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A Molecular Phylogeny of Living Primates
Open accessAbstract
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.
Overview
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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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50 Own result · 35 Not checked yet · 15 Own interpretation · 14 No basis given · 11 Own method
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In the paper
“Here we provide strong evidence that strepsirrhines split with suborder Haplorrhini approximately 87 MYA (node 185).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Resolution of Early Primate Divergence
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“Separate phylogenetic analyses of these data partitions are generally concordant.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion
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“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion
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“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion
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“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion
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“Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered.”
§ A Molecular Phylogeny of Living Primates > Abstract
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In the paper
“Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered.”
§ A Molecular Phylogeny of Living Primates > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered.”
§ A Molecular Phylogeny of Living Primates > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered.”
§ A Molecular Phylogeny of Living Primates > Abstract
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In the paper
“Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered.”
§ A Molecular Phylogeny of Living Primates > Abstract
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In the paper
“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;”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Resolution of Early Primate Divergence
What the sources say
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In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Abstract
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“The ancient lineage is monophyletic and defined by a long branch and eight shared insertions/deletions (indels) (node 144).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Resolution of Early Primate Divergence
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“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion
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“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Strepsirrhini
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“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
What the sources say
- Not checked yetcites [27]-[30]
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In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Strepsirrhini
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“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
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“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Resolution of Early Primate Divergence
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In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Strepsirrhini
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“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Strepsirrhini
What the sources say
- Not checked yetcites [20] JE Horvath, 2007, Primate comparative genomics: lemur biology and evolution., Trends in Genetics source
- Not checked yetcites [19] C Roos, 2004, Primate jumping genes elucidate strepsirrhine phylogeny., Proceedings of the National Academy of Sciences of the United States of America source
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In the paper
“Lorisiformes evolution includes the radiation of Lorisidae (pottos and lorises, 37 MYA, node 179) and Galagidae (19.9 MYA, node 183) species.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Strepsirrhini
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“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Strepsirrhini
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“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
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In the paper
“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
What the sources say
- Not checked yetcites [4] HJ Chatterjee, 2009, Estimating the phylogeny and divergence times of primates using a supermatrix approach., BMC Evolutionary Biology source
- Not checked yetcites [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 yetcites [2] CP Groves, 2001, Primate taxonomy.
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In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
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In the paper
“Colobinae radiation started approximately 12 MYA (node 42) with species adapted to an arboreal, leaf-eating existence.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
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In the paper
“In Callitrichinae, Saguinus is the first to diverge with S. fuscicollis currently distributed south of the Amazon River.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
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In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
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“Cercopithecidae includes two subfamilies, Colobinae and Cercopithecinae, which diverged 18 MYA (node 62)”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
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In the paper
“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)”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
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“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
What the sources say
- Not checked yetcites [33] SJ Cropp, 1999, Historical biogeography of tamarins, genus Saguinus: The molecular phylogenetic evidence., American Journal of Physical Anthropology source
- Not checked yetcites [34] FC Canavez, 1999, Phylogenetic relationships of the callitrichinae (Platyrrhini, Primates) based on beta(2)-microglobulin DNA sequences., American Journal of Primatology source
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“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Hominoidea
What the sources say
- Not checked yetcites [2] CP Groves, 2001, Primate taxonomy.
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“Generally arboreal, Miopithecus and Allenopithecus are early offshoots with respect to the two Cercopithecini subclades formed approximately 7 MYA.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
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In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
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In the paper
“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Hominoidea
What the sources say
- Not checked yetcites [50] N Elango, 2006, Variable molecular clocks in hominoids., Proceedings of the National Academy of Sciences of the United States of America source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“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)”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Hominoidea
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Genome Divergence, Rate Heterogeneity, and Indels
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The Cercopithecus lineage (node 34) radiated after Miopithecus and retained an arboreal lifestyle.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Hominoidea
hedged- Asserted: passes — The authors put it forward as true.
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In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
What the sources say
- Not checked yetcites [2] CP Groves, 2001, Primate taxonomy.
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
What the sources say
- Not checked yetcites [49] T Ziegler, 2007, Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the M. silenus group., Molecular Phylogenetics and Evolution source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Hominoidea
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Genome divergence varies across primate lineages, with the least inter-specific differences observed in Cercopithecidae lineages and the most in Lorisidae”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Genome Divergence, Rate Heterogeneity, and Indels
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The second, rooted by Allenopithecus, forms a terrestrial clade of Erythrocebus patas and Chlorocebus species, with Cercopithecus l'hoesti separated the other Cercopithecus.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
plain- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The highly endangered orangutan forms the single genus Pongo in subfamily Ponginae (nodes 75–76), the sister lineage to Homininae.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Hominoidea
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Conclusions
boosted- Asserted: passes — The authors put it forward as true.
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In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Genome Divergence, Rate Heterogeneity, and Indels
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Further, the pattern of divergence of Callitrichinae is correlated with a gradation in species size, supporting “phyletic dwarfism” [32], [35].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Conclusions
What the sources say
- Not checked yetcites [32] SM Ford, 1992, Systematics and body size: implications for feeding adaptations in New World monkeys., American Journal of Physical Anthropology source
- Not checked yetcites [35] SM Ford, 1980, Callitrichids as phyletic dwarfs, and the place of Callitrichidae in Platyrrhini., Primates source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Genome Divergence, Rate Heterogeneity, and Indels
plaincorrelational- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Approximately half of the 261–377 species and 90% of the genera are included facilitating resolution of long-standing phylogenetic ambiguities.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Conclusions
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Introduction
What the sources say
- Not checked yetcites [1]-[3]
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The exact number of primate genera is controversial and species counts range from 261–377 [1]-[3].”
§ A Molecular Phylogeny of Living Primates > Introduction
What the sources say
- Not checked yetcites [1]-[3]
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“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”
§ A Molecular Phylogeny of Living Primates > Introduction
What the sources say
- Not checked yetcites [1]-[3]
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Strepsirrhini
hedgedconditional- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
What the sources say
- Not checked yetcites [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 yetcites [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 yetcites [46] KP Karanth, 2008, Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae)., Journal of biosciences source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
What the sources say
- Not checked yetcites [32] SM Ford, 1992, Systematics and body size: implications for feeding adaptations in New World monkeys., American Journal of Physical Anthropology source
- Not checked yetcites [35] SM Ford, 1980, Callitrichids as phyletic dwarfs, and the place of Callitrichidae in Platyrrhini., Primates source
- Not checked yetcites [36] M Moynihan, 1976, The New World primates : adaptive radiation and the evolution of social behavior, languages, and intelligence.
hedgedconditional- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > New World Primates (Platyrrhini)
What the sources say
- Not checked yetcites [31] F Ankel-Simons, 2008, Diurnality, Nocturnality, and the Evolution of Primate Visual Systems., American Journal of Physical Anthropology source
hedgedconditionaln = 15- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
hedgedconditional- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“reflecting recent speciation in the former and the more ancient origins of the latter (Figure 3, Table 1, Table 3, Tables S7 and S9).”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Genome Divergence, Rate Heterogeneity, and Indels
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“This paraphyly, also reported in earlier genetic studies [39], [47], [48] and counter to initial morphological classifications [2], suggests taxonomic revision of Cercopithecus.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Old World Primates (Cercopithecoidea)
What the sources say
- Not checked yetcites [39] J Xing, 2007, A mobile element-based evolutionary history of guenons (tribe Cercopithecini)., BMC Biology source
- Not checked yetcites [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 yetcites [48] AJ Tosi, 2003, Cercopithecine Y-chromosome data provide a test of competing morphological evolutionary hypotheses., Molecular Phylogenetics and Evolution source
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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].”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Genome Divergence, Rate Heterogeneity, and Indels
What the sources say
- Not checked yetcites [56] LC Zhu, 2009, Genomewide Association between Insertions/Deletions and the Nucleotide Diversity in Bacteria., Molecular Biology and Evolution source
- Not checked yetcites [57] DC Tian, 2008, Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes., Nature
- Not checked yetcites [58]-[60]
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“B) mean = 43.0 MYA, stdev = 4.5 for TMRCA of Simiiformes [79], [80]”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
What the sources say
- Not checked yetcites [79], [80]
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
- The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Conclusions
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
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Probably not a substantial claim. It may be too vague to check against evidence.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“A negative control (no template) was included in every WGA and was verified by downstream PCR and sequencing.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > DNA Specimens
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Only PCR products that produced single bands were sequenced.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Amplification of Gene Segments
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
In the paper
“Regions of sequence ambiguity within the alignment were identified by GBLOCK version 0.91b [72], and removed from subsequent phylogenetic analyses.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > DNA Sequence Analyses
What the sources say
- Not checked yetcites [72] G Talavera, 2007, Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments., Systematic Biology source
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“consistent with reticulate evolution, recent speciation and possibly augmented by taxonomic over-splitting.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Conclusions
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Phylogenetic Reconstruction of Primates
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may state two separate claims as one.
In the paper
“A) mean = 40.0 MYA, standard deviation (stdev) = 3.0 for time to most recent common ancestor (TMRCA) of galagids and lorisids [78]”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
What the sources say
- Not checked yetcites [78] ER Seiffert, 2003, Fossil evidence for an ancient divergence of lorises and galagos., Nature source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
- The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Conclusions
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > DNA Sequence Analyses
What the sources say
- Not checked yetcites [69], [70]
- Not checked yetcites [71] A Rambaut, 2007, Se-Al. Sequence Alignment Editor.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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).”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Statistical Analyses of Insertion/Deletion Events among Primate Lineages
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Statistical Analyses of Insertion/Deletion Events among Primate Lineages
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Log files from each run were imported into Tracer ver 1.4.1, and trees sampled from the first 1 million generations were discarded.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Mixing of trees was assessed in Tracer by examination of ESS values.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“First, all indels were identified using FASTGAP on GBLOCKED alignments and verified by eye.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Statistical Analyses of Insertion/Deletion Events among Primate Lineages
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“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].”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
What the sources say
- Not checked yetcites [14], [82], [85]
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
- The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“G) mean = 15.5 MYA, stdev = 2.5 for TMRCA of Hominidae [14]”
§ A Molecular Phylogeny of Living Primates > Materials and Methods > Bayesian Analyses of Primate Sequences: Posterior Probability, Node Support, and Divergence Dating
What the sources say
- Not checked yetcites [14] A Matsui, 2009, Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs., Gene source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- The authors state this as an assumption: The ingroup is monophyletic with respect to the outgroup.
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.”
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Based on nuclear data, Callithrix separated from its sister clade of Mico and Cebuella 2.5 million years ago (Perelman et al. 2011), and the young age of Callithrix species probably has not yet allowed for the evolution of either distinct coadapted gene complexes or significant differences in allele frequencies between these species.”
From Morphological Variation in Wild Marmosets (Callithrix penicillata and C. geoffroyi) and Their Hybrids (2014) · cites this paper as Perelman et al. 2011
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“For example, C. penicillata diverged from its species C. jacchus less than a million years ago (Perelman et al. 2011), and these two species showed overlapping allele size frequencies and no diagnostic loci between the two species (loci with non-overlapping alleles between the two species) in a panel of 42 nuclear microsatellite loci (Malukiewicz 2013).”
From Morphological Variation in Wild Marmosets (Callithrix penicillata and C. geoffroyi) and Their Hybrids (2014) · cites this paper as Perelman et al. 2011
Experimental — accuracy not yet measuredIn the citing paper
“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
In the citing paper
“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.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ A Molecular Phylogeny of Living Primates > Results/Discussion
“only 3 of 189 nodes (nodes 28, 38, 158) are polytomies in the bootstrap analyses”
§ A Molecular Phylogeny of Living Primates > Introduction
“| 81 | 1.53 | 0.59 | 2.28 | 6.00 | 1.42 | 13.06 | 11.34 | 21 | 0 | Note A | Note A | 1.00 |”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ A Molecular Phylogeny of Living Primates > Results/Discussion > Resolution of Early Primate Divergence
“eight shared insertions/deletions (indels) (node 144)”
§ A Molecular Phylogeny of Living Primates > Introduction
“| 144 | 68.74 | 58.77 | 76.61 | 9.91 | 5.98 | 14.30 | 188.50 | 591 | 9 | 100 | 100 | 1.00 |”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
“The greatest proportion of phylogenetically informative sites occurred in Y-linked genes (56%)”
§ A Molecular Phylogeny of Living Primates > Results/Discussion
Reported 56 · recomputed 49.885932
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
“Roughly equal amounts of coding (14742 bp) and non-coding (17185 bp) genomic regions were sampled”
§ A Molecular Phylogeny of Living Primates > Results/Discussion
Reported 34927 · recomputed 31927
Citations
Cites
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820 · cited 1×
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MethodBEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 13,104
PAUP^* : Phylogenetic Analysis Using Parsimony (and other methods) 4.0b8
Swofford, D. L. (2001) · Cited by 12,789
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · cited 1×
“3 [76,77].”
Talavera, G., & Castresana, J. (2007) · Systematic Biology · doi:10.1080/10635150701472164 · Cited by 5,599 · cited 1×
“91b [72], and removed from subsequent phylogenetic analyses.”
BackgroundMammal Species of the World: A Taxonomic and Geographic Reference
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Recent developments in the MAFFT multiple sequence alignment program
Katoh, K., & Toh, H. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn013 · Cited by 3,629 · cited 1×
“DNA Sequence Analyses Multiple sequence files for each gene segment amplified were aligned by MAFFT version 6 [69,70], imported into Se-Al ver Figure 2.”
MethodZwickl, D. J. (2006) · Texas ScholarWorks (Texas Digital Library) · Cited by 3,108
Mammal species of the world: a taxonomic and geographic reference
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Cited by
Sorted by citations
Mash: fast genome and metagenome distance estimation using MinHash
Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., & Phillippy, A. M. (2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373
“which the Mash topology is more similar to past phylogenetic studies [27] and mitochondrial trees [13].”
BackgroundThe brain’s default network: updated anatomy, physiology and evolving insights
Buckner, R. L., & DiNicola, L. M. (2019) · Nature Reviews Neuroscience · doi:10.1038/s41583-019-0212-7 · Cited by 1,058
Genetic Management of Fragmented Animal and Plant Populations
Frankham, R., Ballou, J. D., Ralls, K., Eldridge, M. D. B., Dudash, M. R., Fenster, C. B., Lacy, R. C., & Sunnucks, P. (2017) · doi:10.1093/oso/9780198783398.001.0001 · Cited by 540
A developmental coordinate of pluripotency among mice, monkeys and humans
Nakamura, T., Okamoto, I., Sasaki, K., Yabuta, Y., Iwatani, C., Tsuchiya, H., Seita, Y., Nakamura, S., Yamamoto, T., & Saitou, M. (2016) · Nature · doi:10.1038/nature19096 · Cited by 516
Springer, M. S., Meredith, R. W., Gatesy, J., Emerling, C. A., Park, J. S., Rabosky, D. L., Stadler, T., Steiner, C., Ryder, O. A., Janečka, J. E., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049521 · Cited by 518
“[12], who included 219, 271, and 186 primate species, respectively.”
BackgroundResultInfluential
Metadata
- 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
- 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
- gold
- doi.org
- 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
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › 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.
A language model drew the claims from the paper on 2026-10-09, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-09 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
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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