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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.

A full understanding of primate morphological and genomic evolution requires the identification of their closest living relative. In order to resolve the ancestral relationships among primates and their closest relatives, we searched multispecies genome alignments for phylogenetically informative rare genomic changes within the superordinal group Euarchonta, which includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews). We also constructed phylogenetic trees from 14 kilobases of nuclear genes for representatives from most major primate lineages, both extant colugos, and multiple treeshrews, including the pentail treeshrew, Ptilocercus lowii, the only living member of the family Ptilocercidae. A relaxed molecular clock analysis including Ptilocercus suggests that treeshrews arose approximately 63 million years ago. Our data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous.

Plesiadapiforms are central to studies of the origin and evolution of primates and other euarchontan mammals (tree shrews and flying lemurs). We report results from a comprehensive cladistic analysis using cranial, postcranial, and dental evidence including data from recently discovered Paleocene plesiadapiform skeletons (Ignacius clarkforkensis sp. nov.; Dryomomys szalayi, gen. et sp. nov.), and the most plesiomorphic extant tree shrew, Ptilocercus lowii. Our results, based on the fossil record, unambiguously place plesiadapiforms with Euprimates and indicate that the divergence of Primates (sensu lato) from other euarchontans likely occurred before or just after the Cretaceous/Tertiary boundary (65 Mya), notably later than logistical model and molecular estimates. Anatomical features associated with specialized pedal grasping (including a nail on the hallux) and a petrosal bulla likely evolved in the common ancestor of Plesiadapoidea and Euprimates (Euprimateformes) by 62 Mya in either Asia or North America. Our results are consistent with those from recent molecular analyses that group Dermoptera with Scandentia. We find no evidence to support the hypothesis that any plesiadapiforms were mitten-gliders or closely related to Dermoptera.

The data provided here include home range and body sizes for 285 species of mammals in 177 genera. Data were extracted from 552 published sources, and have been used in multiple papers since we originally published results of analyses in 1999 and 2001. While this likely is the most comprehensive such data set available, it is arguably biased taxonomically and geographically. While some mammal orders are well represented taxonomically most are not. Hence, while all genera in Monotremata, Proboscidea, and Pholidota are represented, these comprise only 60, 66, and 20% of species, respectively; moreover, these are relatively minor radiations. In contrast, we have no species of Paucituberculata, Microbiotheria, Notoryctemorphia, Tubulidentata, Hyracoidea, Cingulata, Scandentia, Dermoptera, and Primates (the latter likely reflecting a bias in data acquisition). The modal proportion of genera and species across 27 terrestrial orders is zero; the median values are 10.8% (genera) and 3.7% (species), suggesting that further data should be sought to confirm generalizations provided by these data.

The data provided here include home range and body sizes for 285 species of mammals in 177 genera. Data were extracted from 552 published sources, and have been used in multiple papers since we originally published results of analyses in 1999 and 2001. While this likely is the most comprehensive such data set available, it is arguably biased taxonomically and geographically. While some mammal orders are well represented taxonomically most are not. Hence, while all genera in Monotremata, Proboscidea, and Pholidota are represented, these comprise only 60, 66, and 20% of species, respectively; moreover, these are relatively minor radiations. In contrast, we have no species of Paucituberculata, Microbiotheria, Notoryctemorphia, Tubulidentata, Hyracoidea, Cingulata, Scandentia, Dermoptera, and Primates (the latter likely reflecting a bias in data acquisition). The modal proportion of genera and species across 27 terrestrial orders is zero; the median values are 10.8% (genera) and 3.7% (species), suggesting that further data should be sought to confirm generalizations provided by these data.

Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here, we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) visual sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in the color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination.

The data provided here include home range and body sizes for 285 species of mammals in 177 genera. Data were extracted from 552 published sources, and have been used in multiple papers since we originally published results of analyses in 1999 and 2001. While this likely is the most comprehensive such data set available, it is arguably biased taxonomically and geographically. While some mammal orders are well represented taxonomically most are not. Hence, while all genera in Monotremata, Proboscidea, and Pholidota are represented, these comprise only 60, 66, and 20% of species, respectively; moreover, these are relatively minor radiations. In contrast, we have no species of Paucituberculata, Microbiotheria, Notoryctemorphia, Tubulidentata, Hyracoidea, Cingulata, Scandentia, Dermoptera, and Primates (the latter likely reflecting a bias in data acquisition). The modal proportion of genera and species across 27 terrestrial orders is zero; the median values are 10.8% (genera) and 3.7% (species), suggesting that further data should be sought to confirm generalizations provided by these data.

Endogenous retroviruses are genomic elements formed by germline infiltration by originally exogenous viruses. These molecular fossils provide valuable information about the evolution of the retroviral family. Lentiviruses are an extensively studied genus of retroviruses infecting a broad range of mammals. Despite a wealth of information on their modern evolution, little is known about their origins. This is partially due to the scarcity of their endogenous forms. Recently, an endogenous lentivirus, ELVgv, was discovered in the genome of the Malayan colugo (order Dermoptera). This represents the oldest lentiviral evidence available and promises to lead to further insights into the history of this genus. In this study, we analyzed ELVgv integrations at several genomic locations in four distinct colugo specimens covering all the extant dermopteran species. We confirmed ELVgv integrations in all the specimens examined, which implies that the virus originated before the dermopteran diversification. Using a locus-specific dermopteran substitution rate, we estimated that the proviral integrations occurred 21–40 Ma. Using phylogenetic analysis, we estimated that ELVgv invaded an ancestor of today’s Dermoptera in an even more distant past. We also provide evidence of selective pressure on the TRIM5 antiviral restriction factor, something usually taken as indirect evidence of past retroviral infections. Interestingly, we show that TRIM5 was under strong positive selection pressure only in the common dermopteran ancestor, where the ELVgv endogenization occurred. Further experiments are required to determine whether ELVgv participated in the TRIM5 selection.

Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent incomplete marker fixation in ancestral lineages, led to challenged attempts at phylogenetic reconstructions, particularly for the phylogenetic position of tree shrews. To resolve this conundrum, we sampled genome-wide presence/absence patterns of transposed elements (TEs) from all representatives of Euarchontoglires. This specific marker system has the advantage that phylogenetic diagnostic characters can be extracted in a nearly unbiased fashion genome-wide from reference genomes. Their insertions are virtually free of homoplasy. We simultaneously employed two computational tools, the genome presence/absence compiler (GPAC) and 2-n-way, to find a maximum of diagnostic insertions from more than 3 million TE positions. From 361 extracted diagnostic TEs, 132 provide significant support for the current resolution of Primatomorpha (Primates plus Dermoptera), 94 support the union of Euarchonta (Primates, Dermoptera, plus Scandentia), and 135 marker insertion patterns support a variety of alternative phylogenetic scenarios. Thus, whole genome-level analysis and a virtually homoplasy-free marker system offer an opportunity to finally resolve the notorious phylogenetic challenges that nature produces in rapidly diversifying groups.

Molar morphology plays a key role in the systematics and behavioral interpretation of fossil taxa, so understanding the developmental patterns that shape occlusal morphology in modern taxa is of central importance to informing analysis of the fossil record. The shape of the outer enamel surface (OES) of a tooth is largely the result of the forming and folding of the inner enamel epithelium, which is preserved in fully formed teeth as the enamel-dentine junction (EDJ). Previous research on living primates has shown that the degree of correlation between the EDJ and OES can be used to inform our understanding of developmental patterns because lower correlations imply that later developmental events modify the template provided by the EDJ more extensively. Here, we use three topographic metrics to investigate the degree of correlation between the EDJ and OES across living euarchontans by analyzing treeshrews and dermopterans in addition to primates. We found that all living euarchontans show a high degree of topographical correlation, whereas non-primates, especially basally divergent taxa such as Ptilocercus lowii , show the highest degree of correlation between these two surfaces. Our results indicate, that while it is the earlier stages of dental development that have the most influence on overall crown morphology in euarchontans generally, among primates, anthropoids have a lower degree of correlation, implying a greater emphasis on later phases of dental development. This provides insight relevant to interpreting the evolutionary context of the diversity of dental form observed within Euarchonta.