The tree was rooted with five outgroups from Lagomorpha, Scandentia, and Dermoptera (not shown). All nodes without filled circles were recovered with≥95% bootstrap support in maximum likelihood analyses with RAxML. Black, gray, and white filled circles indicate nodes that were recovered with 70 to<95% bootstrap support, 50 to<70% bootstrap support, and<50% bootstrap support, respectively. The full timetree with 367 primate species and five outgroups is provided in Text S2. Also see Figure 2 (strepsirrhines), Figure 3 (tarsiiforms+platyrrhines), Figure 4 (cercopithecoid), and Figure 5 (hominoids). Calibrated nodes are indicated with numbers and are cross-referenced to Text S3. Paintings by Carl Buell.

The tree was rooted with five outgroups from Lagomorpha, Scandentia, and Dermoptera (not shown). All nodes without filled circles were recovered with≥95% bootstrap support in maximum likelihood analyses with RAxML. Black, gray, and white filled circles indicate nodes that were recovered with 70 to<95% bootstrap support, 50 to<70% bootstrap support, and<50% bootstrap support, respectively. The full timetree with 367 primate species and five outgroups is provided in Text S2. Also see Figure 2 (strepsirrhines), Figure 3 (tarsiiforms+platyrrhines), Figure 4 (cercopithecoid), and Figure 5 (hominoids). Calibrated nodes are indicated with numbers and are cross-referenced to Text S3. Paintings by Carl Buell.

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Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extract...

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... L1RS PRDM4 was heterozygous in ON22212 liver. An analysis of primate reference genome assemblies indicated L1RS PRDM4 was present in the closely related crab-eating macaque (Macaca fascicularis) and absent from the more evolutionarily distant southern pig-tailed macaque (Macaca nemestrina) and green monkey (Chlorocebus sabaeus), suggesting L1RS PRDM4 entered the macaque germline 3-5 million years ago (Kumar et al. 2017;Kent et al. 2002;Springer et al. 2012). The two L1RS PRDM4 alleles carried by ON22213 were identical and deviated from the macaque reference genome L1RS PRDM4 element at a single 5′UTR position (A413G) and two ORF2 nucleotide positions: (A)2312A, which introduced to the reference sequence a premature ORF2p stop codon, and G2891A, a non-synonymous mutation of unclear significance for ORF2p activity (Fig. 2B). ...
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The retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human genome, and continues to drive genetic diversity and germline pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity is poorly defined, and is virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant primate germline. As revealed by case studies, the presently-active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether non-human primate L1s can similarly generate somatic insertions in the brain. Here we applied ~40× single-cell whole genome sequencing (scWGS), and retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques ( Macaca mulatta ). In one animal, we detected and robustly PCR validated a somatic L1 insertion that generated target site duplications, carried a short 5′ transduction, and was present in ~7% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro, and was embedded in PRDM4 , a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a non-human primate, and allude to L1 mobility in the brain over the last 30 million years of human evolution.
... As only a handful of host species have been sampled, we are unable to offer meaningful speculation as to the number of parasite species that have not been discovered yet. However, the phylogeny and the time estimates for the origin of the lemur malaria parasites sampled here were consistent with a scenario where the lineage that gave origin to these parasites was likely introduced into Madagascar by terrestrial vertebrates (Pacheco et al., 2011a;Springer et al., 2012). Narrowing down putative times of introduction is not possible given the limited sampling of parasites (Pacheco et al., 2011a;Springer et al., 2012). ...
... However, the phylogeny and the time estimates for the origin of the lemur malaria parasites sampled here were consistent with a scenario where the lineage that gave origin to these parasites was likely introduced into Madagascar by terrestrial vertebrates (Pacheco et al., 2011a;Springer et al., 2012). Narrowing down putative times of introduction is not possible given the limited sampling of parasites (Pacheco et al., 2011a;Springer et al., 2012). ...
Article
Among the primate malaria parasites, those found in lemurs have been neglected. Here, six Plasmodium lineages were detected in 169 lemurs. Nearly complete mitochondrial genomes (mtDNA, ≈6Kb) and apicoplast loci (≈6Kb) were obtained from these parasites and other Haemosporida species. Plasmodium spp. in lemurs are a diverse clade that shares a common ancestor with other primate parasites from continental Africa. Time-trees for the mtDNA were estimated under different scenarios, and the origin of the lemur clade coincides with the proposed time of their host species' most recent common ancestor (Lemuridae-Indriidae). A time tree with fewer taxa was estimated with mtDNA+Apicoplast loci. Those time estimates overlapped but were younger and had narrower credibility intervals than those from mtDNA alone. Importantly, the mtDNA+Apicoplast estimates that the clade including the most lethal malaria parasite in humans, Plasmodium falciparum, may have originated with Homininae (African apes). Finally, the phylogenetic congruence of the lemurs and their parasites was explored. A statistically significant scenario identified four cospeciation, two duplications, four transfer (host-switches), and zero loss events. Thus, the parasite species sampled in lemurs seem to be radiating with their hosts.
... Despite the stability of inference across most of the tree in the primate data set, there remains disagreement about relationships among the Platyrrhini, a notably contentious node (Perelman et al. 2011;Springer et al. 2012;Perez et al. 2013;Jameson Kiesling et al. 2015;Schrago and Seuánez 2019;Wang et al. 2019;Vanderpool et al. 2020). As in Vanderpool et al. (2020), we find that both concatenated ML and ASTRAL-III based on ML gene trees favor a symmetrical topology (tree 1 in fig. ...
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Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs, and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail, and by analyzing five additional datasets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other datasets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.
... Detailed morphological similarities linking great apes 1 and humans have been noted since anatomical comparisons were carried out in the later half of the 19th century (Huxley, 1863;Haeckel, 1866;Darwin, 1871), and work beginning in the 1960s, including the first long-term field studies of wild great apes, elucidated other shared facets of our biology, including genetics, behavior, cognition, and development (e.g., Goodall, 1964;van Lawick-Goodall, 1973;King and Wilson, 1975;Byrne, 1995;Whiten et al., 1999;Waterson et al., 2005;Russon and Begun, 2007 and references therein). Hominids are estimated to have diverged from hylobatids (gibbons and siamangs) in the Early to Middle Miocene based on fossil calibrated molecular data (Raaum et al., 2005;Steiper and Young, 2006;Perelman et al., 2011;Springer et al., 2012;Pozzi et al., 2014). The orangutan (Pongo) is the sole living member of the subfamily Ponginae and is the extant sister taxon to Homininae. ...
Article
Despite intensive study, many aspects of the evolutionary history of great apes and humans (Hominidae) are not well understood. In particular, the phylogenetic relationships of many fossil taxa remain poorly resolved. This study aims to provide an updated hypothesis of phylogenetic relationships for Middle-Late Miocene fossil apes, focusing on those taxa typically considered to be great apes. The character matrix compiled here samples 274 characters from the skull, dentition, and postcranium. Multiple iterations were performed to examine the effects of ingroup taxon selection, outgroup constraints, treatment of continuous data, character partitions (craniodental, postcranial), and missing data. Parsimony and Bayesian methods were used to infer phylogenetic relationships. Most European hominoids (Hispanopithecus, Rudapithecus, Dryopithecus, Pierolapithecus) are recovered as stem hominids, not more closely related to orangutans or to African apes and humans (Homininae), whereas Ouranopithecus, Graecopithecus, and Nakalipithecus are inferred to be members of the hominine clade. Asian fossil hominoids, with the exception of Lufengpithecus hudienensis, are recovered as part of the orangutan clade (Ponginae). Results suggest that Kenyapithecus and Griphopithecus are possible stem hominids, whereas Equatorius and Nacholapithecus are consistently recovered as stem hominoids. Oreopithecus and Samburupithecus are not recovered as hominids. Results of Bayesian analyses differ from those of parsimony analyses. Craniodental and postcranial character partitions are incongruent in the placement of hylobatids, which is interpreted as evidence that hylobatids and hominids independently evolved adaptations to suspensory positional behaviors. An understanding of phylogenetic relationships is necessary to address many of the questions asked in paleoanthropology. Thus, the updated hypothesis of phylogenetic relationships presented here can be used to gain a better understanding of important morphological transitions that took place during hominid evolution, ancestral morphotypes at key nodes, and the biogeography of the clade.
... M. cyclopis is restricted to Taiwan, and M. fuscata is found only on the three main Japan islands south of Hokkaido and some neighboring small islands just south of Kyushu (Fooden & Aimi, 2005;Fooden & Wu, 2001;Ito et al., 2021). Molecular studies confirm the fascicularis species group forms a monophyletic group with M. fascicularis representing the sister to the other species and rapid diversification from an ancestral M. mulatta population into M. cyclopis and M. fuscata, likely facilitated by dispersals to their respective island distributions (Abegg & Thierry, 2002;Delson, 1980;Ito et al., 2021;Li et al., 2009;Springer et al., 2012;Tosi et al., 2000Tosi et al., , 2003. Across the species group and in M. fascicularis specifically, combinations of natural over-water dispersals, anthropogenically aided dispersals, local extinctions and repeated recolonization of islands, and over-land movement between the Sunda Shelf islands in southeast Asia during glacial periods have contributed to complex patterns of island biogeography and population history, yet most populations appear to follow a consistent latitudinal cline in body size, tail proportions, and cranial length (Abegg & Thierry, 2002;Evans et al., 2020;Fooden, 1991Fooden, , 1995Fooden & Albrecht, 1993;Kawamoto et al., 2007Kawamoto et al., , 2008Yao et al., 2017). ...
... The response to translocation in size and lack thereof in geographic shape in captive M. mulatta suggests that modifications in these broad aspects of cranial form occur at different time scales (Elton et al., 2010;Kuzawa & Thayer, 2011). This corroborates previous studies that show size is a fairly mutable aspect of cranial form (e.g., Cardini & Elton, 2008a, 2008bSingleton, 2002), and strongly suggests that cranial shape has been modified via longer term evolutionary processes, such as selection, drift, or gene flow in these macaques, consistent with the greater developmental and evolutionary constraints on cranial shape fluctuations (Marroig & Cheverud, 2010 (Li et al., 2009;Springer et al., 2012). Estimates of divergence times between subspecies and populations of M. fascicularis in insular southeast Asia are complicated by multiple dispersal events and rapid lineage diversification, but suggest major dispersals occurred $1.7-0.5 Ma (Evans et al., 2020;Liedigk et al., 2015;Yao et al., 2017). ...
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Geographic variation is an important feature among primates, but the mechanisms underlying it are not well understood. Macaques are geographically widespread and have been translocated to captive populations, providing a prime opportunity to evaluate changes in cranial form in response to a novel environment. Clinal variation was assessed among wild fascicularis‐group macaques and compared to two translocated populations to explore the relative contributions of developmental plasticity and microevolutionary forces in producing geographic variation in cranial form. Forty‐five 3D coordinates over the cranium were taken on 380 wild macaques and 56 captive Macaca mulatta from Cayo Santiago, PR and Beaverton, OR. Geographic shape, represented by the singular warp scores from a two‐block partial least squares analysis, and centroid size were regressed against latitude, mean annual temperature, and mean annual precipitation among wild macaques. The two captive populations were compared to wild M. mulatta to assess potential changes in cranial form. Size and geographic shape were highly correlated with latitude in wild macaques, but neither ecological variable was important across the entire cline. Precipitation was important for shape only outside the tropics. Translocated M. mulatta are significantly larger, but not different in shape, compared to wild M. mulatta. These results are consistent with previous studies demonstrating cranial form is latitudinally variable among fascicularis‐group macaques, but the potential drivers remain unclear. Size is highly plastic while geographic shape has evolved differentiation at interpopulation and interspecific levels. Variation in cranial morphology likely arises first in size, followed relatively rapidly by evolved modifications to shape.
... While originally controversial, this proposal has now been supported by microstimulation and inactivation studies replicated in several laboratories and across a wide variety of species, including macaques [172,[186][187][188], galagos and squirrel monkeys [165,175,189,190], tree shrews [167] and rodents [191]. In particular, the similarity of the maps observed in macaques and galagos [165] suggests that this organization emerged at the root of primates about 70 Ma [192]. In the context of the hypothetical brain organization of ancestral mammals shown in figure 6b, I propose that the expansion of primate fronto-parietal cortex primarily involved the circuits formerly responsible for 'handling' activities, making possible the many highly diverse ways of interacting with the environment of which primates are capable. ...
Article
This article outlines a hypothetical sequence of evolutionary innovations, along the lineage that produced humans, which extended behavioural control from simple feedback loops to sophisticated control of diverse species-typical actions. I begin with basic feedback mechanisms of ancient mobile animals and follow the major niche transitions from aquatic to terrestrial life, the retreat into nocturnality in early mammals, the transition to arboreal life and the return to diurnality. Along the way, I propose a sequence of elaboration and diversification of the behavioural repertoire and associated neuroanatomical substrates. This includes midbrain control of approach versus escape actions, telencephalic control of local versus long-range foraging, detection of affordances by the dorsal pallium, diversified control of nocturnal foraging in the mammalian neocortex and expansion of primate frontal, temporal and parietal cortex to support a wide variety of primate-specific behavioural strategies. The result is a proposed functional architecture consisting of parallel control systems, each dedicated to specifying the affordances for guiding particular species-typical actions, which compete against each other through a hierarchy of selection mechanisms. This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.
... Of the living guenons, Cercopithecus and Chlorocebus are craniodentally similar and were considered congeneric until molecular studies demonstrated the arrangement was polyphyletic (Groves, 1989(Groves, , 2001Tosi et al., 2004Tosi et al., , 2005Xing et al., 2007). Uncertainty remains in the placement of Miopithecus and Allenopithecus and the relationships among the Cercopithecus species groups, with different molecular markers recovering alternative topologies (e.g., Tosi et al., 2002aTosi et al., , 2005Xing et al., 2007;Perelman et al., 2011;Springer et al., 2012). However, the monophyly of each genus, as well as the monophyly of the terrestrial clade, appears well supported ( Fig. 1; Tosi et al., 2004;Xing et al., 2007;Perelman et al., 2011;Springer et al., 2012). ...
... Uncertainty remains in the placement of Miopithecus and Allenopithecus and the relationships among the Cercopithecus species groups, with different molecular markers recovering alternative topologies (e.g., Tosi et al., 2002aTosi et al., , 2005Xing et al., 2007;Perelman et al., 2011;Springer et al., 2012). However, the monophyly of each genus, as well as the monophyly of the terrestrial clade, appears well supported ( Fig. 1; Tosi et al., 2004;Xing et al., 2007;Perelman et al., 2011;Springer et al., 2012). ...
... 12.3e9.8 Ma (Raaum et al., 2005;Steiper and Young, 2006;Fabre et al., 2009;Springer et al., 2012;Guschanski et al., 2013;Linden et al., 2020), the fossil record of the guenons is limited. Few specimens have been recovered from otherwise productive Plio-Pleistocene sites in eastern Africa (Eck and Howell, 1972;Eck, 1987;Leakey, 1988;Harrison and Harris, 1996;Frost and Alemseged, 2007;Jablonski et al., 2008;Jablonski and Frost, 2010;Plavcan et al., 2019;Frost et al., 2020) and Middle to Late Pleistocene sites in South Africa (Klein, 1977;Ogola, 2009;Mokokwe, 2016;Fig. ...
Article
The living guenons (Cercopithecini, Cercopithecidae) are speciose and widely distributed across sub-Saharan Africa but are poorly represented in the fossil record. In addition, the craniodental and skeletal similarity of the guenons has hampered the identification of fragmentary material, likely obscuring the taxonomic diversity represented in the fossil record. Here, we describe a new fossil guenon specimen (LAET 75-3703) from the Lower Ngaloba Beds, Laetoli in Tanzania, dated to ∼1.7–1.2 Ma and preserving the lower face and mandible. Comparison to 278 extant guenon specimens, representing all six extant genera, identified several informative traits for distinguishing between the morphologically similar Chlorocebus and Cercopithecus, and these support the attribution of LAET 75-3703 to Chlorocebus. A discriminant function analysis of seven craniodental indices on a subsample of Chlorocebus and Cercopithecus was robust with an overall correct classification rate of 80.4%, and it classified LAET 75-3703 as a member of Chlorocebus with a posterior probability of 92.7%. LAET 75-3703 shares with Chlorocebus the presence of small ‘thumbprint’ depressions on the maxilla; a tall, narrow, and diamond-shaped nasal aperture; a relatively longer and shallower face; relatively buccolingually broader molars; and a shallow mandible that decreases in depth posteriorly. In addition, LAET 75-3703 is distinguished from all extant guenons, including other species of Chlorocebus, in having a very small P³ relative to M¹ area. As such, LAET 75-3703 is assigned to a new species, Chlorocebus ngedere sp. nov. This specimen represents the first cercopithecin from Laetoli, as well as the oldest fossil cercopithecin confidently attributed to a modern genus.
... The applications of dated phylogenetic trees to evolutionary biology and anthropology are multi-fold. [1][2][3][4][5] Because dated phylogenies represent both the historical relationships between taxa and the timing of cladogenetic events, they are critical for understanding patterns and processes of species diversification and adaptation. ...
... Phylogenies are thus commonly used to address questions in biogeography, comparative analyses, behavioral ecology, and many other fields. 1,3,6,7 For instance, divergence times between clades are pivotal to understanding the role of geological or climatic events in the diversification of a taxonomic group because these age estimates provide a timeline for biological events. 6 Similarly, dated phylogenies can provide essential evidence in understanding the timing of colonization of a particular island 8,9 or the impact of human activity in species extinction. ...
... The figure also includes the main nodes that can be used as calibration points in the primate tree (see Table 1). Phylogenetic relationships are based on Springer et al. 1 T A B L E 1 Commonly used node calibrations for dating the primate tree with minimum bound (informed by the oldest known fossils for a specific clade) and suggested 95% prior distribution intervals 3 and updated with more recent findings. This table is not meant to provide an exhaustive list of all the fossils that can be used as calibration points, but a summary of the most commonly used calibration intervals for some of the major primate clades. ...
Article
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In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total‐evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever‐increasing availability of genomic‐level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
... The ASTRAL-Pro, FastMulRFS, MiniNJ, and DupTree tools all group Aotidate with Cebus/Saimiri. There exist studies that agree with the SpeciesRax (Perelman et al. 2011;Springer et al. 2012) but also the ASTRAL-Pro (Fabre et al. 2009) resolutions of these clades. ...
Article
Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modelling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated datasets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large datasets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31612 gene families in one hour using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.
... According to all the commonalities between humans and other catarrhine primates regarding gestural laterality and the associated brain asymmetries, several evolutionary hypotheses proposed that a left-lateralized gestural communication system may have already existed in the brain of the common ancestor of African and Asian primates, over 29 million years ago [8,295,300,302,303,318]. The neural substrates of human intentional communication would then have derived from this hemispheric specialization for gestures, under different evolutionary constraints and at different phylogenetic levels [8,303,319]. ...
Article
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Until the 1990s, the notion of brain lateralization—the division of labor between the two hemispheres—and its more visible behavioral manifestation, handedness, remained fiercely defined as a human specific trait. Since then, many studies have evidenced lateralized functions in a wide range of species, including both vertebrates and invertebrates. In this review, we highlight the great contribution of comparative research to the understanding of human handedness’ evolutionary and developmental pathways, by distinguishing animal forelimb asymmetries for functionally different actions—i.e., potentially depending on different hemispheric specializations. Firstly, lateralization for the manipulation of inanimate objects has been associated with genetic and ontogenetic factors, with specific brain regions’ activity, and with morphological limb specializations. These could have emerged under selective pressures notably related to the animal locomotion and social styles. Secondly, lateralization for actions directed to living targets (to self or conspecifics) seems to be in relationship with the brain lateralization for emotion processing. Thirdly, findings on primates’ hand preferences for communicative gestures accounts for a link between gestural laterality and a left-hemispheric specialization for intentional communication and language. Throughout this review, we highlight the value of functional neuroimaging and developmental approaches to shed light on the mechanisms underlying human handedness.