A Molecular Phylogeny of Living Primates

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;”

What the sources say

• Not checked yetcites [16] JE Janecka, 2007, Molecular and genomic data identify the closest living relative of primates., Science source
• Not checked yetcites [17] JO Kriegs, 2007, Evolutionary history of 7SL RNA-derived SINEs in supraprimates., Trends in Genetics source

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.”

In the paper

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

In the paper

“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).”

In the paper

“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).”

In the paper

“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].”

What the sources say

• Not checked yetcites [27]-[30]

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.”

In the paper

“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).”

In the paper

“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).”

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).”

In the paper

“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].”

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

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.”

In the paper

“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.”

In the paper

“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.”

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].”

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.

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.”

In the paper

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

In the paper

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

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).”

In the paper

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

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)”

In the paper

“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].”

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

In the paper

“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.”

What the sources say

• Not checked yetcites [2] CP Groves, 2001, Primate taxonomy.

In the paper

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

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.”

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].”

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

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)”

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).”

In the paper

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

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).”

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).”

What the sources say

• Not checked yetcites [2] CP Groves, 2001, Primate taxonomy.

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].”

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

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.”

In the paper

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

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.”

In the paper

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

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).”

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.”

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).”

In the paper

“Further, the pattern of divergence of Callitrichinae is correlated with a gradation in species size, supporting “phyletic dwarfism” [32], [35].”

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

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).”

In the paper

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

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.”

What the sources say

• Not checked yetcites [1]-[3]

In the paper

“The exact number of primate genera is controversial and species counts range from 261–377 [1]-[3].”

What the sources say

• Not checked yetcites [1]-[3]

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”

What the sources say

• Not checked yetcites [1]-[3]

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.”

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.”

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

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].”

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.

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.”

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

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.”

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).”

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.”

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

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].”

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]

In the paper

“B) mean = 43.0 MYA, stdev = 4.5 for TMRCA of Simiiformes [79], [80]”

What the sources say

• Not checked yetcites [79], [80]

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.”

In the paper

“A negative control (no template) was included in every WGA and was verified by downstream PCR and sequencing.”

In the paper

“Only PCR products that produced single bands were sequenced.”

In the paper

“Regions of sequence ambiguity within the alignment were identified by GBLOCK version 0.91b [72], and removed from subsequent phylogenetic 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

In the paper

“consistent with reticulate evolution, recent speciation and possibly augmented by taxonomic over-splitting.”

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.”

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]”

What the sources say

• Not checked yetcites [78] ER Seiffert, 2003, Fossil evidence for an ancient divergence of lorises and galagos., Nature source

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.”

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.”

What the sources say

• Not checked yetcites [69], [70]
• Not checked yetcites [71] A Rambaut, 2007, Se-Al. Sequence Alignment Editor.

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).”

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.”

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.”

In the paper

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

In the paper

“First, all indels were identified using FASTGAP on GBLOCKED alignments and verified by eye.”

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.”

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].”

What the sources say

• Not checked yetcites [14], [82], [85]

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.”

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.”

In the paper

“G) mean = 15.5 MYA, stdev = 2.5 for TMRCA of Hominidae [14]”

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