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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×
“7 [73] and the optimal model of nucleotide substitution was selected using the AIC criterion.”
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
Schmid, R., Wilson, D. E., & Reeder, D. M. (1993) · Taxon · doi:10.2307/1223169 · Cited by 5,384
Nowak, R. (1999) · doi:10.56021/9780801857898 · Cited by 4,102
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
(2006) · Choice Reviews Online · doi:10.5860/choice.44-1281 · Cited by 3,008
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.”
BackgroundResultInfluentialCaptivity humanizes the primate microbiome
Clayton, J. B., Vangay, P., Huang, H., Ward, T., Hillmann, B., Al‐Ghalith, G. A., Travis, D. A., Long, H. T., Tuan, B. V., Minh, V. V., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521835113 · Cited by 524
“(22) for the 10 unique primate species sampled in this study.”
BackgroundA glimpse on the pattern of rodent diversification: a phylogenetic approach
Fabre, P., Hautier, L., Dimitrov, D., & Douzery, E. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-88 · Cited by 521
“Fabre PH, Rodrigues A, Douzery EJP: Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.”
BackgroundParham, P., & Moffett, A. (2013) · Nature reviews. Immunology · doi:10.1038/nri3370 · Cited by 489
Primate brain size is predicted by diet but not sociality
DeCasien, A. R., Williams, S. A., & Higham, J. P. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0112 · Cited by 479
Reveley, C., Seth, A. K., Pierpaoli, C., Silva, A. C., Yu, D., Saunders, R. C., Leopold, D. A., & Ye, F. Q. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418198112 · Cited by 417
“Moreover, although in many respects the macaque brain is a good approximation of the human brain, both species have undergone profound evolutionary changes since the time of their most recent common ancestor living more than 20 million years ago (10), particularly in regard to the massive expansion of the cerebral cor…”
BackgroundSelf-citationLactobacilli Dominance and Vaginal pH: Why Is the Human Vaginal Microbiome Unique?
Miller, E. A., Beasley, D. E., Dunn, R. R., & Archie, E. A. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01936 · Cited by 411
“…University, Raleigh, NC, USA, 4Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark, 5 Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya The human vaginal microbiome is dominated by bacteria from…”
BackgroundEvolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes
Amato, K. R., Sanders, J. G., Song, S. J., Nute, M., Metcalf, J. L., Thompson, L., Morton, J. T., Amir, A., McKenzie, V. J., Humphrey, G., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0175-0 · Cited by 381
Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes
Pozzi, L., Hodgson, J. A., Burrell, A. S., Sterner, K. N., Raaum, R. L., & Disotell, T. R. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.02.023 · Cited by 327
“, 2013), but in contrast with nuclear data (Perelman et al., 2011; but see Guschanski et al., 2013).”
InfluentialTransposable elements are the primary source of novelty in primate gene regulationPreprint
Trizzino, M., Park, Y., Beltrame, M. H., Aracena, K. A., Mika, K. M., Çalışkan, M., Perry, G. H., Lynch, V. J., & Brown, C. D. (2017) · Genome Research · doi:10.1101/gr.218149.116 · Cited by 286
“We performed ChIP-seq for histone H3 lysine 27 acetylation (H3K27ac)andhistoneH3lysine4monomethylation(H3K4me1), whichmarkfunctionalandpoisedregulatoryelements,intheliver of six primate species, including at least one species from each major primate clade (Perelman et al. 2011).”
Springer, M. S., & Gatesy, J. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.07.018 · Cited by 281
Onabajo, O. O., Banday, A. R., Stanifer, M. L., Yan, W., Obajemu, A., Santer, D. M., Florez-Vargas, O., Piontkivska, H., Vargas, J. M., Ring, T. J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-00731-9 · Cited by 261
Rossier, B. C., Baker, M. E., & Studer, R. A. (2015) · Physiological Reviews · doi:10.1152/physrev.00011.2014 · Cited by 269
“(255), based on a wealth of new genomic data, comparative genomic analyses of primates allow resolving the primate phylogeny with a much greater accuracy.”
BackgroundThe common marmoset genome provides insight into primate biology and evolution
Worley, K. C., Rogers, J., Muzny, D. M., Weinstock, G. M., Chandrabose, M. N., Cree, A., Dao, M., Dinh, H. H., Fowler, R. G., Gabisi, R. A., et al. (2014) · Nature Genetics · doi:10.1038/ng.3042 · Cited by 264
A Mitogenomic Phylogeny of Living Primates
Finstermeier, K., Zinner, D. P., Brameier, M., Meyer, M., Kreuz, E., Hofreiter, M., & Roos, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069504 · Cited by 276
“In our mt genome data, Erythrocebus clusters with Cercopithecus and not with Chlorocebus as suggested by all available nuclear sequence and retroposon data [18,42,58,59], but monophyly of Erythrocebus and Chlorocebus is not rejected by alternative tree topology tests (P > 0.”
BackgroundMethodResultInfluentialSelf-citationLim, E. S., Fregoso, O. I., McCoy, C. O., Matsen, F. A., IV, Malik, H. S., & Emerman, M. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.01.004 · Cited by 271
“The phylogeny constructed from the primate SAMHD1 sequences was congruent with the generally accepted primate species phylogeny (Perelman et al., 2011), confirming that the sequences are orthologous.”
The Genome Landscape of the African Green Monkey Kidney-Derived Vero Cell Line
Osada, N., Kohara, A., Yamaji, T., Hirayama, N., Kasai, F., Sekizuka, T., Kuroda, M., & Hanada, K. (2014) · DNA Research · doi:10.1093/dnares/dsu029 · Cited by 259
“42, 43 The estimated divergence between the rhesus macaque and Vero cell line genomes was 2.2%.”
BackgroundInfluentialPlohl, M., Meštrović, N., & Mravinac, B. (2012) · Genome dynamics · doi:10.1159/000337122 · Cited by 238
Next-Generation Museomics Disentangles One of the Largest Primate Radiations
Guschanski, K., Krause, J., Sawyer, S., Valente, L., Bailey, S., Finstermeier, K., Sabin, R., Gilissen, E., Sonet, G., Nagy, Z. T., et al. (2013) · Systematic Biology · doi:10.1093/sysbio/syt018 · Cited by 235
Evolution of Multilevel Social Systems in Nonhuman Primates and Humans
Grueter, C. C., Chapais, B., & Zinner, D. P. (2012) · International Journal of Primatology · doi:10.1007/s10764-012-9618-z · Cited by 230
“On the other hand, when OMUs congregate on an irregular basis and bands are more fluid and not as consistently assembled or behaviorally integrated as in strict modular systems, this would constitute a flexible system, e.g., Theropithecus gelada (Table II; see also Grueter and Zinner 2004).”
BackgroundHERV Envelope Proteins: Physiological Role and Pathogenic Potential in Cancer and Autoimmunity
Grandi, N., & Tramontano, E. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00462 · Cited by 233
“The estimated period in which the different primate species evolutionary diverged (as derived from Steiper and Young, 2006; Perelman et al., 2011) is indicated in the underlying tree at each node of separation, and is depicted in the graph by colored blocks corresponding to the first primate…”
BackgroundStegelmeier, A. A., Müller, K. M., Weese, J. S., & Neufeld, J. D. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1801302115 · Cited by 224
Molecular ecology and adaptation of visual photopigments in craniates
Davies, W. I. L., Collin, S. P., & Hunt, D. M. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05617.x · Cited by 217
A comprehensive atlas of immunological differences between humans, mice, and non-human primates
Bjornson-Hooper, Z. B., Fragiadakis, G. K., Spitzer, M. H., Chen, H., Madhireddy, D., Hu, K., Lundsten, K., McIlwain, D. R., & Nolan, G. P. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.867015 · Cited by 215
Byrne, H., Rylands, A. B., Carneiro, J. C., Alfaro, J. W. L., Bertuol, F., da Silva, M. N. F., Messias, M. R., Groves, C. P., Mittermeier, R. A., Farias, I. P., et al. (2016) · Frontiers in Zoology · doi:10.1186/s12983-016-0142-4 · Cited by 215
“1758. Syst. Nat. 10th ed., 1: 25. In part. Humboldt, A. von. 1811. Rec. Obs. Zool. Anat. Comp. 1: 319. Simia lugens (= Callicebus lugens). Cebus Erxleben, C. P. 1777. Systema Regni Anim. Mammalia, p. 44. In part. Hoffmannsegg, G. von. 1807. Mag. Ges. Naturf. Freunde, Berlin, 9: 97. Cebus moloch (= Callicebus moloch).…”
BackgroundKelava, I., Reillo, I., Murayama, A. Y., Kalinka, A. T., Stenzel, D., Tomančák, P., Matsuzaki, F., Lebrand, C., Sasaki, E., Schwamborn, J. C., et al. (2011) · Cerebral Cortex · doi:10.1093/cercor/bhr301 · Cited by 217
“Therefore, we assembled an anthropoid phylogeny using topology and branch lengths estimated previously (Perelman et al. 2011) based on ~8 Mb of genomic sequence (Supplementary Fig.”
A global catalog of whole-genome diversity from 233 primate species
Kuderna, L. F. K., Gao, H., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T. M., Manu, S., Valenzuela, A., Bergman, J., Rousselle, M. M. C., et al. (2023) · Science · doi:10.1126/science.abn7829 · Cited by 222
Self-citationThe Ancient Evolutionary History of Polyomaviruses
Buck, C. B., Doorslaer, K. V., Peretti, A., Geoghegan, E. M., Tisza, M. J., An, P., Katz, J. P., Pipas, J. M., McBride, A. A., Camus, A. C., et al. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005574 · Cited by 211
“Based on the posterior distributions obtained for the host [84, 100], normal priors were imposed on specific nodes used to calibrate the evolutionary rates (S5 File).”
MethodMetabolic rate and body size are linked with perception of temporal information
Healy, K., McNally, L., Ruxton, G. D., Cooper, N., & Jackson, A. L. (2013) · Animal Behaviour · doi:10.1016/j.anbehav.2013.06.018 · Cited by 202
“We used Benton & Donoghue’s (2007) estimation of divergence time between anopsids (Testudines and Aves) and suarapids (Squamata and Rhynchocephalia) while Perelman et al. (2011) was used for the divergence and phylogenetic relationships among Squamata, Rhynchocephalia, Testudines and Aves.”
dos Reis, M., Gunnell, G. F., Barba‐Montoya, J., Wilkins, A., Yang, Z., & Yoder, A. D. (2018) · Systematic Biology · doi:10.1093/sysbio/syy001 · Cited by 190
“…been inordinately and repeatedly the subject of divergence time analysis, with the first studies appearing at the very outset of molecular clock studies (Sarich and Wilson 1967), up to phylogenomic studies encompassing a large set of primate species (Perelman et al. 2011; Springer et al. 2012).”
BackgroundMethodThe ABO blood group is a trans-species polymorphism in primates
Ségurel, L., Thompson, E. E., Flutre, T., Lovstad, J. N., Venkat, A., Margulis, S. W., Moyse, J. A., Ross, S., Gamble, K. C., Sella, G., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210603109 · Cited by 189
“We assumed that B arose ∼8 Mya (the minimum age indicated by Fig.”
InfluentialGlutaredoxin: Discovery, redox defense and much more
Ogata, F. T., Branco, V., Vale, F. F., & Coppo, L. (2021) · Redox Biology · doi:10.1016/j.redox.2021.101975 · Cited by 198
Centromere repositioning in mammals
Rocchi, M., Archidiacono, N., Schempp, W., Capozzi, O., & Stanyon, R. (2011) · Heredity · doi:10.1038/hdy.2011.101 · Cited by 183
“15 MYA (Perelman et al., 2011), therefore the origin of the ENC has to be somewhere between 15 and 1.”
BackgroundInfluentialBraga, R. M., Van Dijk, K. R. A., Polimeni, J. R., Eldaief, M. C., & Buckner, R. L. (2019) · Journal of Neurophysiology · doi:10.1152/jn.00808.2018 · Cited by 162
Alfaro, J. W. L., Boubli, J. P., Paim, F. P., RIBAS, C. C., da Silva, M. N. F., Messias, M. R., Röhe, F., Mercês, M. P., Júnior, J. S. S., Silva, C. R., et al. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.09.004 · Cited by 180
Hecht, E. E., Gutman, D. A., Bradley, B. A., Preuss, T. M., & Stout, D. (2015) · NeuroImage · doi:10.1016/j.neuroimage.2014.12.039 · Cited by 175
“In this scenario, the macaque–chimpanzee–human last common ancestor (~25–32 million years ago (Goodman et al., 1998; Chatterjee et al., 2009; Perelman et al., 2011)) did not have SLF”
Phylogenomic analyses provide insights into primate evolution
Shao, Y., Zhou, L., Li, F., Zhao, L., Zhang, B.-L., Shao, F., Chen, J., Chen, C., Bi, X., Zhuang, X.-L., et al. (2023) · Science · doi:10.1126/science.abn6919 · Cited by 185
“2B), which contradicts the 218 Hominini slowdown hypothesis on the nucleotide substitution rates (35).”
BackgroundMethodInfluentialSelf-citationLaguette, N., Rahm, N., Sobhian, B., Chable-Bessia, C., Münch, J., Snoeck, J., Sauter, D., Switzer, W. M., Heneine, W., Kirchhoff, F., et al. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.01.007 · Cited by 184
Human mortality improvement in evolutionary context
Bürger, O., Baudisch, A., & Vaupel, J. W. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1215627109 · Cited by 172
“6 million years (14), since the split from a common ancestor with chimpanzees.”
BackgroundA quantitative review of MHC ‐based mating preference: the role of diversity and dissimilarity
Kamiya, T., O’Dwyer, K., Westerdahl, H., Senior, A. M., & Nakagawa, S. (2014) · Molecular Ecology · doi:10.1111/mec.12934 · Cited by 170
“taxonomy database, and polytomies were resolved using the following studies (Steppan et al. 2004; Hackett et al. 2008; Perelman et al. 2011; Crête-Lafreni ere et al. 2012).”
MethodThe Ancient Evolutionary History of Polyomaviruses
Buck, C., Van Doorslaer, K., Peretti, A., Geoghegan, E., Tisza, M., An, P., Katz, J., Pipas, J., McBride, A., Camus, A., et al. (2016) · D-Scholarship@Pitt (University of Pittsburgh) · Cited by 170
Fan, H., Ives, A. R., Surget‐Groba, Y., & Cannon, C. H. (2015) · BMC Genomics · doi:10.1186/s12864-015-1647-5 · Cited by 175
“1) as those previously published using traditional methods [30, 31], even though AAF did not use any information about assembly or alignment.”
BackgroundMethodResultInfluentialPrimate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance
Yıldırım, S., Yeoman, C. J., Janga, S. C., Thomas, S. M., Ho, M., Leigh, S. R., Microbiome, P., White, B. A., Wilson, B. A., & Stumpf, R. M. (2014) · The ISME Journal · doi:10.1038/ismej.2014.90 · Cited by 169
“The aligned sequences based on 54 concatenated primate genes were used to build the maximum parsimony tree (Perelman et al., 2011).”
MethodMolecular evolution of hydrogen peroxide degrading enzymes
Zámocký, M., Gasselhuber, B., Furtmüller, P. G., & Obinger, C. (2012) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2012.01.017 · Cited by 172
Pacheco, M. A., Matta, N. E., Valkiūnas, G., Parker, P. G., Mello, B., Stanley, C. E., Lentino, M., García-Amado, M. A., Cranfield, M. R., Pond, S. L. K., et al. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx285 · Cited by 169
“This event is used to inform a calibration prior with a maximum of 65 Ma that allows this parasite clade to be as old as the origin of primates, if the data support that (Perelman et al. 2011).”
Mitchell, P. S., Patzina, C., Emerman, M., Haller, O., Malik, H. S., & Kochs, G. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.09.005 · Cited by 142
“A phylogenetic tree generated from these MxA sequences was congruent with a previously published primate phylogeny (Perelman et al., 2011) confirming that the MxA sequences obtained were orthologous (Figure 1A).”
ResultPhylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree
Herrera, J. P., & Dávalos, L. M. (2016) · Systematic Biology · doi:10.1093/sysbio/syw035 · Cited by 156
Conservation Genomics of Threatened Animal Species
Steiner, C., Putnam, A. S., Hoeck, P. E. A., & Ryder, O. A. (2013) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-031412-103636 · Cited by 169
Crottini, A., Madsen, O., Poux, C., Strauß, A., Vieites, D. R., & Vences, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1112487109 · Cited by 158
Roux, C., Tsagkogeorga, G., Bierne, N., & Galtier, N. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst066 · Cited by 154
“This is equivalent to the divergence between humans and marmosets 1581 Downloaded from https://academic.oup.com/mbe/article-abstract/30/7/1574/972546 by guest on 29 July 2018 (Perelman et al. 2011).”
BackgroundEarly primate evolution in Afro‐Arabia
Seiffert, E. R. (2012) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21335 · Cited by 152
The systematics and evolution of New World primates – A review
Schneider, H., & Sampaio, I. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.10.017 · Cited by 159
“were based on Perelman et al. (2011) estimates.”
BackgroundMethodInfluentialExonization of transposed elements: A challenge and opportunity for evolution
Schmitz, J., & Brosius, J. (2011) · Biochimie · doi:10.1016/j.biochi.2011.07.014 · Cited by 158
Marine origin of retroviruses in the early Palaeozoic Era
Aiewsakun, P., & Katzourakis, A. (2017) · Nature Communications · doi:10.1038/ncomms13954 · Cited by 152
Ebeling, M., Küng, E., See, A., Broger, C., Steiner, G., Berrera, M., Heckel, T., Iniguez, L. A., Albert, T., Schmucki, R., et al. (2011) · Genome Research · doi:10.1101/gr.123117.111 · Cited by 146
“These primates share a commonancestorwithhumans that is estimated to have lived about 32million years ago (Perelman et al. 2011).”
BackgroundComparative RNA sequencing reveals substantial genetic variation in endangered primatesPreprint
Perry, G. H., Melsted, P., Marioni, J. C., Wang, Y., Bainer, R. O., Pickrell, J. K., Michelini, K., Zehr, S. M., Yoder, A. D., Stephens, M., et al. (2011) · Genome Research · doi:10.1101/gr.130468.111 · Cited by 149
“This conclusion is further supported by our ability to nearly perfectly recapitulate the known primate phylogeny (Perelman et al. 2011) based on either the sequence data or the estimates of gene expression levels (Fig.”
BackgroundMeaning, intention, and inference in primate vocal communication
Fischer, J., & Price, T. (2016) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2016.10.014 · Cited by 144
Steiper, M. E., & Seiffert, E. R. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119506109 · Cited by 143
“(7); green, theCYP7A1 region (16); blue, Jamesonet al.”
BackgroundBaboon phylogeny as inferred from complete mitochondrial genomes
Zinner, D. P., Wertheimer, J., Liedigk, R., Groeneveld, L. F., & Roos, C. (2012) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22185 · Cited by 150
“Estimated divergence times for all nodes are in a similar range as dates from other molecular studies (Chan et al., 2010; Perelman et al., 2011; Roos et al., 2011; Liedigk et al., 2012; Steiper and Seiffert, 2012).”
ResultSelf-citationTime-Dependent Rate Phenomenon in Viruses
Aiewsakun, P., & Katzourakis, A. (2016) · Journal of Virology · doi:10.1128/jvi.00593-16 · Cited by 132
“On the basis of these observations, their rates have been estimated to be of the order of 10 7 to 10 9 nucleotide substitutions per site per year (s/n/y) (1–5), comparable to those of their hosts (6, 7).”
BackgroundNiimura, Y., Matsui, A., & Touhara, K. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy042 · Cited by 134
Faurby, S., & Svenning, J. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.11.001 · Cited by 137
“Family monophyly and family assignment in the New World monkeys are unsettled, although the monophyly of the NewWorld monkey superfamily is settled beyond doubt (Perelman et al., 2011).”
BackgroundSystems Biology of the Vervet Monkey
Jasinska, A. J., Schmitt, C. A., Service, S. K., Cantor, R. M., Dewar, K., Jentsch, J. D., Kaplan, J. R., Turner, T. R., Warren, W. C., Weinstock, G. M., et al. (2013) · ILAR Journal · doi:10.1093/ilar/ilt049 · Cited by 131
“…differentiation of the vervet from other members of its tribe is estimated to be about 1.5 to 3 million years ago, based on molecular phylogeny analyses from 54 nuclear genes in 191 primate taxa (Perelman et al. 2011) and similar analyses from mitochondrial genome data (Wertheim and Worobey 2007).”
InfluentialAnimal models of human pregnancy and placentation: alternatives to the mouse
Carter, A. M. (2020) · Reproduction · doi:10.1530/rep-20-0354 · Cited by 130
“Figure 5 Classification of primates (Perelman et al. 2011).”
Manipulation complexity in primates coevolved with brain size and terrestriality
Heldstab, S. A., Kosonen, Z. K., Koski, S. E., Burkart, J. M., van Schaik, C. P., & Isler, K. (2016) · Scientific Reports · doi:10.1038/srep24528 · Cited by 128
Münk, C., Willemsen, A., & Bravo, I. G. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-71 · Cited by 134
“This timing could be compatible with the Hylobatidae/Hominidae split some 18–24 Mya, although it matches well the Cercopithecidae/Hominoidea split some 26–34 Mya [44].”
ResultVoice pitch: a window into the communication of social power
Aung, T., & Puts, D. A. (2019) · Current Opinion in Psychology · doi:10.1016/j.copsyc.2019.07.028 · Cited by 126
Kay, R. F. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.12.002 · Cited by 125
“phylogeny (Opazo et al., 2006; Osterholz et al., 2009; Wildman et al., 2009; Perelman et al., 2011; Springer et al., 2012).”
ResultInfluentialLinking the Investigations of Character Evolution and Species Diversification
Magnuson-Ford, K., & Otto, S. P. (2012) · The American Naturalist · doi:10.1086/666649 · Cited by 123
“…of primate diversification, we recommend that future analyses include trait information for more species, use the most recent molecular data (e.g., see Perelman et al. 2011), and be conducted over a set of trees that are consistent with the data, to account for phylogenetic uncertainty.”
MethodCortés‐Ortiz, L., Rylands, A. B., & Mittermeier, R. A. (2014) · Springer eBooks · doi:10.1007/978-1-4939-1957-4_3 · Cited by 121
Esselstyn, J. A., Oliveros, C. H., Swanson, M. T., & Faircloth, B. C. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx168 · Cited by 123
Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Palesch, D., Bosinger, S. E., Tharp, G. K., Vanderford, T. H., Paiardini, M., Chahroudi, A., Johnson, Z. P., Kirchhoff, F., Hahn, B. H., Norgren, R. B., et al. (2018) · Nature · doi:10.1038/nature25140 · Cited by 119
“…more closely related to sooty mangabeys and drills than to rhesus macaques, the phylogeny of Old World monkeys is compatible with the possibility of a single G-to-A mutation creating the truncated form of the protein in the common ancestor of baboons, rhesus macaques and sooty mangabeys 12,14 (Fig.”
BackgroundIdentification of a Genomic Reservoir for New TRIM Genes in Primate Genomes
Han, K., Lou, D. I., & Sawyer, S. L. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002388 · Cited by 120
“(C) The relationships of the species discussed in this study are shown, along with approximate dates of divergence [78,79].”
BackgroundThe evolution and functions of nuclei of the visual pulvinar in primates
Baldwin, M. K. L., Balaram, P., & Kaas, J. H. (2017) · The Journal of Comparative Neurology · doi:10.1002/cne.24272 · Cited by 119
“Thus, current classification schemes divide living primates into two large clades, the strepsirrhine (prosimians, except for tarsiers), and the haplorhines (tarsiers and anthropoids (Kay, Ross, & Williams, 1997; Jameson et al., 2011; Perelman et al., 2011).”
BackgroundRabenold, D., & Pearson, O. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028379 · Cited by 116
“(DOC) Figure S1 Phylogeny of the species included in the study with ages of splits indicated in millions of years (data from Perelman et al., 2011 [70]).”
BackgroundMethodBiogeography of the marmosets and tamarins (Callitrichidae)
Buckner, J. C., Alfaro, J. W. L., Rylands, A. B., & Alfaro, M. E. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.04.031 · Cited by 116
Compton, A. A., & Emerman, M. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003135 · Cited by 117
“The resulting A3G phylogeny and the currently accepted phylogeny of OWM species [37] are similar but not identical, most likely due to rampant selection.”
BackgroundMethodInfluentialOld World Monkeys Compare to Apes in the Primate Cognition Test Battery
Schmitt, V., Pankau, B., & Fischer, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032024 · Cited by 112
“Within the hominoidea (apes and humans), the last common ancestor of humans and their closest relatives, the chimpanzees and bonobos, is dated at about 6 mya [1], while the split between the Hominoidea and the Cercopithecoidea (Old World monkeys) occurred between 29 and 24 mya [2].”
The population genomics of rhesus macaques ( Macaca mulatta ) based on whole-genome sequencesPreprint
Xue, C., Raveendran, M., Harris, R. A., Fawcett, G. L., Liu, X., White, S. J., Dahdouli, M., Deiros, D. R., Below, J. E., Salerno, W. J., et al. (2016) · Genome Research · doi:10.1101/gr.204255.116 · Cited by 117
“caques are Old World monkeys (Family Cercopithecidae, Superfamily Cercopithecoidea) and thus are phylogenetically closely related to humans, sharing a common ancestor roughly 25million years ago (Perelman et al. 2011).”
BackgroundSelf-citationHuman KIR repertoires: shaped by genetic diversity and evolution
Manser, A. R., Weinhold, S., & Uhrberg, M. (2015) · Immunological Reviews · doi:10.1111/imr.12316 · Cited by 118
“5 million years of evolution from humans (97, 98).”
BackgroundMorphology of the Nasal Capsule of Primates—With Special Reference to D aubentonia and H omo
Maier, W., & Ruf, I. (2014) · The Anatomical Record · doi:10.1002/ar.23023 · Cited by 112
“Phylogenetically, Daubentonia seems to be a basal branch to the Madagascan strepsirhines, which probably arrived on this island somewhat <60 million year ago (Roos et al., 2004; Perelman et al., 2011).”
BackgroundEvidence of Alternative Dietary Syndromes and Nutritional Goals in the Genus Alouatta
Garber, P. A., Righini, N., & Kowalewski, M. M. (2014) · Springer eBooks · doi:10.1007/978-1-4939-1960-4_4 · Cited by 110
Schlenker, P., Chemla, E., Schel, A. M., Fuller, J. L., Gautier, J., Kuhn, J. D., Veselinović, D., Arnold, K., Cäsar, C., Keenan, S., et al. (2016) · Theoretical Linguistics · doi:10.1515/tl-2016-0001 · Cited by 110
“Colobus monkeys and cercopithecines probably have a most recent common ancestor that lived – very approximately – 18 million years ago (Perelman et al. 2011).”
New approaches for genome assembly and scaffolding
Rice, E. S., & Green, R. E. (2019) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-115344 · Cited by 110
Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors
Blanco-Melo, D., Gifford, R. J., & Bieniasz, P. D. (2017) · eLife · doi:10.7554/elife.22519 · Cited by 109
“Expected branch lengths were calculated for the minimum and maximum estimates of the origin of hominids (13.45 and 19.68 MY respectively) (Perelman et al., 2011) using the neutral substitution for humans.”
MethodInfluentialA Severe Lack of Evidence Limits Effective Conservation of the World's Primates
Junker, J., Petrovan, S. O., Arroyo‐Rodríguez, V., Boonratana, R., Byler, D., Chapman, C. A., Chetry, D., Cheyne, S. M., Cornejo, F. M., Cortés‐Ortiz, L., et al. (2020) · BioScience · doi:10.1093/biosci/biaa082 · Cited by 108
Self-citationViral evolution in deep time: lentiviruses and mammals
Gifford, R. J. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.11.003 · Cited by 117
McCord, A. I., Chapman, C. A., Weny, G., Tumukunde, A., Hyeroba, D., Klotz, K., Koblings, A. S., Mbora, D. N. M., Cregger, M. A., White, B. A., et al. (2013) · American Journal of Primatology · doi:10.1002/ajp.22238 · Cited by 108
“Specifically, although black‐and‐white colobus and red colobus are closely related [Perelman et al., 2011], microbiomes of these two colobine species were as different from each other as either was from the microbiomes of more distantly related red‐tailed guenons.”
S cones: Evolution, retinal distribution, development, and spectral sensitivity
HUNT, D. M., & Peichl, L. (2013) · Visual Neuroscience · doi:10.1017/s0952523813000242 · Cited by 103
“If codon changes at site 86 are placed on to a primate phylogeny (Perelman et al., 2011 ) using the tree shrew as an outgroup (Petry & Harosi, 1990 ; Hunt et al., 2009 a ), then this codon would appear to have passed unchanged into the SWS1 pigment of the aye-aye ( Fig.”
Primate mosaic brain evolution reflects selection on sensory and cognitive specialization
DeCasien, A. R., & Higham, J. P. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0969-0 · Cited by 105
Compton, A. A., Hirsch, V. M., & Emerman, M. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2011.11.010 · Cited by 107
“Despite sharing a recent common ancestor 1–3 million years ago (Perelman et al., 2011; Wertheim and Worobey, 2007), each subspecies is naturally infected with a distinct subtype of SIV, aptly named after the specific host it infects: SIVagm.”
Hybridization in human evolution: Insights from other organisms
Ackermann, R., Arnold, M. L., Baiz, M. D., Cahill, J. A., Cortés‐Ortiz, L., Evans, B. J., Grant, B. R., Grant, P. R., Hallgrímsson, B., Humphreys, R. A., et al. (2019) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21787 · Cited by 101
“penicillata.(74,75) Experimental interspecific crosses revealed different levels”
Self-citationEvolutionary loss of complexity in human vocal anatomy as an adaptation for speech
Nishimura, T., Tokuda, I. T., Miyachi, S., Dunn, J. C., Herbst, C. T., Ishimura, K., Kaneko, A., Kinoshita, Y., Koda, H., Saers, J. P. P., et al. (2022) · Science · doi:10.1126/science.abm1574 · Cited by 102
The genome of the vervet (Chlorocebus aethiops sabaeus)
Warren, W. C., Jasinska, A. J., García-Pérez, R., Svardal, H., Tomlinson, C., Rocchi, M., Archidiacono, N., Capozzi, O., Minx, P., Montague, M. J., et al. (2015) · Genome Research · doi:10.1101/gr.192922.115 · Cited by 123
“…vervet provides a different kind of model for studying chromosome stability since the fission events are likely more recent, having occurred since the split between Cercopithecini and other members of Cercopi-thecinae ∼ 11.5 – 14.1 million years ago (Mya) (Perelman et al. 2011; Pozzi et al. 2014).”
BackgroundResultInfluentialSpecial issue: Comparative biogeography of Neotropical primates
Alfaro, J. W. L., Cortés‐Ortiz, L., Fiore, A. D., & Boubli, J. P. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.09.027 · Cited by 105
“In the case of Alouatta, the genus as a whole is relatively old, with the initial cis- and trans-Andean split estimated, using different kinds of molecular markers, variously as 6.8 Ma (Cortés-Ortiz et al., 2003), 6.0 Ma (Perelman et al., 2011) or 3.7 Ma (Springer et al., 2012).”
BackgroundMethodInfluentialThe Genetic and Evolutionary Drives behind Primate Color Vision
Carvalho, L. S., Pessoa, D. M. A., Mountford, J. K., Davies, W. I. L., & Hunt, D. M. (2017) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2017.00034 · Cited by 100
“Atelidae, and Pitheciidae (Perelman et al., 2011), trichromacy appears to have followed the same evolutionary process seen in the Cebinae family (Riba-Hernandez et al.”
BackgroundInfluential
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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