Structurally divergent and recurrently mutated regions of primate genomes.

We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.

Identification of constrained sequence elements across 239 primate genomes.

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

New records of early Paleocene (earliest Torrejonian) plesiadapiforms from northeastern Montana, USA, provide a window into the diversification of stem primates.

Plesiadapiforms (putative stem primates) appear in the fossil record shortly after the Cretaceous/Paleogene boundary and subsequently radiated throughout the Paleocene into a taxonomically and ecomorphologically diverse group. The oldest known plesiadapiforms come from early Puercan (the oldest North American Land Mammal 'age' [NALMA] of the Cenozoic) deposits in northeastern Montana, and all records of Puercan plesiadapiforms are taxonomically restricted to members of the Purgatoriidae and the enigmatic genus Pandemonium. Plesiadapiform diversity substantially increased in the following Torrejonian NALMA, but the sparse record of faunas between the Puercan and the well-known middle and late Torrejonian has hampered our understanding of this important interval in early primate evolution. Here we report new plesiadapiform dental fossils from early Torrejonian (To1) deposits from the Tullock Member of the Fort Union Formation in northeastern Montana that record several poorly known taxa including members of the Purgatoriidae, Paromomyidae and Pandemonium, and that document the largest and most diverse assemblage of To1 plesiadapiforms known. We describe a new species of the purgatoriid Ursolestes (Ursolestes blissorum, sp. nov.) that represents the largest plesiadapiform known from the early Paleocene and, among other taxa, provides additional evidence that the temporal range of purgatoriids extended into the Torrejonian. Large sample sizes of the oldest known paromomyid, Paromomys farrandi, allowed us to document intraspecific variability and one undescribed tooth locus. Our observations illuminate changes in dental morphology of some taxa that occurred in To1 and may inform the acquisition of certain diagnostic plesiadapiform dental characters. We evaluate plesiadapiform species richness, mean body mass and body-mass disparity through the Paleocene and reveal unrecognized levels of richness in To1 and a general trend of stable body mass and body-mass disparity. Our findings contribute to documented patterns of plesiadapiform provincialism in the early Paleocene and shed light on the early stages of their Torrejonian radiation.

Early anthropoid primates: New data and new questions.

Although the evolutionary history of anthropoid primates (monkeys, apes, and humans) appears relatively well-documented, there is limited data available regarding their origins and early evolution. We review and discuss here the earliest records of anthropoid primates from Asia, Africa, and South America. New fossils provide strong support for the Asian origin of anthropoid primates. However, the earliest recorded anthropoids from Africa and South America are still subject to debate, and the early evolution and dispersal of platyrhines to South America remain unclear. Because of the rarity and incomplete nature of many stem anthropoid taxa, establishing the phylogenetic relationships among the earliest anthropoids remains challenging. Nonetheless, by examining evidence from anthropoids and other mammalian groups, we demonstrate that several dispersal events occurred between South Asia and Afro-Arabia during the middle Eocene to the early Oligocene. It is possible that a microplate situated in the middle of the Neotethys Ocean significantly reduced the distance of overseas dispersal.

Rapid evolution of the primate larynx?

Tissue vibrations in the larynx produce most sounds that comprise vocal communication in mammals. Larynx morphology is thus predicted to be a key target for selection, particularly in species with highly developed vocal communication systems. Here, we present a novel database of digitally modeled scanned larynges from 55 different mammalian species, representing a wide range of body sizes in the primate and carnivoran orders. Using phylogenetic comparative methods, we demonstrate that the primate larynx has evolved more rapidly than the carnivoran larynx, resulting in a pattern of larger size and increased deviation from expected allometry with body size. These results imply fundamental differences between primates and carnivorans in the balance of selective forces that constrain larynx size and highlight an evolutionary flexibility in primates that may help explain why we have developed complex and diverse uses of the vocal organ for communication.

Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage.

The steroid hormone progesterone, acting through the progesterone receptor (PR), a ligand-activated DNA-binding transcription factor, plays an essential role in regulating nearly every aspect of female reproductive biology. While many reproductive traits regulated by PR are conserved in mammals, Catarrhine primates evolved several derived traits including spontaneous decidualization, menstruation, and a divergent (and unknown) parturition signal, suggesting that PR may also have evolved divergent functions in Catarrhines. There is conflicting evidence, however, whether the progesterone receptor gene (PGR) was positively selected in the human lineage. Here we show that PGR evolved rapidly in the human stem-lineage (as well as other Catarrhine primates), which likely reflects an episode of relaxed selection intensity rather than positive selection. Coincident with the episode of relaxed selection intensity, ancestral sequence resurrection and functional tests indicate that the major human PR isoforms (PR-A and PR-B) evolved divergent functions in the human stem-lineage. These results suggest that the regulation of progesterone signaling by PR-A and PR-B may also have diverged in the human lineage and that non-human animal models of progesterone signaling may not faithfully recapitulate human biology.

Do zoo-housed primates retreat from crowds? A simple study of five primate species.

An animal's welfare state is directly influenced by the mental state, which is shaped by experiences within the environment throughout the animal's life. For zoo-housed animals, visitors to the zoo are a large part of that environment and a fluctuating influence within it. This study examines the impact of zoo visitors on the space use of five species of zoo-housed primates (Eastern black-and-white colobus monkeys, Colobus guereza, n = 5, Allen's swamp monkeys, Allenopithecus nigroviridis, n = 2, DeBrazza's monkeys, Cercopithecus neglectus, n = 3, Bolivian gray titi monkeys, Callicebus donacophilus, n = 3, and crowned lemurs, Eulemur coronatus, n = 3). Specifically, we considered whether primates' distance from visitor areas changed as crowd sizes increased. Data were collected using the ZooMonitor app. Observers recorded spatial coordinates for each animal over periods ranging from 12 to 32 months. Data were analyzed using two types of regression models (linear and logistic) to examine the influence of visitors on the location of the primates. Both analyses revealed a statistically significant but small decrease in primate distance from visitor viewing glass as the number of visitors increased. Behavioral indicators of welfare were also unaffected by the presence of visitors. These results suggest that, with additional validation, distance from visitors may be one promising, simple way to evaluate the influence of visitors on primate welfare.

A robust alternative to assessing three-dimensional relative enamel thickness for the use in taxonomic assessment.

OBJECTIVE: Three-dimensional relative enamel thickness (3DRET) is important for assessing hypotheses about taxonomy, phylogeny, and dietary reconstruction for primates. However, its weaknesses have not been thoroughly investigated. Here, we analyze its weaknesses and propose an index aiming at better taxonomic discrimination. MATERIALS AND METHODS: The dimensionless 3D index, ratio of enamel-thickness to dentine-thickness (3DRED), which is defined as the cubic root of the ratio of 3D average enamel thickness (3DAET) to 3D average dentine thickness (3DADT), is proposed here. To compare 3DRET and 3DRED and their sensitivity to voxel size, a fossil orangutan molar was scanned 14 times with different resolutions ranging from 10 to 50 µm. Enamel thickness analysis was carried out for each resultant digital model. In addition, enamel thickness measurements of 179 mandibular permanent molars (eight genera) were analyzed, followed by investigating the relationship between 3DRET and 3DAET and between 3DRED and 3DAET. RESULTS: Regarding sensitivity, 3DRED is more robust than 3DRET. In addition, 3DRET is correlated with 3DAET by linear curve with regression coefficients approximating or larger than 0.8 in most cases, while 3DRED shows less correlation with 3DAET. Furthermore, there are clear separations between different taxa in the bivariate plot of 3DRED against 3DAET, indicative of the taxonomic value of 3DRED. CONCLUSION: Under certain conditions, 3DRED promises to be a robust and reliable alternative to 3DRET in taxonomic study.

Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates.

BACKGROUND: Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression. RESULTS: We examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential. CONCLUSIONS: The pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.

Evolution of HLA-F and its orthologues in primate species: a complex tale of conservation, diversification and inactivation.

HLA-F represents one of the nonclassical MHC class I molecules in humans. Its main characteristics involve low levels of polymorphism in combination with a restricted tissue distribution. This signals that the gene product executes a specialised function, which, however, is still poorly understood. Relatively little is known about the evolutionary equivalents of this gene in nonhuman primates, especially with regard to population data. Here we report a comparative genetic analysis of the orthologous genes of HLA-F in various great ape, Old World monkey (OWM), and New World monkey (NWM) species. HLA-F-related transcripts were found in all subjects studied. Low levels of polymorphism were encountered, although the length of the predicted gene products may vary. In most species, one or two transcripts were discovered, indicating the presence of only one active F-like gene per chromosome. An exception was provided by a New World monkey species, namely, the common marmoset. In this species, the gene has been subject to duplication, giving rise to up to six F-like transcripts per animal. In humans, great apes, and OWM, and probably the majority of the NWM species, the evolutionary equivalents of the HLA-F gene experienced purifying selection. In the marmoset, however, the gene was initially duplicated, but the expansion was subjected afterwards to various mechanisms of genetic inactivation, as evidenced by the presence of pseudogenes and an array of genetic artefacts in a section of the transcripts.

True Homoplasy of Retrotransposon Insertions in Primates.

How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, which were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multigenome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages and twelve incidences of precise deletions of previously established SINEs. Correspondingly, eight precise parallel insertions and no exact deletions were detected in a comparison of lemuriform primate and human insertions spanning the range of primate diversity. With an overall frequency of homoplasious Alu insertions of only 0.01% (for human-chimpanzee-rhesus macaque) and 0.02-0.04% (for human-bushbaby-lemurs) and precise Alu deletions of 0.001-0.002% (for human-chimpanzee-rhesus macaque), real homoplasy is not considered to be a quantitatively relevant source of evolutionary noise. Thus, presence/absence patterns of Alu retrotransposons and, presumably, all LINE1-mobilized elements represent indeed the virtually homoplasy-free markers they are considered to be. Therefore, ancestral incomplete lineage sorting and hybridization remain the only serious sources of conflicting presence/absence patterns of retrotransposon insertions, and as such are detectable and quantifiable. [Homoplasy; precise deletions; precise parallel insertions; primates; retrotransposons.].

Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments.

The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. However, profound changes in taxonomy and species concepts have led to the proliferation of Neotropical primate taxa, which may have reduced support for their results. Using the most recent taxonomic assessments and distribution maps, we tested the effect of increasing river size on the similarity of opposite riverbank primate communities in the Amazon. First, we conducted a literature review of primate taxonomy and developed a comprehensive spatial database, then applied geographical information system to query mapped primate ranges against the riverine geography of the Amazon watershed to produce a similarity index for opposite riverbank communities. Finally, we ran models to test how measures of river size predicted levels of similarity. We found that, almost without exception, similarity scores were lower than scores from Ayres and Clutton-Brock (1992) for the same rivers. Our model showed a significant negative relationship between streamflow and similarity in all tests, and found river width significant for the segmented Amazon, but not for multiple Amazon watershed rivers. Our results support the RBH insofar as they provide evidence for the prediction that rivers with higher streamflow act as more substantial barriers to dispersal, and accordingly exhibit greater variation in community composition between riverbanks.

Abundance, Diversity, and Distribution of Primates at Welel Mountain, Kellem Wollega Zone, Oromia Region, Ethiopia.

Primates are the mammals of the order Primate that is characterized by advanced development of binocular vision and enlargement of the cerebral hemispheres. The aim of this study was to investigate the abundance, diversity, and distribution of primates on Welel Mountain. From August 2017 to February 2018, we collected data from different parts of Welel Mountain during wet and dry seasons of the year and analyzed them using SPSS version 20. We identified four primate species: Chlorocebus aethiops, Cercopithecus mitis, Papio anubis, and Colobus guereza. We conducted t-test analysis for abundance and distribution of primates in wet and dry season of the year, and the P value obtained was 0.20. The mean percentages of primates in forest, woodland, and shrubs were 43.16%, 32.26%, and 24.58%, respectively. Shannon-Wiener diversity index (H') value was higher in wet season than in dry season. The current study showed that the species are distributed more evenly in wet season than in dry season, and the number of young individuals is more than that of adults. This indicates that currently the status of primates population on Welel Mountain is good. Therefore, to keep the status of primates in the study area effective, wildlife management and conservation policy should be formulated.

Daily Distance Traveled Is Associated with Greater Brain Size in Primates.

Explanations for the brain size increments through primate and, particularly, human evolution are numerous. Commonly, these hypotheses rely on the influence that behavioral and ecological variables have on brain size in extant primates, such as diet quality, social group size, or home range (HR) area. However, HR area does not reflect the time spent moving. As such, it has not been properly addressed whether the effort involved in movement could have affected brain size evolution in primates. This study aimed to test the influence of daily movement on primates' brain sizes, controlling for these other behavioral and ecological factors. We used a large comparative dataset of extant primate species and phylogenetic comparative methods. Our results show a significant correlation between daily movement and brain mass, which is not explained by the influence of diet, social group size, HR, or body mass. Hence, from an evolutionary timescale, a longer daily movement distance is not a constraining factor for the energetic investment in a larger brain. On the contrary, increased mobility could have contributed to brain mass incrementations through evolution.

Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene.

BACKGROUND: The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our previous study, we identified an intriguing unreported transcript of the BLOC1S2 gene that has a novel exon derived from two transposable elements (TEs), MIR and AluSp. To investigate the evolutionary footprint and molecular mechanism of action of this transcript, we performed PCR and RT-PCR experiments and sequencing analyses using genomic DNA and RNA samples from humans and various non-human primates. RESULTS: The results showed that the MIR element had integrated into the genome of our common ancestor, specifically in the BLOC1S2 gene region, before the radiation of all primate lineages and that the AluSp element had integrated into the genome of our common ancestor, fortunately in the middle of the MIR sequences, after the divergence of Old World monkeys and New World monkeys. The combined MIR and AluSp sequences provide a 3' splice site (AG) and 5' splice site (GT), respectively, and generate the Old World monkey-specific transcripts. Moreover, branch point sequences for the intron removal process are provided by the MIR and AluSp combination. CONCLUSIONS: We show for the first time that sequential integration into the same location and sequence divergence events of two different TEs generated lineage-specific transcripts through sequence collaboration during primate evolution.

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission.

Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST. We modeled host species as a discrete character trait on the viral phylogeny and inferred historical host switches and the pairwise transmission rates between each pair of 24 primate hosts. We identify 14 novel, well-supported, ancient cross-species transmission events. We also find that lentiviral lineages vary widely in their ability to infect new host species: SIVcol (from colobus monkeys) is evolutionarily isolated, while SIVagms (from African green monkeys) frequently move between host subspecies. We also examine the origins of SIVcpz (the predecessor of HIV-1) in greater detail than previous studies, and find that there are still large portions of the genome with unknown origins. Observed patterns of CST are likely driven by a combination of ecological circumstance and innate immune factors.

Endometrium and endometriosis tissue mitochondrial energy metabolism in a nonhuman primate model.

BACKGROUND: Endometriosis is the growth of uterine lining (endometrium) outside of the uterus. In other chronic inflammatory diseases, mitochondrial dysfunction is suspected of playing a role in disease pathogenesis. However, little is known about endometriosis mitochondrial function or its effects on tissue metabolism. The objectives of this study were to analyze mitochondrial function in nonhuman primate (NHP) endometrium and endometriosis tissue and to identify the metabolic features of these tissues that may contribute to disease. METHODS: Mitochondrial function in endometriosis tissue and endometrium was measured using mitochondrial respirometry analysis to determine if changes in oxidative phosphorylation exist in endometrium and endometriosis tissue compared to control endometrium from clinically healthy NHPs. Targeted metabolomics and multidimensional statistical analysis were applied to quantify key metabolites in energy and amino acid biosynthesis pathways. RESULTS: Mitochondrial respirometry assays showed endometrium from NHPs with endometriosis had reduced complex II-mediated oxygen consumption rates (OCR) across all energy states (basal, p = 0.01; state 3, p = 0.02; state 3u, p = 0.04; state 4o, p = 0.008) and endometriosis tissue had reduced state 3, complex I-mediated OCR (p = 0.02) and respiratory control rates (p = 0.01) compared to normal endometrium. Targeted metabolomics performed on tissue revealed carnitine (p = 0.001), creatine phosphate (p = 0.01), NADH (p = 0.0001), FAD (p = 0.001), tryptophan (p = 0.0009), and malic acid (p = 0.005) were decreased in endometriosis tissue compared to normal endometrium samples. FAD (p = 0.004), tryptophan (p = 0.0004) and malic acid (p = 0.03) were significantly decreased in endometrium from NHPs with endometriosis compared to normal endometrium. Significant metabolites identified in endometriosis and endometrium samples from animals with endometriosis were part of amino acid biosynthesis or energy metabolism pathways. CONCLUSIONS: Here, endometrial mitochondrial energy production and metabolism were decreased in endometrium and endometriosis tissue. Decreased mitochondrial energy production may be due to oxidative stress-induced damage to mitochondrial DNA or membranes, a shift in cell metabolism, or decreased energy substrate; however, the exact cause remains unknown. Additional research is needed to determine the implications of reduced mitochondrial energy production and metabolism on endometriosis and endometrium.

New fossils, systematics, and biogeography of the oldest known crown primate Teilhardina from the earliest Eocene of Asia, Europe, and North America.

Omomyiform primates are among the most basal fossil haplorhines, with the oldest classified in the genus Teilhardina and known contemporaneously from Asia, Europe, and North America during the Paleocene-Eocene Thermal Maximum (PETM) ∼56 mya. Characterization of morphology in this genus has been limited by small sample sizes and fragmentary fossils. A new dental sample (n = 163) of the North American species Teilhardina brandti from PETM strata of the Bighorn Basin, Wyoming, documents previously unknown morphology and variation, prompting the need for a systematic revision of the genus. The P4 of T. brandti expresses a range of variation that encompasses that of the recently named, slightly younger North American species 'Teilhardina gingerichi,' which is here synonymized with T. brandti. A new partial dentary preserving the alveoli for P1-2 demonstrates that T. brandti variably expresses an unreduced, centrally-located P1, and in this regard is similar to that of T. asiatica from China. This observation, coupled with further documentation of variability in P1 alveolar size, position, and presence in the European type species T. belgica, indicates that the original diagnosis of T. asiatica is insufficient at distinguishing this species from either T. belgica or T. brandti. Likewise, the basal omomyiform 'Archicebus achilles' requires revision to be distinguished from Teilhardina. Results from a phylogenetic analysis of 1890 characters scored for omomyiforms, adapiforms, and other euarchontan mammals produces a novel clade including T. magnoliana, T. brandti, T. asiatica, and T. belgica to the exclusion of two species previously referred to Teilhardina, which are here classified in a new genus (Bownomomys americanus and Bownomomys crassidens). While hypotheses of relationships and inferred biogeographic patterns among species of Teilhardina could change with the discovery of more complete fossils, the results of these analyses indicate a similar probability that the genus originated in either Asia or North America.

Skeletal morphology of the early Paleocene plesiadapiform Torrejonia wilsoni (Euarchonta, Palaechthonidae).

Plesiadapiforms, like other Paleogene mammals, are known mostly from fossil teeth and jaw fragments. The several families of plesiadapiforms known from partial skeletons have all been reconstructed as arborealists, but differences in postcranial morphology among these taxa indicate a diversity of positional behaviors. Here we provide the first detailed descriptions and comparisons of a dentally associated partial skeleton (NMMNH P-54500) and of the most complete dentary with anterior teeth (NMMNH P-71598) pertaining to Torrejonia wilsoni, from the early Paleocene (late Torrejonian To3 interval zone) of the Nacimiento Formation, San Juan Basin, New Mexico, USA. NMMNH P-54500 is the oldest known partial skeleton of a plesiadapiform and the only known postcrania for the Palaechthonidae. This skeleton includes craniodental fragments with all permanent teeth fully erupted, and partial forelimbs and hind limbs with some epiphyses unfused, indicating that this individual was a nearly fully-grown subadult. Analysis of the forelimb suggests mobile shoulder and elbow joints, a habitually flexed forearm, and capacity for manual grasping. The hip joint allowed abduction and lateral rotation of the thigh and provides evidence for frequent orthograde postures on large diameter supports. Other aspects of the hind limb suggest a habitually flexed thigh and knee with no evidence for specialized leaping, and mobile ankle joints capable of high degrees of inversion and eversion. Although it is likely that some variability exists within the group, analysis of this skeleton suggests that palaechthonids are most like paromomyids among plesiadapiforms, but retain more plesiomorphic postcranial features than has been documented for the Paromomyidae. These observations are congruent with craniodental evidence supporting palaechthonids and paromomyids as closely related within the Paromomyoidea. The skeleton of T. wilsoni also demonstrates that many regions of the postcranium were already well adapted for arboreality within the first few million years of the diversification of placental mammals following the Cretaceous-Paleogene extinction event.

An In Silico Comparison of Protocols for Dated Phylogenomics.

In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to perform in silico extractions from genomes and create directly comparable data sets for each class of marker. We then compare these data sets in terms of both phylogenetic resolution and ability to consistently and precisely estimate clade ages using fossil-calibrated molecular-clock models. Furthermore, we were also able to directly compare these results to previously published data sets from Sanger-sequenced nuclear exons and mitochondrial genomes under the same analytical conditions. Our results show-although with the exception of the mitochondrial genome data set and the smallest ddRADseq data set-that for uncontroversial nodes all data classes performed equally well, that is they recovered the same well supported topology. However, for one difficult-to-resolve node comprising a rapid diversification, we report well supported but conflicting topologies among the marker classes consistent with the mismodeling of gene tree heterogeneity as demonstrated by species tree analyses of single nucleotide polymorphisms. Likewise, clade age estimates showed consistent discrepancies between data sets under strict and relaxed clock models; for recent nodes, clade ages estimated by nuclear exon data sets were younger than those of the UCE, RADseq and mitochondrial data, but vice versa for the deepest nodes in the primate phylogeny. This observation is explained by temporal differences in phylogenetic informativeness (PI), with the data sets with strong PI peaks toward the present underestimating the deepest node ages. Finally, we conclude by emphasizing that while huge numbers of loci are probably not required for uncontroversial phylogenetic questions-for which practical considerations such as ease of data generation, sharing, and aggregating, therefore become increasingly important-accurately modeling heterogeneous data remains as relevant as ever for the more recalcitrant problems.