadequate sampling, the indel frequency per branch varies by a factor of 20 (Table 1, Table 2, Table 3; Tables S7, S8, S9) with the greatest accumulation within Lorisidae (particularly Arctocebus calabarensis) and the least in Cercopithecidae (Figure 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    The pattern of divergence of Callitrichinae is correlated with a gradation in species size, supporting "phyletic dwarfism".

    “Further, the pattern of divergence of Callitrichinae is correlated with a gradation in species size, supporting “phyletic dwarfism” [32], [35].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [32] SM Ford, 1992, Systematics and body size: implications for feeding adaptations in New World monkeys., American Journal of Physical Anthropology source

      Not checked in the free run.

    • cites [35] SM Ford, 1980, Callitrichids as phyletic dwarfs, and the place of Callitrichidae in Platyrrhini., Primates source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The distribution of indels is ubiquitous in both coding and noncoding segments, but is markedly disjunct among primate lineages.

    “Here, the distribution of indels is ubiquitous in both coding and noncoding segments (Tables S4, S5, S6), but is markedly disjunct among primate lineages (Figure 3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    Approximately half of the 261-377 species and 90% of the genera are included, facilitating resolution of long-standing phylogenetic ambiguities.

    “Approximately half of the 261–377 species and 90% of the genera are included facilitating resolution of long-standing phylogenetic ambiguities.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Current views concur that 67-69 primate genera originated from a common ancestor during the Cretaceous/Paleocene boundary roughly 80-90 MYA.

    “Primate taxonomy has undergone considerable revision but current views [1]-[3] concur that 67–69 primate genera originated from a common ancestor during the Cretaceous/Paleocene boundary roughly 80–90 MYA.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [1]-[3]

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The exact number of primate genera is controversial and species counts range from 261-377.

    “The exact number of primate genera is controversial and species counts range from 261–377 [1]-[3].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [1]-[3]

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    An Eocene expansion formed the major extant primate lineages: Strepsirrhini (Lorisiformes, Chiromyiformes, Lemuriformes), Tarsiiformes, and Simiiformes (Platyrrhini and Catarrhini).

    “An Eocene expansion formed the major extant lineages of 1) Strepsirrhini, which is composed of Lorisiformes (galagos, pottos, lorises), Chiromyiformes (Malagasy aye-aye) and Lemuriformes (Malagasy lemurs); 2) Tarsiiformes (tarsiers) and 3) Simiiformes composed of Platyrrhini (New World monkeys) and Catarrhini”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [1]-[3]

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Optimal resolution of node 158 is observed with exon sequences, indicating that intron sites may be saturated, while more conserved coding regions remain informative and reflect the ancient rapid radiation of Lemuriformes families.

    “Optimal resolution of this node is observed with exon sequences (Figures S8 and S9), indicating that intron sites may be saturated, while more conserved coding regions remain informative and reflect the ancient rapid radiation of Lemuriformes families.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Inter-specific genetic differences are roughly half those observed among other colobine genera and may indicate that recent speciation, taxonomic over-splitting, reticulate evolution, or a combination thereof are common within the Asian Colobinae radiation.

    “Inter-specific genetic differences are roughly half those observed among other colobine genera (Figure 2, Figure S1, Table 3, Table S9) and may indicate that recent speciation, taxonomic over-splitting, reticulate evolution, or a combination thereof, (e. g. see [40], [44], [46]) are common within the Asian Colobinae radiation.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [40] N Ting, 2008, Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys., Molecular Phylogenetics and Evolution source

      Not checked in the free run.

    • cites [44] KP Karanth, 2008, Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates : Colobinae)., Molecular Phylogenetics and Evolution source

      Not checked in the free run.

    • cites [46] KP Karanth, 2008, Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae)., Journal of biosciences source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    This phylogenetic depiction of Callitrichinae is concordant with several other morphological and reproductive traits related to dwarfism and perhaps reflects adaptive evolution selected by fluctuating resource availability within the Amazon and Atlantic coast rainforests.

    “This phylogenetic depiction of Callitrichinae is concordant with several other morphological and reproductive traits [32], [35] related to dwarfism and perhaps reflects adaptive evolution selected by fluctuating resource availability within the Amazon and Atlantic coast rainforests [36].”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [32] SM Ford, 1992, Systematics and body size: implications for feeding adaptations in New World monkeys., American Journal of Physical Anthropology source

      Not checked in the free run.

    • cites [35] SM Ford, 1980, Callitrichids as phyletic dwarfs, and the place of Callitrichidae in Platyrrhini., Primates source

      Not checked in the free run.

    • cites [36] M Moynihan, 1976, The New World primates : adaptive radiation and the evolution of social behavior, languages, and intelligence.

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The unusual depth of divergence in Aotus may exemplify adaptive speciation as Aotus are the only nocturnal Simiiformes, and thereby may have reduced competition with diurnal small-bodied platyrrhines inhabiting the same neotropical environments.

    “The unusual depth of divergence (i.e. sizeable nucleotide substitutions/site; high indel frequency) may exemplify adaptive speciation as Aotus are the only nocturnal Simiiformes [31], and thereby may have reduced competition with diurnal small-bodied platyrrhines inhabiting the same neotropical environments.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] F Ankel-Simons, 2008, Diurnality, Nocturnality, and the Evolution of Primate Visual Systems., American Journal of Physical Anthropology source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    As odd-nosed species are not exclusively arboreal and folivorous, the results indicate either morphological convergence between Presbytis with Trachypithecus and Semnopithecus, adaptation for an expanded diet in the odd-nosed group, or that a folivorous diet is a symplesiomorphic trait within Asian colobines.

    “As odd-nosed species are not exclusively arboreal and folivorous, the results indicate either 1) morphological convergence between Presbytis with Trachypithecus and Semnopithecus, 2) adaptation for an expanded diet in the odd-nosed group, or 3) that a folivorous diet is a symplesiomorphic trait within Asian colobines.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The least inter-specific differences in Cercopithecidae reflect recent speciation, and the most in Lorisidae reflect the more ancient origins of the latter.

    “reflecting recent speciation in the former and the more ancient origins of the latter (Figure 3, Table 1, Table 3, Tables S7 and S9).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    This paraphyly, also reported in earlier genetic studies and counter to initial morphological classifications, suggests taxonomic revision of Cercopithecus.

    “This paraphyly, also reported in earlier genetic studies [39], [47], [48] and counter to initial morphological classifications [2], suggests taxonomic revision of Cercopithecus.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [39] J Xing, 2007, A mobile element-based evolutionary history of guenons (tribe Cercopithecini)., BMC Biology source

      Not checked in the free run.

    • cites [47] AJ Tosi, 2004, Sex chromosome phylogenetics indicate a single transition to terrestriality in the guenons (tribe Cercopithecini)., Journal of Human Evolution source

      Not checked in the free run.

    • cites [48] AJ Tosi, 2003, Cercopithecine Y-chromosome data provide a test of competing morphological evolutionary hypotheses., Molecular Phylogenetics and Evolution source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Large-scale genome sequence analysis demonstrate that indel formation is an indicator of genome plasticity, positively correlated with adjacent nucleotide substitution rate, gene segmental duplication, chromosomal position, hybridization between species and speciation, and is enhanced by molecular mechanisms of recombination among repetitive elements.

    “Further, large-scale genome sequence analysis demonstrate that indel formation is an indicator of genome plasticity, positively correlated with adjacent nucleotide substitution rate [56], [57], gene segmental duplication, chromosomal position, hybridization between species and speciation, and is enhanced by molecular mechanisms of recombination among repetitive elements [58]-[60].”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [56] LC Zhu, 2009, Genomewide Association between Insertions/Deletions and the Nucleotide Diversity in Bacteria., Molecular Biology and Evolution source

      Not checked in the free run.

    • cites [57] DC Tian, 2008, Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes., Nature

      Not checked in the free run.

    • cites [58]-[60]

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    The TMRCA of Simiiformes is 43.0 MYA (stdev 4.5).

    “B) mean = 43.0 MYA, stdev = 4.5 for TMRCA of Simiiformes [79], [80]”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [79], [80]

      Not checked in the free run.

    • The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    Resolution of the primate species phylogeny here provides a validated framework essential in the development, interpretation and discovery of the genetic underpinnings of human adaptation and disease.

    “Resolution of the primate species phylogeny here provides a validated framework essential in the development, interpretation and discovery of the genetic underpinnings of human adaptation and disease.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    A negative control (no template) was included in every whole-genome amplification and was verified by downstream PCR and sequencing.

    “A negative control (no template) was included in every WGA and was verified by downstream PCR and sequencing.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Only PCR products that produced single bands were sequenced.

    “Only PCR products that produced single bands were sequenced.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Regions of sequence ambiguity within the alignment were identified by GBLOCK and removed from subsequent phylogenetic analyses.

    “Regions of sequence ambiguity within the alignment were identified by GBLOCK version 0.91b [72], and removed from subsequent phylogenetic analyses.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [72] G Talavera, 2007, Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments., Systematic Biology source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The low divergence in Cercopithecoidea is consistent with reticulate evolution, recent speciation and possibly augmented by taxonomic over-splitting.

    “consistent with reticulate evolution, recent speciation and possibly augmented by taxonomic over-splitting.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    Support for nodes within the phylogeny used bootstrap analysis with identical settings established for each method of phylogenetic reconstruction and values greater than 50% were retained.

    “Support for nodes within the phylogeny used bootstrap analysis with identical settings established for each method of phylogenetic reconstruction and values greater than 50% were retained.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    The TMRCA of galagids and lorisids is 40.0 MYA (stdev 3.0).

    “A) mean = 40.0 MYA, standard deviation (stdev) = 3.0 for time to most recent common ancestor (TMRCA) of galagids and lorisids [78]”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [78] ER Seiffert, 2003, Fossil evidence for an ancient divergence of lorises and galagos., Nature source

      Not checked in the free run.

    • The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.

  • May combine two claims.

    Interpretationreasoning

    A parsimonious interpretation of the present data suggests an Asian origin for primates because the ancient Asian Tarsiiformes and the strepsirrhine Lorisinae are most basal and the closest relatives of primates, Dermoptera and Scandentia, are also exclusive to Asia.

    “A parsimonious interpretation of the present data would suggest an Asian origin as the ancient Asian Tarsiiformes and the strepsirrhine Lorisinae are most basal and the closest relatives of primates, Dermoptera and Scandentia, are also exclusive to Asia.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductcitation

    Multiple sequence files for each gene segment were aligned by MAFFT, imported into Se-Al, and verified by eye.

    “Multiple sequence files for each gene segment amplified were aligned by MAFFT version 6 [69], [70], imported into Se-Al ver 2.0a11 [71] and verified by eye.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [69], [70]

      Not checked in the free run.

    • cites [71] A Rambaut, 2007, Se-Al. Sequence Alignment Editor.

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Only indels that correctly conformed to the species associations of the primate phylogeny were used and identified as a subset of synapomorphic events.

    “Second, only indels that correctly conformed to the species associations of the primate phylogeny (Figure 2) were used and identified as a subset of synapomorphic events (Table 1, Table 2, Table 3; Tables S5, S6).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Indels in regions that did not amplify across all species were identified as synapomorphic for a lineage providing ∼70% of the relevant species were successfully PCR amplified, and that species with missing sequence for the indel did not all occur on the same node within the lineage.

    “Infrequently, some indels included in the analysis were positioned in regions that did not amplify across all species. In these cases, indels were identified as synapomorphic for a lineage providing ∼70% of the relevant species were successfully PCR amplified, and that species with missing sequence for the indel did not all occur on the same node within the lineage.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Trees sampled from the first 1 million generations were discarded.

    “Log files from each run were imported into Tracer ver 1.4.1, and trees sampled from the first 1 million generations were discarded.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Mixing of trees was assessed in Tracer by examination of ESS values.

    “Mixing of trees was assessed in Tracer by examination of ESS values.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    All indels were identified using FASTGAP on GBLOCKED alignments and verified by eye.

    “First, all indels were identified using FASTGAP on GBLOCKED alignments and verified by eye.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Four to seven independent MCMC runs for each analysis were run for 20-100 million generations to ensure sampling of ESS values.

    “Four to seven independent Markov chain Monte Carlo (MCMC) runs for each analysis were run for 20–100 million generations to ensure sampling of estimated sample size (ESS) values.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    The mean root height of all Primates is 90.0 MYA (stdev 6.0) based on molecular estimates.

    “A normal prior for the mean root height of 90.0 MYA with stdev = 6.0 was used based on molecular estimates of MRCA of all Primates [14], [82], [85].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [14], [82], [85]

      Not checked in the free run.

    • The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.

  • Classified as probably not a substantial claim. May combine two claims.

    Premisenone given

    The calibration points selected are based on fossil dates that have undergone extensive review in previous publications and are supported by a consensus of paleoanthropologists.

    “The calibration points selected are based on fossil dates that have undergone extensive review in previous publications and are supported by a consensus of paleoanthropologists.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    The number of MCMC steps was more than adequate, with ESS of all parameters often exceeding 200, and Tracer plots showing strong equilibrium after discarding burn-in.

    “Analysis of these parameters in Tracer suggested that the number of MCMC steps was more than adequate, with ESS of all parameters often exceeding 200, and Tracer plots showing strong equilibrium after discarding burn-in.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The TMRCA of Hominidae is 15.5 MYA (stdev 2.5).

    “G) mean = 15.5 MYA, stdev = 2.5 for TMRCA of Hominidae [14]”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [14] A Matsui, 2009, Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs., Gene source

      Not checked in the free run.

    • The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.
73 of 73

  • The paper relies on this without support.

    Primate taxonomy is complex and controversial, with marginal unifying consensus on the evolutionary hierarchy of extant primate species.

    “However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species.”

  • The paper relies on this without support.

    The phylogenetic hierarchy of primate species has only modest local (family and genus level) molecular resolution with little consensus on overall primate radiations.

    “Markedly absent from these many advances however, is a formal evolutionary context to interpret these findings, as the phylogenetic hierarchy of primate species has only modest local (family and genus level) molecular resolution with little consensus on overall primate radiations.”

  • The paper relies on this without support.

    Recent application of molecular genetic data to resolve primate systematics has been informative but limited in scope and constrained to specific subsets of taxa.

    “Recent application of molecular genetic data to resolve primate systematics has been informative, but limited in scope and constrained to just specific subsets of taxa.”

  • The paper relies on this without support.

    Whole genome sequencing of 12 primate species is now completed or nearly so.

    “Although whole genome sequencing of 12 primate species are now completed, or nearly so, broader genome representation of man's closest relatives is necessary to interpret human evolution, adaptation and genome structure to assist in biomedical advances.”

  • The authors state this as an assumption.

    The ingroup is monophyletic with respect to the outgroup.

    “with the ingroup assumed to be monophyletic with respect to the outgroup.”
5 of 5

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • New World monkeys comprise the parvorder Platyrrhini, and divergence of this taxon from Old World primates and hominoids occurred approximately 43 million years ago.

    “NWM comprise the parvorder Platyrrhini, and estimates based on molecular clocks suggest a divergence of this taxon from Old World primates and hominoids ~43 Mya”

    From Neuropeptide diversity and the regulation of social behavior in New World primates (2016) · cites this paper as Perelman et al., 2011

  • Primates as an Order diverged from other mammalian forms approximately 80-90 million years ago.

    “Primates as an Order diverged from other mammalian forms approximately 80-90 million years ago (Mya; (Perelman et al., 2011)”

    From Neuropeptide diversity and the regulation of social behavior in New World primates (2016) · cites this paper as Perelman et al., 2011

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • A fourth node is marked as collapsed in bootstrap analyses

    Minor

    The text names only nodes 28, 38, and 158 as bootstrap polytomies, but Table 2 marks node 81 with Note A for both bootstrap analyses. Note A is defined as a node collapsed into a polytomy by bootstrap analyses.

  • Node 144 has eight indels in the text but nine in Table 1

    Minor

    The text assigns eight shared indels to node 144, whereas Table 1 lists nine indels for that node.

  • Y-linked informative-site proportion is overstated

    Minor

    Table 4 gives 1,312 informative Y-linked sites out of 2,630 Y-linked sites, or 49.89%, rather than the stated 56%. Its tabulated value of 55.59% is also inconsistent with those counts.

    Reported 56 · recomputed 49.885932

  • Coding and non-coding lengths do not total the analyzed sequence

    Minor

    The stated coding and non-coding lengths sum to 31,927 bp, not the reported 34,927 bp analyzed.

    Reported 34927 · recomputed 31927

4 of 4

Cites

Flagged first, then by citations

3 of the 89 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Related

Authors
Perelman, P., Johnson, W. E., Roos, C., Seuánez, H. N., Horvath, J. E., Moreira, M. A. M., Kessing, B., Pontius, J., Roelke, M., Rumpler, Y., Schneider, M. P. C., Silva, A., O'Brien, S. J., & Pecon-Slattery, J.
Affiliations
  • Frederick National Laboratory for Cancer Research (US)
  • National Cancer Institute (US)
  • German Primate Center (DE)
  • Universidade Federal do Rio de Janeiro (BR)
  • Duke University (US)
  • Université de Strasbourg (FR)
  • Universidade Federal do Pará (BR)
ORCID
Venue
PLoS Genetics
Publisher
Public Library of Science (PLoS)
Published
2011-03-17
Volume
7
Issue
3
Pages
e1001342
ISSN
  • 1553-7390 (ISSN-L)
  • 1553-7404
DOI
10.1371/journal.pgen.1001342
PMC
PMC3060065
OpenAlex
W2144820135
Semantic Scholar
fe3c21d27cf4a3bb815467dcde063248e497b923
Cited by
1,414
References
89
Citations by year
2026: 43 · 2025: 53 · 2024: 53 · 2023: 62 · 2022: 91 · 2021: 79 · 2020: 132 · 2019: 81 · 2018: 157 · 2017: 120 · 2016: 111 · 2015: 94 · 2014: 127 · 2013: 99 · 2012: 82
FWCI
74.43
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Genetics (publishedVersion, public-domain)
  • PubMed Central (publishedVersion, public-domain)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
  • GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
Funders
  • U.S. Department of Health and Human Services (N01-CO-12400)
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico
  • National Institutes of Health (n01co12400-79-0-22, N01-CO-12400)
  • National Cancer Institute (CO-12400, N01CO12400, N01-CO-012400)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Social Sciences › Psychology › Social Psychology › Primate Behavior and Ecology
Keywords
primate phylogeny, comparative genomics, primate taxonomy, human evolution, primate genomics, Dermoptera, tree shrew, lagomorphs, reticulate evolution, speciation, zoonotic emergence, endangered species conservation
MeSH terms
Animals, Female, Male, Phylogeny, Primates, Genetic Variation, Genome, Computational Biology

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-09.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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