Primate Evolution Research Articles

Evolution of Hepatitis B Virus Receptor NTCP Reveals Differential Pathogenicities and Species Specificities of Hepadnaviruses in Primates, Rodents, and Bats.

Human hepatitis B virus (HBV) is a global health problem, affecting more than 250 million people worldwide. HBV-like viruses, named orthohepadnaviruses, also naturally infect nonhuman primates, rodents, and bats, but their pathogenicity and evolutionary history are unclear. Here, we determined the evolutionary history of the HBV receptors NTCP and GPC5 over millions of years of primate, rodent, and bat evolution. We use this as a proxy to understand the pathogenicity of orthohepadnaviruses in mammalian hosts and to determine the implications for species specificity. We found that NTCP, but not GPC5, has evolved under positive selection in primates (27 species), rodents (18 species), and bats (21 species) although at distinct residues. Notably, the positively selected codons map to the HBV-binding sites in primate NTCP, suggesting past genetic "arms races" with pathogenic orthohepadnaviruses. In rodents, the positively selected codons fall outside and within the presumed HBV-binding sites, which may contribute to the restricted circulation of rodent orthohepadnaviruses. In contrast, the presumed HBV-binding motifs in bat NTCP are conserved, and none of the positively selected codons map to this region. This suggests that orthohepadnaviruses may bind to different surfaces in bat NTCP. Alternatively, the patterns may reflect adaptive changes associated with metabolism rather than pathogens. Overall, our findings further point to NTCP as a naturally occurring genetic barrier for cross-species transmissions in primates, which may contribute to the narrow host range of HBV. In contrast, this constraint seems less important in bats, which may correspond to greater orthohepadnavirus circulation and diversity.IMPORTANCE Chronic infection with hepatitis B virus (HBV) is a major cause of liver disease and cancer in humans. Mammalian HBV-like viruses are also found in nonhuman primates, rodents, and bats. As for most viruses, HBV requires a successful interaction with a host receptor for replication. Cellular receptors are thus key determinants of host susceptibility as well as specificity. One hallmark of pathogenic virus-host relationships is the reciprocal evolution of host receptor and viral envelope proteins, as a result of their antagonistic interaction over time. The dynamics of these so-called "evolutionary arms races" can leave signatures of adaptive selection, which in turn reveal the evolutionary history of the virus-host interaction as well as viral pathogenicity and the genetic determinants of species specificity. Here, we show how HBV-like viruses have shaped the evolutionary history of their mammalian host receptor, as a result of their ancient pathogenicity, and decipher the genetic determinants of cross-species transmissions.

Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys.

The phylogenetic position of owl monkeys, grouped in the genus Aotus, has been a controversial issue for understanding Neotropical primate evolution. Explanations of the difficult phylogenetic assignment of owl monkeys have been elusive, frequently relying on insufficient data (stochastic error) or scenarios of rapid speciation (adaptive radiation) events. Using a coalescent-based approach, we explored the population-level mechanisms likely explaining these topological discrepancies. We examined the topological variance of 2,192 orthologous genes shared between representatives of the three major Cebidae lineages and the outgroup. By employing a methodological framework that allows for reticulated tree topologies, our analysis explicitly tested for non-dichotomous evolutionary processes impacting the finding of the position of owl monkeys in the cebid phylogeny. Our findings indicated that Aotus is a sister lineage of the callitrichines. Most gene trees (>50%) failed to recover the species tree topology, although the distribution of gene trees mismatching the true species topology followed the standard expectation of the multispecies coalescent without reticulation. We showed that the large effective population size of the common ancestor of Aotus and callitrichines was the most likely factor responsible for generating phylogenetic uncertainty. On the other hand, fast speciation scenarios or introgression played minor roles. We propose that the difficult phylogenetic placement of Aotus is explained by population-level processes associated with the large ancestral effective size. These results shed light on the biogeography of the early cebid diversification in the Miocene, highlighting the relevance of evaluating phylogenetic relationships employing population-aware approaches.

A comprehensive analysis of chimpanzee (Pan troglodytes)-specific LINE-1 retrotransposons

Long interspersed element-1 (LINE-1 or L1) is one of the most abundant retrotransposons in the primate genomes and has contributed to their genome diversity and variations during the primate evolution. Among primate L1 subfamilies, L1Pt subfamilies include Pan troglodytes-specific L1s. L1Pt elements have been successfully expanded in the chimpanzee genome since the divergence of human and chimpanzee lineages. However, only a few full-length L1Pt copies were previously detected in the chimpanzee genome due to incomplete chimpanzee reference genome sequences at the time. In the present study, we aimed to identify chimpanzee-specific L1s using the most recent version of the chimpanzee reference genome (May 2016, panTro5). We identified a total of 3731 chimpanzee-specific L1s. This is much more than previously reported chimpanzee-specific L1 copies. Among these, 223 are full-length (>6 kb), and we annotated their subfamilies and examined their retrotransposition-competency. The result showed that there are two L1Pt subfamilies in the chimpanzee genome, and the nine structurally intact elements belong to L1Pt-1, L1Pt-2, and L1PA2 subfamilies. In addition, we found that the intact full-length L1 group showed significantly higher L1 expression level than the non-intact full-length L1 group using limited RNA-seq data. It is interesting to notice that the number of retrotransposition-competent elements is much less in the chimpanzee genome than that in the human genome. In conclusion, there is increasing evidence to indicate that chimpanzee-specific L1s have changed the chimpanzee genome, causing genomic difference from other primate genomes.

Chromatin features constrain structural variation across evolutionary timescales

The potential impact of structural variants includes not only the duplication or deletion of coding sequences, but also the perturbation of noncoding DNA regulatory elements and structural chromatin features, including topological domains (TADs). Structural variants disrupting TAD boundaries have been implicated both in cancer and developmental disease; this likely occurs via "enhancer hijacking," whereby removal of the TAD boundary exposes enhancers to new target transcription start sites (TSSs). With this functional role, we hypothesized that boundaries would display evidence for negative selection. Here we demonstrate that the chromatin landscape constrains structural variation both within healthy humans and across primate evolution. In contrast, in patients with developmental delay, variants occur remarkably uniformly across genomic features, suggesting a potentially broad role for enhancer hijacking in human disease.

Expression of two near absent dental traits, mesial cuspule and paraconid, on one Archaic period modern human from the Ohio Valley

Presented here are the linugal cuspule and paraconid; two traits considered near absent (occurring <1%) in world populations. Both traits were found on lower third molars of one individual from late Archaic (2500-500BC) site of Shick in, Handcock County, Ohio. Rare dental anomalies in modern humans inform about biological variation and evolutionary changes. The Lingual Cuspule has only been reported in one other world population, thus very little is known about this anomaly. It was thought that paraconids have been otherwise lost in primate evolution starting in the Oligocene (34-23 MYA). The expression of a paraconid in modern humans could suggest secondary evolution of this trait. Further reporting of both traits is necessary to discuss the implications of human dental evolution which result from the presence of these variants.

Absolute brain size predicts dog breed differences in executive function.

Large-scale phylogenetic studies of animal cognition have revealed robust links between absolute brain volume and species differences in executive function. However, past comparative samples have been composed largely of primates, which are characterized by evolutionarilyderived neural scaling rules. Therefore, it is currently unknown whether positive associations between brain volume and executive function reflect a broad-scale evolutionary phenomenon, or alternatively, a unique consequence of primate brain evolution. Domestic dogs provide a powerful opportunity for investigating this question due to their close genetic relatedness, but vast intraspecific variation. Using citizen science data on more than 7000 purebred dogs from 74 breeds, and controlling for genetic relatedness between breeds, we identify strong relationships between estimated absolute brain weight and breed differences in cognition. Specifically, larger-brained breeds performed significantly better on measures of short-term memory and self-control. However, the relationships between estimated brain weight and other cognitive measures varied widely, supporting domain-specific accounts of cognitive evolution. Our results suggest that evolutionary increases in brain size are positively associated with taxonomic differences in executive function, even in the absence of primate-like neuroanatomy. These findings also suggest that variation between dog breeds may present a powerful model for investigating correlated changes in neuroanatomy and cognition among closely related taxa.

Conserved sequences identify the closest living relatives of primates

Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.

Primate neocortex development and evolution: Conserved versus evolved folding.

The neocortex, the seat of higher cognitive functions, exhibits a key feature across mammalian species-a highly variable degree of folding. Within the neocortex, two distinct subtypes of cortical areas can be distinguished, the isocortex and the proisocortex. Here, we have compared specific spatiotemporal aspects of folding between the proisocortex and the isocortex in 13 primates, including human, chimpanzee, and various Old World and New World monkeys. We find that folding at the boundaries of the dorsal isocortex and the proisocortex, which gives rise to the cingulate sulcus (CiS) and the lateral fissure (LF), is conserved across the primates studied and is therefore referred to as conserved folding. In contrast, the degree of folding within the dorsal isocortex exhibits huge variation across these primates, indicating that this folding, which gives rise to gyri and sulci, is subject to major changes during primate evolution. We therefore refer to the folding within the dorsal isocortex as evolved folding. Comparison of fetal neocortex development in long-tailed macaque and human reveals that the onset of conserved folding precedes the onset of evolved folding. Moreover, the analysis of infant human neocortex exhibiting lissencephaly, a developmental malformation thought to be mainly due to abnormal neuronal migration, shows that the evolved folding is perturbed more than the conserved folding. Taken together, our study presents a two-step model of folding that pertains to primate neocortex development and evolution. Specifically, our data imply that the conserved folding and the evolved folding constitute two distinct, sequential events.

Evolution in primates by "Catastrophic-selection" interplay between enveloped virus epidemics, mutated genes of enzymes synthesizing carbohydrate antigens, and natural anti-carbohydrate antibodies.

"Catastrophic-selection" is an evolutionary mechanism, by which entire parental-populations are eliminated but very few mutated offspring survive and replace extinct parental-populations. The human natural anti-carbohydrate antibodies, anti-Gal and anti-Neu5Gc suggest the occurrence of catastrophic-selection events in primate evolution. Parental-populations synthesizing corresponding carbohydrate-antigens underwent extinction in viral epidemics, and few offspring survived. These offspring carried accidental mutations that inactivated carbohydrate-antigen synthesis and produced natural-antibody against the lost antigen. Such natural anti-carbohydrate antibody was produced against environmental carbohydrate-antigens (e.g., gastrointestinal bacteria). The carbohydrate-antigen in infected parental-populations was also synthesized on viruses by the host glycosylation-machinery. The natural-antibody in the offspring bound to the carbohydrate-antigen on infecting viruses produced in parental-populations, destroyed the viruses and protected these offspring from extinction. This process occurred in ancestral Old-World monkeys and apes synthesizing α-gal epitopes, which were replaced 20-30 million-years-ago by offspring lacking α-gal epitopes and producing natural anti-Gal antibody against this antigen, and later in hominins synthesizing the sialic-acid antigen Neu5Gc, which were replaced by offspring lacking Neu5Gc and producing anti-Neu5Gc antibody. A present-day example for accidental mutations in very few humans that lost a common carbohydrate-antigen and produce a natural antibody against it is the rare blood-group "Bombay" individuals. These individuals lack the H-antigen (blood-group O) which is synthesized in all other humans, and produce the natural anti-H antibody against blood-group O. Overall, it is suggested that natural anti-carbohydrate antibodies played a critical role in preventing complete extinction of mammalian species in epidemics of highly virulent viruses and may have similar role in future events.

Evolution of DNA Methylation in Papio Baboons.

Changes in gene regulation have long been thought to play an important role in primate evolution. However, although a number of studies have compared genome-wide gene expression patterns across primate species, fewer have investigated the gene regulatory mechanisms that underlie such patterns, or the relative contribution of drift versus selection. Here, we profiled genome-scale DNA methylation levels in blood samples from five of the six extant species of the baboon genus Papio (4-14 individuals per species). This radiation presents the opportunity to investigate DNA methylation divergence at both shallow and deeper timescales (0.380-1.4 My). In contrast to studies in human populations, but similar to studies in great apes, DNA methylation profiles clearly mirror genetic and geographic structure. Divergence in DNA methylation proceeds fastest in unannotated regions of the genome and slowest in regions of the genome that are likely more constrained at the sequence level (e.g., gene exons). Both heuristic approaches and Ornstein-Uhlenbeck models suggest that DNA methylation levels at a small set of sites have been affected by positive selection, and that this class is enriched in functionally relevant contexts, including promoters, enhancers, and CpG islands. Our results thus indicate that the rate and distribution of DNA methylation changes across the genome largely mirror genetic structure. However, at some CpG sites, DNA methylation levels themselves may have been a target of positive selection, pointing to loci that could be important in connecting sequence variation to fitness-related traits.

More intelligent chimpanzees (Pan troglodytes) have larger brains and increased cortical thickness

Though sometimes controversial, there is growing consensus that human general intelligence is associated with variation in a number of aspects of cortical organization including brain volume, white and gray matter volume, connectivity, and cortical thickness. Recent studies in great apes have shown, like humans, they exhibit both general and domain specific forms of intelligence when tested on a wide range of cognitive tests; however, whether individual variation in intelligence is associated with measures of cortical organization remains untested. Here we show that general intelligence in chimpanzees is associated with total brain volume, total gray matter volume, mean cortical thickness and regional variation in both gray matter volume and cortical thickness. These results suggest that increased gray matter volume and cortical thickness may produce enhanced computational cognitive processes and may have been selected for during primate brain evolution.

A Review of Experimental, Natural, and Anthropogenic Hybridization in Callithrix Marmosets

Natural and anthropogenic hybridization both occur in primates, but the effects of these distinct processes on primate evolution and population dynamics can be difficult to disentangle from one another. With most primate species being endangered, conservation prioritizes natural over anthropogenic hybrids. However, anthropogenic hybridization can generate genetic diversity and novelty, and fully understanding hybridization is important for primate conservation and evolutionary biology. The neotropical genus Callithrix, an emerging hybridization model, provides a good opportunity to study natural and anthropogenic hybridization separately, and here I review Callithrix hybridization work from the 1970s to the 2010s. Natural hybridization in these species occurs under secondary contact at their distribution borders. In contrast, C. jacchus and C. penicillata, species native to northern, northeastern, and central-eastern Brazil, have been widely introduced in southeastern Brazil. Such introductions have resulted in artificial sympatry and hybridization between exotic C. jacchus and C. penicillata with themselves or with native Callithrix species. Hybridization between native C. aurita and exotic Callithrix results in mixed pure species and hybrid groups, whereas hybridization between pairings of C. jacchus, C. penicillata, and C. geoffroyi results in populations of advanced hybrids. These findings indicate differences in reproductive isolation, and as such, distinct genomic and evolutionary consequences of these hybridization events. Genomic and genetic work is still rare for wild Callithrix populations, and most hybridization studies have been qualitative or descriptive. I point future priorities for Callithrix hybridization research toward hybrid fitness, reproduction, and health as well as investigation of genetic introgression among hybrids and nonhybrids.

High-Expanding Regions in Primate Cortical Brain Evolution Support Supramodal Cognitive Flexibility.

Primate cortical evolution has been characterized by massive and disproportionate expansion of a set of specific regions in the neocortex. The associated increase in neocortical neurons comes with a high metabolic cost, thus the functions served by these regions must have conferred significant evolutionary advantage. In the present series of analyses, we show that evolutionary high-expanding cortex - as estimated from patterns of surface growth from several primate species - shares functional connections with different brain networks in a context-dependent manner. Specifically, we demonstrate that high-expanding cortex is characterized by high internetwork functional connectivity; is recruited flexibly over many different cognitive tasks; and changes its functional coupling pattern between rest and a multimodal task-state. The capacity of high-expanding cortex to connect flexibly with various specialized brain networks depending on particular cognitive requirements suggests that its selective growth and sustainment in evolution may have been linked to an involvement in supramodal cognition. In accordance with an evolutionary-developmental view, we find that this observed ability of high-expanding regions - to flexibly modulate functional connections as a function of cognitive state - emerges gradually through childhood, with a prolonged developmental trajectory plateauing in young adulthood.

Female Power in Primates and the Phenomenon of Female Dominance

Sex-biased power structures are common in human and nonhuman primate societies. “Female dominance” is a term applied to a wide range of female-biased power structures. However, the full extent of this variation remains obscure because an adequate vocabulary of power has not been adopted consistently. Female power occurs throughout primates and other animals, even in male-dominant societies, but the legacy of patriarchy persists in primatologists’ use of language and implicit assumptions about intersexual power. While explanations for the occurrence of female power can be accommodated within existing ethological theory, many hypotheses seeking to explain the evolution of female power are narrowly focused on particular taxa. Theories about primate social evolution would benefit from a synthesis of the disparate literature on power, increased emphasis on intersexual social relationships, and comparative studies that include the full behavioral diversity of primates and other mammals.

Effects of Environmental Stress on Primate Populations

Environmental stress on primate populations can take many forms. Abiotic factors, such as temperature and precipitation, may directly influence the behavior of primates owing to physiological demands of thermoregulation or through indirect influences on vegetation that primates rely on for food. These effects can also scale up to the macro scale, impacting primate distributions and evolution. Primates also encounter stress during interactions within and between species (i.e., biotic interactions). For example, selective pressure from male-perpetrated infanticide can drive the development of female counterstrategies and can impact life-history traits. Predation on primates can modify group size, ranging behavior, and habitat use. Finally, humans have influenced primate populations for millennia. More recently, hunting, habitat disturbance, disease, and climate change have increased in frequency and severity with detrimental impacts on primate populations worldwide. These effects and recent evidence from camera traps emphasize the importance of maintaining protected areas for conserving primate populations.

Primate tails: Ancestral state reconstruction and determinants of interspecific variation in primate tail length.

Living primates vary considerably in tail length-body size relation, ranging from tailless species to those where the tail is more than twice as long as the body. Because the general pattern and determinants of tail evolution remain incompletely known, we reconstructed evolutionary changes in relative tail length across all primates and sought to explain interspecific variation in this trait. We combined data on tail length, head-body length, intermembral index (IMI), habitat use, locomotion type, and range latitude for 340 species from published sources. We reconstructed the evolution of relative tail length to identify all independent cases of regime shifts on a primate phylogeny, using several methods based on Ornstein-Uhlenbeck (OU) models. Accounting for phylogeny, we also examined the effects of habitat, locomotion type, distance from the equator and IMI on interspecific variation in tail length-body size relation. Primate tail length is not sexually dimorphic. A phylogenetic reconstruction allowing multiple optima explains the observed regime shifts best. During the evolutionary history of primates, relative tail length changed 50 times under an OU model. Specifically, relative tail length increased 26 and decreased 24 times. Most of these changes occurred among Old World primates. Among the variables tested here, interspecific variation in IMI and the difference between leaping and non-leaping locomotion explained interspecific variation in relative tail length: Evolutionary decreases in relative tail length are generally associated with an increase in IMI and an absence of leaping behavior. Regime shifts for relative tail length in living primates occurred in concert with fundamental changes in IMI and a change from leaping to non-leaping locomotion, or vice versa. Exceptions from this general pattern are linked to the presence of a prehensile tail or specialized foraging strategies. Thus, the primate tail appears to have evolved in functional coordination with limb proportions, presumably to assist body balance.

Locomotor kinematics of tree squirrels (Sciurus carolinensis) in free‐ranging and laboratory environments: Implications for primate locomotion and evolution

The grasping capabilities and gait kinematics characteristic of primates are often argued to be adaptations for safely moving on small terminal branches. The goal of this study was to identify whether Eastern gray squirrels (Sciurus carolinensis)-arboreal rodents that frequently move and forage on small branches, lack primate-like grasping and gait patterns, and arguably represent extant analogs of a stem primate ancestor-adjust gait kinematics to narrow and nonhorizontal branches. We studied locomotor kinematics of free-ranging and laboratory-housed squirrels moving over various substrates. We used high-speed video to film (a) a population of free-ranging squirrels moving on natural substrates and (b) laboratory-housed squirrels moving on horizontal poles. Substrates were coded as small, medium, or large relative to squirrel trunk diameter, and as inclined, declined, or horizontal. Free-ranging squirrels used more gallops and half-bounds on small- and medium-sized substrates, and more high-impact bounds, with reduced limb-lead durations, on declined substrates. Laboratory squirrels moved at higher speeds than free-ranging squirrels and responded to decreasing diameter by using more gallops and half-bounds, lowering speed, and-controlling for speed-increasing mean duty factor, mean number of supporting limbs, and relative forelimb lead duration. Our inability to detect substantial diameter or orientation-related gait adjustments in the wild may be due to a limited accounting of confounding influences (e.g., substrate compliance). Ultimately, studies assessing stability measures (e.g., center of mass fluctuations and peak vertical force) are required to assess whether primates' enhanced grasping and gait patterns engender performance advantages on narrow or oblique substrates.

A 3D population-based brain atlas of the mouse lemur primate with examples of applications in aging studies and comparative anatomy

The gray mouse lemur (Microcebus murinus) is a small prosimian of growing interest for studies of primate biology and evolution, and notably as a model organism of brain aging. As brain atlases are essential tools for brain investigation, the objective of the current work was to create the first 3D digital atlas of the mouse lemur brain. For this, a template image was constructed from in vivo magnetic resonance imaging (MRI) data of 34 animals. This template was then manually segmented into 40 cortical, 74 subcortical and 6 cerebro-spinal fluid (CSF) regions. Additionally, we generated probability maps of gray matter, white matter and CSF. The template, manual segmentation and probability maps, as well as imaging tools used to create and manipulate the template, can all be freely downloaded. The atlas was first used to automatically assess regional age-associated cerebral atrophy in a cohort of mouse lemurs previously studied by voxel based morphometry (VBM). Results based on the atlas were in good agreement with the VBM ones, showing age-associated atrophy in the same brain regions such as the insular, parietal or occipital cortices as well as the thalamus or hypothalamus. The atlas was also used as a tool for comparative neuroanatomy. To begin with, we compared measurements of brain regions in our MRI data with histology-based measures from a reference article largely used in previous comparative neuroanatomy studies. We found large discrepancies between our MRI-based data and those of the reference histology-based article. Next, regional brain volumes were compared amongst the mouse lemur and several other mammalian species where high quality volumetric MRI brain atlases were available, including rodents (mouse, rat) and primates (marmoset, macaque, and human). Unlike those based on histological atlases, measures from MRI atlases indicated similar cortical to cerebral volume indices in all primates, including in mouse lemurs, and lower values in mice. On the other hand, white matter to cerebral volume index increased from rodents to small primates (mouse lemurs and marmosets) to macaque, reaching their highest values in humans.

Gorongosa by the sea: First Miocene fossil sites from the Urema Rift, central Mozambique, and their coastal paleoenvironmental and paleoecological contexts

The East African Rift System (EARS) has played a central role in our understanding of human origins and vertebrate evolution in the late Cenozoic of Africa. However, the distribution of fossil sites along the rift is highly biased towards its northern extent, and the types of paleoenvironments are primarily restricted to fluvial and lacustrine settings. Here we report the discovery of the first fossil sites from the Urema Rift at Gorongosa National Park (central Mozambique) at the southern end of the EARS, and reconstruct environmental contexts of the fossils. In situ and surface fossils from the lower member of the Mazamba Formation, estimated to be of Miocene age, comprise mammals, reptiles, fishes, invertebrates, palms, and dicot trees. Fossil and geological evidence indicates a coastal-plain paleoenvironmental mosaic of riverine forest/woodland and estuarine habitats that represent the first coastal biomes identified in the Neogene EARS context. Receiving continental sediment from source terranes west of today's Urema Graben, estuarine sequences accumulated prior to rifting as compound incised-valley fills on a low-gradient coastal plain following transgression. Modern environmental analogues are extremely productive habitats for marine and terrestrial fauna, including primates. Thus, our discoveries raise the possibility that the Miocene coastal landscapes of Gorongosa were ecologically-favorable habitats for primates, providing relatively stable maritime climate and ecosystem conditions, year-round freshwater availability, and food both from terrestrial and marine sources. The emerging fossil record from Gorongosa is beginning to fill an important gap in the paleobiogeography of Africa as no fossil sites of Neogene age have previously been reported from the southernmost part of the EARS. Furthermore, this unique window into past continental-margin ecosystems of central Mozambique may allow us to test key paleobiogeographic hypotheses during critical periods of primate evolution.

Reevaluating cases of trait-dependent diversification in primates.

Previous investigations have identified several ecological traits that may have shaped differences in species richness among primate clades by influencing speciation and extinction probabilities. In this study, I reevaluate these cases in light of concerns about high false-positive rates of the methods used to detect trait-dependent diversification. Data for six traits were taken from the literature: activity pattern, sociality, mating system, terrestriality, frugivory, and mutualistic interactions with angiosperms (i.e., seed dispersal and pollination). These traits were treated as binary variables and analyzed in a phylogenetic framework using likelihood-based and nonparametric methods for estimating trait-specific diversification rates. Of the traits analyzed here, only activity pattern was found by all methods to be correlated with diversification: diurnal primates diversify at higher rates than nocturnal primates. Solitary foragers have a lower rate of diversification than group-living primates, but this link is driven by the association between solitariness and nocturnality. These results indicate that ecological traits have had a more limited influence on primate diversification than suggested by previous studies. The false positives detected here can be linked with heterogeneity in diversification caused by sources other than the focal traits. One of these sources is the very high rate of diversification in Cercopithecoidea found in previous investigations. Another is the correlation between activity patterns and diversification. The underlying causal mechanism for the contrast in diversification dynamics between diurnal and nocturnal primates is unclear, but this correlation highlights the important role of activity pattern in shaping primate evolutionary history.