Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families

Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution.

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

BACKGROUND

Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates.

RESULTS

Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates.

CONCLUSIONS

Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.

Metagenomic analyses reveal previously unrecognized variation in the diets of sympatric Old World monkey species

Insectivory, or the consumption of insects and other arthropods, is a significant yet cryptic component of omnivorous primate diets. Here, we used high-throughput DNA sequencing to identify arthropods from fecal DNA and assess variation in insectivory by closely-related sympatric primates. We identified arthropod prey taxa and tested the hypothesis that variation in insectivory facilitates niche differentiation and coexistence among closely-related species with high dietary overlap. We collected 233 fecal samples from redtail (Cercopithecus ascanius; n = 118) and blue monkeys (C. mitis; n = 115) and used a CO1 metabarcoding approach to identify arthropod DNA in each fecal sample. Arthropod DNA was detected in 99% of samples (N = 223 samples), and a total of 68 families (15 orders) were identified. Redtails consumed arthropods from 54 families, of which 12 (21.8%) were absent from blue monkey samples. Blue monkeys consumed arthropods from 56 families, of which 14 (24.6%) were absent from redtail samples. For both species, >97% of taxa present belonged to four orders (Araneae, Diptera, Hymenoptera, Lepidoptera). Redtail samples contained more Lepidoptera taxa (p<0.05), while blue monkey samples contained more Araneae (p<0.05). Blue monkeys consumed a greater diversity of arthropod taxa than redtail monkeys (p<0.05); however, the average number of arthropod families present per fecal sample was greater in the redtail monkey samples (p<0.05). These results indicate that while overlap exists in the arthropod portion of their diets, 20-25% of taxa consumed are unique to each group. Our findings suggest that variation in arthropod intake may help decrease dietary niche overlap and hence facilitate coexistence of closely-related primate species.

Functional characterization of enhancer evolution in the primate lineage

BACKGROUND

Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Previous efforts to understand the evolution of enhancers in primates have typically studied many enhancers at low resolution, or single enhancers at high resolution. Although comparative genomic studies reveal large-scale turnover of enhancers, a specific understanding of the molecular steps by which mammalian or primate enhancers evolve remains elusive.

RESULTS

We identified candidate hominoid-specific liver enhancers from H3K27ac ChIP-seq data. After locating orthologs in 11 primates spanning around 40 million years, we synthesized all orthologs as well as computational reconstructions of 9 ancestral sequences for 348 active tiles of 233 putative enhancers. We concurrently tested all sequences for regulatory activity with STARR-seq in HepG2 cells. We observe groups of enhancer tiles with coherent trajectories, most of which can be potentially explained by a single gain or loss-of-activity event per tile. We quantify the correlation between the number of mutations along a branch and the magnitude of change in functional activity. Finally, we identify 84 mutations that correlate with functional changes; these are enriched for cytosine deamination events within CpGs.

CONCLUSIONS

We characterized the evolutionary-functional trajectories of hundreds of liver enhancers throughout the primate phylogeny. We observe subsets of regulatory sequences that appear to have gained or lost activity. We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution.

Genetic Diversity and Structure among Isolated Populations of the Endangered Gees Golden Langur in Assam, India

Gee’s golden langur (Trachypithecus geei) is an endangered colobine primate, endemic to the semi-evergreen and mixed-deciduous forests of Indo-Bhutan border. During the last few decades, extensive fragmentation has caused severe population decline and local extinction of golden langur from several fragments. However, no studies are available on the impact of habitat fragmentation and the genetic diversity of golden langur in the fragmented habitats. The present study aimed to estimate the genetic diversity in the Indian population of golden langur. We sequenced and analyzed around 500 bases of the mitochondrial DNA (mtDNA) hypervariable region-I from 59 fecal samples of wild langur collected from nine forest fragments. Overall, genetic diversity was high (h = 0.934, π = 0.0244) and comparable with other colobines. Populations in smaller fragments showed lower nucleotide diversity compared to the larger forest fragments. The median-joining network of haplotypes revealed a genetic structure that corresponded with the geographical distribution. The Aie and Champabati Rivers were found to be a barrier to gene flow between golden langur populations. In addition, it also established that T. geei is monophyletic but revealed possible hybridization with capped langur, T. pileatus, in the wild. It is hoped that these findings would result in a more scientific approach towards managing the fragmented populations of this enigmatic species.

Evolutionary history of the odd-nosed monkeys and the phylogenetic position of the newly described Myanmar snub-nosed monkey Rhinopithecus strykeri

Odd-nosed monkeys represent one of the two major groups of Asian colobines. Our knowledge about this primate group is still limited as it is highlighted by the recent discovery of a new species in Northern Myanmar. Although a common origin of the group is now widely accepted, the phylogenetic relationships among its genera and species, and the biogeographic processes leading to their current distribution are largely unknown. To address these issues, we have analyzed complete mitochondrial genomes and 12 nuclear loci, including one X chromosomal, six Y chromosomal and five autosomal loci, from all ten odd-nosed monkey species. The gene tree topologies and divergence age estimates derived from different markers were highly similar, but differed in placing various species or haplogroups within the genera Rhinopithecus and Pygathrix. Based on our data, Rhinopithecus represent the most basal lineage, and Nasalis and Simias form closely related sister taxa, suggesting a Northern origin of odd-nosed monkeys and a later invasion into Indochina and Sundaland. According to our divergence age estimates, the lineages leading to the genera Rhinopithecus, Pygathrix and Nasalis+Simias originated in the late Miocene, while differentiation events within these genera and also the split between Nasalis and Simias occurred in the Pleistocene. Observed gene tree discordances between mitochondrial and nuclear datasets, and paraphylies in the mitochondrial dataset for some species of the genera Rhinopithecus and Pygathrix suggest secondary gene flow after the taxa initially diverged. Most likely such events were triggered by dramatic changes in geology and climate within the region. Overall, our study provides the most comprehensive view on odd-nosed monkey evolution and emphasizes that data from differentially inherited markers are crucial to better understand evolutionary relationships and to trace secondary gene flow.

Evolution of the antiretroviral restriction factor TRIMCyp in Old World primates

The retroviral restriction factor TRIMCyp, which is a fusion protein derived from the TRIM5 gene, blocks replication at a post-entry step. Among Old World primates, TRIMCyp has been found in four species of Asian macaques, but not in African monkeys. To further define the evolutionary origin of Old World TRIMCyp, we examined two species of baboons (genus Papio) and three additional macaque species, including M. sylvanus, which is the only macaque species found outside Asia, and represents the earliest diverging branch of the macaque lineage. None of four P. cynocephalus anubis, one P. hamadryas, and 36 M. sylvanus had either TRIMCyp mRNA or the genetic features required for its expression. M. sylvanus genomic sequences indicated that the lack of TRIMCyp in this species was not due to genetic homogeneity among specimens studied and revealed the existence of four TRIM5α alleles, all distinct from M. mulatta and Papio counterparts. Together with existing data on macaque evolution, our findings indicate that TRIMCyp evolved in the ancestors of Asian macaques approximately 5-6 million years before present (ybp), likely as a result of a retroviral threat. TRIMCyp then became fixed in the M. nemestrina lineage after it diverged from M. nigra, approximately 2 million ybp. The macaque lineage is unique among primates studied so far due to the presence and diversity of both TRIM5 and TRIMCyp restriction factors. Studies of these antiviral proteins may provide valuable information about natural antiviral mechanisms, and give further insight into the factors that shaped the evolution of macaque species.

Fossil cercopithecidae from the Middle Pleistocene Dawaitoli formation, Middle Awash valley, Afar region, Ethiopia

A series of fossil cercopithecoids has been recovered from the Dawaitoli Formation, in the Middle Awash study area, Ethiopia. The Dawaitoli Fm. has been dated to approximately 600 Ka. This series includes several partial crania of Theropithecus oswaldi leakeyi as well as other cranial and postcranial fragments. This material is some of the most complete to date and adds considerably to what is known of this widespread and abundant taxon. There are also two isolated papionin molars here allocated to Papio cf. hamadryas based largely on size grounds and similarity to contemporary material from other sites in the Afar Depression. Cercopithecoids are rare in the Dawaitoli Fm., and among them only large papionins are known. This is unique among known Pleistocene sites in the Afar region, but is most similar to the Daka Member of the Bouri Formation. It is quite different from the other known Middle Pleistocene sites in the Afar: Asbole and the geologically younger Andalee where cercopithecoids are abundant and colobines predominate.

Middle Pleistocene fossil Cercopithecidae from Asbole, Afar Region, Ethiopia

A sample of 117 fossil cercopithecids has been collected from the Middle Pleistocene site of Asbole, Afar Region, Ethiopia. A minimum of five species is present. There are two species of Cercopithecini, here recognized as cf. Chlorocebus aff. aethiops, and cf. Chlorocebus cf. patas. There are also two species of Papionini: Papio hamadryas ssp. indet. and Theropithecus oswaldi leakeyi. Finally, there is a single species of colobine present, Colobus sp. indet. The assemblage is chronologically constrained and is derived from sediments dated to approximately 600 ka. Within this sample Colobus sp. is by far the most common species present, outnumbering the other four species combined. The cercopithecid assemblage is most consistent with a woodland habitat, corroborating an earlier interpretation based on the non-primate fauna. Taxonomic, biogeographic, and evolutionary implications of the assemblage are also discussed.

Morphology of the enamel-dentine junction in sections of anthropoid primate maxillary molars

The shape of the enamel-dentine junction (EDJ) in primate molars is regarded as a potential indicator of phylogenetic relatedness because it may be morphologically more conservative than the outer enamel surface (OES), and it may preserve vestigial features (e.g., cuspules, accessory ridges, and remnants of cingula) that are not manifest at the OES. Qualitative accounts of dentine-horn morphology occasionally appear in character analyses, but little has been done to quantify EDJ shape in a broad taxonomic sample. In this study, we examine homologous planar sections of maxillary molars to investigate whether measurements describing EDJ morphology reliably group extant anthropoid taxa, and we extend this technique to a small sample of fossil catarrhine molars to assess the utility of these measurements in the classification of fossil teeth. Although certain aspects of the EDJ are variable within a taxon, a taxon-specific cross-sectional EDJ configuration predominates. A discriminant function analysis classified extant taxa successfully, suggesting that EDJ shape may a reliable indicator of phyletic affinity. When considered in conjunction with aspects of molar morphology, such as developmental features and enamel thickness, EDJ shape may be a useful tool for the taxonomic assessment of fossil molars.

Genetic relationships of langur species using AFLP markers

Cytogenetic studies of five langur species using conventional banding pattern were investigated. All species studied have an identical number of 44 diploid chromosomes, they are assumed to have common evolutionary relationships. For in depth study, molecular markers were assessed using the Amplified Fragment Length Polymorphism (AFLP) method. With seven successful primer combinations, a total of 1043 scorable bands were generated. The percentage of polymorphic bands for each primer ranged from 48.60 to 94.12%. The resulting bands were used for dendrogram construction. From the dendrogram, the individuals of Trachypithecus species are grouped into two major clusters, T. phayrei is clustered with T. obscurus, while T. cristatus is clustered with T. francoisi. The bootstrap value between two groups is 94%. The other cluster, Presbytis femoralis is separated from the Trachypithecus species with a bootstrap value of 94%. Averages of inter-specific genetic similarity values among all langur species studied are 70.16% (between T. obscurus and P. femoralis) to 88.12% (between T. phayrei and T. obscurus). In summary T. phayrei might be a subspecies of T. obscurus. The development of specific molecular markers of a species is beneficial for genetic differentiation of this group of primates.

Evolutionary and comparative anatomical investigations of the autonomic cardiac nervous system in the African cercopithecidae

The purpose of this study was to clarify the general architecture and morphological variations of the autonomic cardiac nervous system (ACNS) in the African Cercopithecidae (Old World monkeys), and to discuss the evolutionary changes between this system in African/Asian Cercopithecidae and humans. A detailed macroscopic comparative morphological investigation of the ACNS was performed by examining the left and right sides of 11 African cercopithecid specimens, including some previously unreported species (Abyssinian colobus, Angola pied colobus, Savanna monkey, and lesser white-nosed guenon). The common characteristics of the ACNS in the African Cercopithecidae are described in detail. Consequently, homologies of the ACNS between Asian (macaques) and African Cercopithecidae, and differences between the Asian/African Cercopithecidae and humans, were found. In particular, differences in the sympathetic (cardiac) systems of the Cercopithecidae and humans were recognized, despite the similar morphology of the parasympathetic vagal (cardiac) system. These differences include the composition of the cervicothoracic ganglion, the lower positions of the middle cervical and cervicothoracic ganglia, and the narrow range for the origin of the cardiac nerves in the Cercopithecidae, compared with that in humans. In conclusion, these findings are considered with regard to the morphology of the last common ancestors of the Cercopithecidae.

Growth hormone locus expands and diverges after the separation of New and Old World Monkeys

While most mammals including the prosimians have a single copy of the growth hormone (GH) gene, anthropoids possess a cluster of GH-related genes. Throughout the evolution of the main anthropoid groups [New World Monkeys (NWM), Old World Monkeys (OWM), and apes], two features stand out of the GH loci. The first is the appearance of chorionic somatommamotropin hormone (CSH) genes within the OWM lineage and the second is the expansion of the loci intergenic regions in the OWM and apes. In relation with this loci expansion, the NWM possess intergenic regions of homogeneous lengths (3.5 kb). In contrast, heterogeneous lengths (6 and 13 kb) have been reported for species of the OWM. At the present, none of the OWM genomic GH loci organizations have been described. Here, we report the genomic organization of the GH locus in the rhesus monkey, this locus has six GH-related genes separated by five intergenic regions. The 5' end gene (GH-1) encodes for the pituitary GH and is followed by CSH-1, GH-2, CSH-2, CSH-3 and CSH-4 genes. The five intergenic regions have heterogeneous lengths and also present more or less the same Alu distribution as the human GH locus. To analyze the events that contributed to the extension of the intergenic regions of the GH locus and the emergence of the regulatory elements, the five GH locus intergenic regions of the spider monkey (NWM) were sequenced. The results of comparing the loci from both species suggest that the long intergenic regions (13 kb) of the rhesus GH locus share a common ancestor with the 3.5 kb intergenic regions of the spider monkey. However, the observed increased length of the former is due to an insertion (approximately 8.7 kb) at their 3' end. Interestingly in this insert, we discovered a DNA element resembling the enhancer of the CSH genes of the human GH locus. On the other hand, we observed that the short intergenic regions (6 kb) increased by a different recombination event.

Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences

The effective sizes of ancestral populations and species divergence times of six primate species (humans, chimpanzees, gorillas, orangutans, and representatives of Old World monkeys and New World monkeys) are estimated by applying the two-species maximum likelihood (ML) method to intron sequences of 20 different loci. Examination of rate heterogeneity of nucleotide substitutions and intragenic recombination identifies five outrageous loci (ODC1, GHR, HBE, INS, and HBG). The estimated ancestral polymorphism ranges from 0.21 to 0.96% at major divergences in primate evolution. One exceptionally low polymorphism occurs when African and Asian apes diverged. However, taking into consideration the possible short generation times in primate ancestors, it is concluded that the ancestral population size in the primate lineage was no smaller than that of extant humans. Furthermore, under the assumption of 6 million years (myr) divergence between humans and chimpanzees, the divergence time of humans from gorillas, orangutans. Old World monkeys, and New World monkeys is estimated as 7.2, 18, 34, and 65 myr ago, respectively, which are generally older than traditional estimates. Beside the intron sequences, three other data sets of orthologous sequences are used between the human and the chimpanzee comparison. The ML application to these data sets including 58,156 random BAC end sequences (BES) shows that the nucleotide substitution rate is as low as 0.6-0.8 x 10(-9) per site per year and the extent of ancestral polymorphism is 0.33-0.51%. With such a low substitution rate and short generation time, the relatively high extent of polymorphism suggests a fairly large effective population size in the ancestral lineage common to humans and chimpanzees.

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo

What do functionally important DNA sites, those scrutinized and shaped by natural selection, tell us about the place of humans in evolution? Here we compare approximately 90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. On a time scale, the coding DNA divergencies separate the human-chimpanzee clade from the gorilla clade at between 6 and 7 million years ago and place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago. The evolutionary rate of coding DNA in the catarrhine clade (Old World monkey and ape, including human) is much slower than in the lineage to mouse. Among the genes examined, 30 show evidence of positive selection during descent of catarrhines. Nonsynonymous substitutions by themselves, in this subset of positively selected genes, group humans and chimpanzees closest to each other and have chimpanzees diverge about as much from the common human-chimpanzee ancestor as humans do. This functional DNA evidence supports two previously offered taxonomic proposals: family Hominidae should include all extant apes; and genus Homo should include three extant species and two subgenera, Homo (Homo) sapiens (humankind), Homo (Pan) troglodytes (common chimpanzee), and Homo (Pan) paniscus (bonobo chimpanzee).

Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates

Cytochrome c oxidase (COX) is a 13-subunit protein complex that catalyzes the last step in mitochondrial electron transfer in mammals. Of the 10 subunits encoded by nuclear DNA (three are mtDNA products), some are expressed as tissue- and/or development-specific isoforms. For COX subunit VIII, previous work showed that expression of the contractile muscle-specific isoform gene, COX8H, is absent in humans and Old World monkeys, and the other isoform gene, COX8L, is expressed ubiquitously. Here, we show that COX8H is transcribed in most primate clades, but its expression is absent in catarrhines, that is, in Old World monkeys and hominids (apes, including humans), having become a pseudogene in the stem of the catarrhines. The ubiquitously expressed isoform, COX8L, underwent nonsynonymous rate acceleration and elevation in the ratio of nonsynonymous/synonymous changes in the stem of anthropoid primates (New World monkeys and catarrhines), possibly setting the stage for loss of the heart-type (H) isoform. The most rapidly evolving region of VIII-L is one that interacts with COX I, suggesting that the changes are functionally coadaptive. Because accelerated rates of nonsynonymous substitutions in anthropoids such as observed for COX8L are also shown by genes for at least 13 other electron transport chain components, these encoded amino acid replacements may be viewed as part of a series of coadaptive changes that optimized the anthropoid biochemical machinery for aerobic energy metabolism. We argue that these changes were linked to the evolution of an expanded neocortex in anthropoid primates.

Long bone articular and diaphyseal structure in old world monkeys and apes. I: locomotor effects

The relationship between locomotor behavior and long bone structural proportions is examined in 179 individuals and 13 species of hominoids and cercopithecoids. Articular surface areas, estimated from linear caliper measurements, and diaphyseal section moduli (strengths), determined from CT scans, were obtained for the femur, tibia, humerus, radius, and ulna. Both within-bone (articular to shaft) and between-bone (forelimb to hindlimb) proportions were calculated and compared between taxa. It was hypothesized that: 1) species emphasizing slow, cautious movement and/or more varied limb positioning (i.e., greater joint excursion) would exhibit larger articular to cross-sectional shaft proportions, and 2) species with more forelimb suspensory behavior would have relatively stronger/larger forelimbs, while those with more leaping would have relatively stronger/larger hindlimbs. The results of the analysis generally confirm both hypotheses. Several partial exceptions can be explained on the basis of more detailed structural-functional considerations. Associations between locomotion and structural proportions can be demonstrated both across major groupings (hominoids and cercopithecoids) and between relatively closely related taxa, e.g., mountain and lowland gorillas, siamangs and gibbons, and Trachypithecus and other colobines. Furthermore, structure and function do not always covary with taxonomy. For example, compared to cercopithecoids, mountain gorillas have relatively larger joints, like other hominoids, but do not have relatively stronger forelimbs, unlike other hominoids. This is consistent with a locomotor repertoire emphasizing relatively slow movement but with very little forelimb suspension. Proportions of Proconsul nyanzae, Proconsul heseloni, Morotopithecus bishopi, and Theropithecus oswaldi are compared with modern distributions to illustrate the application of the techniques to fossil taxa.

Taxonomic affinities of the Eppelsheim femur

The taxonomic affinities of the Eppelsheim femur, known as Paidopithex, have been unclear for more than a century. Over the years, due to similarities with Pliopithecus, some authors have considered it a large pliopithecid, while others refer to it as Dryopithecus. The issue could not be resolved, because no definitive Dryopithecus femora were available. With the discovery of the Dryopithecus laietanus skeleton from Can Llobateres (CLl 18800), it has become possible to test the attribution of the Eppelsheim femur to Dryopithecus on the basis of direct morphological and metrical comparisons. By means of allometric techniques, we show that the Eppelsheim and D. laietanus femora fit different hindlimb morphologies with regard to relative length and relative head/neck size, with Paidopithex significantly differing from Dryopithecus, but more closely resembling Pliopithecus. Paidopithex also differs from Dryopithecus in other important aspects, such as its lower neck/shaft angle, lack of elevation of the femoral head above the greater trochanter, more posteriorly oriented lesser trochanter, and proximal shaft diameter thicker anteroposteriorly than mediolaterally. In these features, Paidopithex most closely resembles Pliopithecus in spite of differences in body mass (ca. 22 kg vs. ca. 10 kg, respectively). These features suggest that Paidopithex used a primitive locomotor pattern associated with arboreal quadrupedalism, instead of the more derived pattern displayed by Dryopithecus. Currently available evidence confirms that the attribution of Paidopithex to Dryopithecus can be rejected. Paidopithex could be a large and otherwise unknown pliopithecid, but the possibility cannot be ruled out that it represents a third kind of catarrhine.

Paranasal sinus anatomy of Aegyptopithecus: implications for hominoid origins

The East African Early Miocene apes, or proconsulids, have often been considered to be among the earliest members of the Hominoidea, as defined by the divergence of the Cercopithecoidea, but this hypothesis is only weakly supported by available fossil evidence. The ethmofrontal sinus is one of a few morphological features that may link proconsulids with later hominoids. Here we present direct evidence of an ethmofrontal sinus in an early Oligocene stem catarrhine, Aegyptopithecus zeuxis. The presence of this sinus in Aegyptopithecus suggests that its presence in proconsulids is most likely to be a retained primitive condition. The morphological evidence bearing on proconsulids' purported hominoid affinities is further weakened by this conclusion, and alternative phylogenetic possibilities, such as the placement of proconsulids as stem catarrhines are considered more likely.

Egarapithecus narcisoi, a new genus of Pliopithecidae (primates, catarrhini) from the Late Miocene of Spain

Pliopithecid remains from the Spanish locality of Torrent de Febulines (Late Vallesian, MN 10), consisting of right and left mandibular fragments with partial tooth rows and an isolated P(3) probably belonging to the same individual, are described and assigned to Egarapithecus narcisoi gen. et sp. nov. (Pliopithecidae, Crouzeliinae). This is a highly derived species dated at around 9 Ma (Ma = 10(6) years), representing the latest appearance of the family in the European continent. Morphologically it is the most distant member from the inferred primitive pliopithecid morphotype, displaying many autapomorphies that notably accentuate those of the remaining Crouzeliinae. A cladistic analysis based on lower cheek teeth, performed in order to tentatively assess the phylogenetic relationships of Egarapithecus within the Crouzeliinae, indicates that several equally parsimonious cladograms are possible in the light of current evidence. This is due to uncertainties regarding the position of Plesiopliopithecus and Crouzelia (here considered distinct genera), as a result of missing characters and the significant degree of homoplasy apparently involved in crouzeliine dental evolution. Whether Egarapithecus is more closely related to Crouzelia or to Anapithecus (the latter hypothesis tentatively favored here) cannot be definitively resolved with the currently available material and deserves further investigation. It is clear, however, that Egarapithecus is one of the more derived and specialized members of the Pliopithecidae.

A note on a review of the taxonomic status of Phayre's langur (Trachypithecus phayrei) in Tripura, north-east India

Phayre’s langur, Trachypithecus phayrei (= Presbytis phayrei), belongs to the family Colobidae. Its previous synonyms are Presbytis obscurus [1], P. barbei [2] and P. melamerus [3]. After 1847, when Blyth first described this species, subsequent descriptions by many scientists, including Blyth himself [4], led to confusion about the taxonomic status of this langur.Since the last review on the taxonomic status of this species by Agrawal [5], confusion has persisted as it is referred to by different names, for example, Presbytis phayrei, P. barbei and Trachypithecus phayrei.

MHC diversity in Caucasians, investigated using highly heterogeneous noncoding sequence motifs at the DQB1 locus including a retroviral long terminal repeat element, and its comparison to nonhuman primate homologues

Long terminal repeats (LTRs) are common retrovirus-related sequences spread throughout the human genome. We previously reported the human-specific integration of one LTR (DQLTR3) located 15 kb upstream of HLA DQB1. To elucidate the contribution of retroviral sequences to the variability and phylogenetic background of HLA DQB1 we investigated another LTR (DQLTR13), located 1.3 kb upstream of HLA DQB1, in German families, great apes, and Old World monkeys. Within German families, DQLTR13 presence was strongly linked to HLA DQB1*0302, *0303, and *0402 haplotypes. All other haplotypes had a low frequency or were devoid of DQLTR13. Phylogenetic analysis of DQLTR13 and adjacent nucleotide sequences in humans and non-human primates revealed a high degree of similarity and recent origin of HLA DQB1*0302, *0303, and *0402. Nevertheless, two lineages leading to DQB1*0301 and *0302 were generated by an ancient split of a DQB1*0301, *0302 progenitor. A third lineage consisting of DQB1*05/*06-related sequences may have evolved from the DQB1*0302 lineage, and a DQB1*0201-related sequence shared common ancestry with DQB1*0301. Among the human haplotypes, HLA DQB1*0201 and *0301 are linked to two different DQA1 alleles. Based on the small genetic distance of DQLTR13 as well as the adjacent sequences on these haplotypes, we suggest that a recent recombination is responsible for these associations. In the analysis of nonhuman primate species, we detected DQLTR13 in two lowland gorillas, dating the integration at at least 8 million years ago. We therefore conclude that noncoding sequences up to 1.3 kb upstream of DQB1 provide novel insight into the generation of MHC gene diversity.

Molecular phylogeny of Old World monkeys (Cercopithecidae) as inferred from gamma-globin DNA sequences

DNA sequence data of the nuclear-encoded gamma1-gamma2-globin duplication region were used to examine the phylogenetic relationships of 16 cercopithecid (Old World monkey) species representing 12 extant genera. Morphology- and molecular-based hypotheses of Old World monkey branching patterns are generally congruent, except for generic relationships within the subtribe Papionina. The cercopithecids divide into colobines (leaf-eating monkeys) and cercopithecines (cheek-pouched monkeys). The colobines examined by the DNA data divide into an Asian clade (Nasalis, proboscis monkeys; Trachypithecus, langurs) and an African clade (Colobus, colobus monkeys). The cercopithecines divide into tribes Cercopithecini (Erythrocebus, patas monkey; Chlorocebus, green monkeys; Cercopithecus, guenons) and Papionini. Papionins divide into subtribes Macacina (Macaca, macaques) and Papionina (Papio, hamadryas baboons; Mandrillus, drills and mandrills; Theropithecus, gelada baboons; Lophocebus, arboreal mangabeys; Cercocebus, terrestrial mangabeys). In a morphologically based classification, Mandrillus is a subgenus of Papio, whereas Lophocebus is a subgenus of Cercocebus. In contrast, the molecular evidence treats Mandrillus as a subgenus of Cercocebus, and treats both Theropithecus and Lophocebus as subgenera of Papio. Local molecular clock divergence time estimates were used as a yardstick in a "rank equals age" system to propose a reduction in taxonomic rank for most clades within Cercopithecidae.

Taxonomy and phylogenetic relationships of early Miocene catarrhines from Sihong, China

Paleontological investigations at sites in Sihong County, Jiangsu Province, China since 1981 have yielded a sizeable collection of previously undescribed fossil catarrhines from the Xiacaowan Formation. The associated vertebrate fauna indicates a late early Miocene age (correlating with MN 4, late Orleanian of Europe, approximately 17-18 Ma), which establishes the Sihong primates as the earliest known catarrhines from Eurasia. The fossil primates are assigned to two species: Dionysopithecus shuangouensis Li, 1978 and Platodontopithecus jianghuaiensis Gu & Lin, 1983. Although the new material from Sihong consists mainly of isolated teeth, it does provide important new information on the anatomy of Dionysopithecus and Platodontopithecus that helps to clarify their phylogenetic and taxonomic status. Previous studies have suggested that the Sihong catarrhines might be closely related to the proconsulids from the early Miocene of East Africa. However, with more extensive material available for comparison, the Sihong primates can now be shown to share a number of key derived features with pliopithecids. This new evidence helps to resolve a longstanding problem concerning the origins of the Pliopithecidae. It was previously considered that specialized pliopithecids migrated into Europe during MN 5, originating from an unknown antecedent and location in Africa. Recognition that the Sihong primates have affinities with pliopithecids, but are more primitive, suggests that the initial differentiation and diversification of the clade may have taken place in Asia rather than Africa. The earliest Eurasian catarrhines probably migrated into tropical Asia as part of a major faunal interchange with Africa that occurred during MN 3.

Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates

Over the past 60 million years, or so, approximately one million copies of Alu DNA repeats have accumulated in the genome of primates, in what appears to be an ongoing process. We determined the phylogenetic distribution of specific Alu (and other) DNA repeats in the genome of several primates: human, chimpanzee, gorilla, orangutan, baboon, rhesus, and macaque. At the population level studied, the majority of the repeats was found to be fixed in the primate species. Our data suggest that new Alu elements arise in unique, irreversible events, in a mechanism that seems to preclude precise excision and loss. The same insertions did not arise independently in two species. Once inserted and genetically fixed, the DNA elements are retained in all descendant lineages. The irreversible expansion of Alu s introduces a vector of time into the evolutionary process, and provides realistic (rather than statistical) answers to questions on phylogenies. In contrast to point mutations, the present distribution of individual Alu s is congruent with just one phylogeny. We submit that only irreversible and taxonomically relevant events are at the molecular basis of evolution. Most point mutations do not belong to this category.

Theropithecus atlanticus (Thomas, 1884) (Primates: Cercopithecidae) from the late Pliocene of Ahl al Oughlam, Casablanca, Morocco

The site of Ahl al Oughlam near Casablanca, Morocco, dated to ca. 2.5 Ma, has yielded a good sample of Theropithecus atlanticus (Thomas, 1884), a North African late Pliocene species previously known only by its holotype, a lower molar from Algeria. Theropithecus atlanticus, which can now be much better defined, is clearly distinct from other species of the genus, which is thus more diverse than previously thought. The mandible of T. atlanticus has a very characteristic deep and long post-molar sulcus and a deep and well excavated supra-lateral triangular depression of the ramus, with a sharp postero-inferior ridge. The upper and lower canines are rather large but low. The male P3 is very wide, with well developed posterior crests; the P4 is rounded, with a large talonid and weak notches and clefts. Median lingual notches of the lower molars form an acute angle. Although our incomplete knowledge of T. atlanticus precludes a detailed phylogenetic analysis, we suggest that it arose by cladogenesis from the T. darti-T. oswaldi lineage; it is replaced by the latter species in the Pleistocene.

Earliest known Old World monkey skull

Similarities of the skull are commonly used to support hypotheses of ancestor-descendant relationships between fossil and living ape genera, especially between the late Miocene apes Sivapithecus and Dryopithecus from Eurasia and the living orang-utan (Pongo) from Borneo and Sumatra. Yet determining whether craniofacial traits shared by extant and Miocene apes are primitive or derived is severely hampered by the rarity of well-preserved fossil crania, particularly of early members of their closest outgroup, the Old World monkeys (Cercopithecoidea). The discovery of a complete and undistorted skull of Victoriapithecus at middle Miocene deposits from Maboko Island, Kenya, provides evidence of intact cranial-vault and basicranial morphology, brain size and craniofacial hafting for a primate from between 32 and 7 million years ago. Victoriapithecus represents a branch of Old World monkey that is intermediate between extant cercopithecids (Colobinae and Cercopithecinae) and the common ancestor they shared with apes (Hominoidea). The skull preserves traits widely thought to be derived for extant and fossil members of a proposed Sivapithecus/Pongo clade, but which now appear to be primitive features of ancestral Old World higher primates in general.

Phylogenetic relationships among two species of golden monkey and three species of leaf monkey inferred from rDNA variation

Restriction maps of rDNA repeats of five species of Colobinae and three outgroup taxa, Hylobates leucogenys, Macaca mulatta, and Macaca irus, were constructed using 15 restriction endonucleases and cloned 18S and 28S rRNA gene probes. The site variation between Rhinopithecus roxellana and Rhinopithecus bieti is comparable to that between Presbytis françoisi and Preshytis phayrei, implying that R. bieti is a valid species rather than a subspecies of R. roxellana. Phylogenetic analysis on the 47 informative sites supports the case for Rhinopithecus being an independent genus and closely related to Presbytis. Furthermore, branch lengths of the tree seem to support the hypothesis that the leaf monkeys share some ancestral traits as well as some automorphic characters.

Chromosomal painting shows that "marked chromosomes" in lesser apes and Old World monkeys are not homologous and evolved by convergence

Cytogeneticists have long held that the single pair of metacentric, NOR-bearing "marked chromosomes" in lesser apes (Hylobatidae) and Old World monkeys (Cercopithecidae) are homologous. Hylobatids have sometimes been excluded from Hominoidea (great apes and humans) and phylogenetically allied with the lower primates, primarily on the basis of this shared "trait." However, in situ hybridization of human chromosome-specific DNA probes to chromosomes of Hylobates lar, H. syndactylus, H. concolor, Cercopithecus aethiops, Macaca fuscata, Colobus guereza, and Presbytis cristata showed that the so-called "marked chromosomes" in Hylobatidae and Cercopithecidae evolved by convergence. Therefore, "marked chromosomes" cannot be used to exclude gibbons from Hominoidea or to link Hylobatidae with monkeys. Chromosomal painting is a powerful tool to resolve problems of chromosomal homology and helps eliminate phylogenetic errors due to confusing convergence with homology. Chromosomal painting improves the confidence in using cytogenetic data for evolutionary studies, especially in phylogeny and taxonomy.

The phylogenetic relationships and classification of the doucs and snub-nosed langurs of China and Vietnam

The taxonomy of the douc and snub-nosed langurs has changed several times during the 20th century. The controversy over the systematic position of these animals has been due in part to difficulties in studying them: both the doucs and the snub-nosed langurs are rare in the wild and are generally poorly represented in institutional collections. This review is based on a detailed examination of relatively large numbers of specimens of most of the species of langurs concerned. An attempt was made to draw upon as many types of information as were available in order to make an assessment of the phyletic relationships between the langur species under discussion. Toward this end, quantitative and qualitative features of the skeleton, specific features of visceral anatomy and characteristics of the pelage were utilized. The final data matrix comprised 178 characters. The matrix was analyzed using the program Hennig86. The results of the analysis support the following conclusions: (1) that the douc and snub-nosed langurs are generically distinct and should be referred to as species of Pygathrix and Rhinopithecus, respectively; (2) that the Tonkin snub-nosed langur be placed in its own subgenus as Rhinopithecus (Presbytiscus) avunculus and that the Chinese snub-nosed langur thus be placed in the subgenus Rhinopithecus (Rhinopithecus); (3) that four extant species of Rhinopithecus be recognized: R. (Rhinopithecus) roxellana Milne Edwards, 1870; R. (Rhinopithecus) bieti Milne Edwards, 1897; R. (Rhinopithecus) brelichi Thomas, 1903, and R. (Presbytiscus) avunculus Dollman, 1912; (4) that the Chinese snub-nosed langurs fall into northern and southern subgroups divided by the Yangtze river; (5) that R. lantianensis Hu and Qi, 1978, is a valid fossil species, and (6) the precise affinities and taxonomic status of the fossil species R. tingianus Matthew and Granger, 1923, are unclear because the type specimen is a subadult.

Classification and evolution of Asian colobines

In order to study the differentiation of Asian colobines, 14 variables measured on 123 skulls, including Rhinopithecus, Presbytis, Presbytiscus (Rhinopithecus avunculus), Pygathrix and Nasalis were analyzed by one-way, cluster and discriminant function analyses. Information on paleoenvironmental changes in China and southeast Asia since the late Tertiary was used to examine the influences of migratory routes and range of distribution in Asian colobines. A cladogram for 6 genera of Asian colobines was constructed from the results of various analyses. Some new points or revisions were suggested: (1) Following one of two migratory routes, ancient species of Asian colobines perhaps passed through Xizang (Tibet) along the northern bank of the Tethys sea and through the Heng Duan Shan regions of Yunnan into Vietnam. An ancient landmass linking Yunnan and Xizang was already present on the east bank of the Tethys sea. Accordingly, Asian colobines would have two centers of evolutionary origin: Sundaland and the Heng Duan Shan regions of China. (2) Pygathrix shares more cranial features with Presbytiscus than with Rhinopithecus. This differs somewhat from the conclusion reached by Groves. (3) Nasalis (karyotype: 2n = 48) may be the most primitive genus among Asian colobines. Certain features shared with Rhinopithecus, e.g. large body size, terrestrial activity and limb proportions, can be interpreted as symplesiomorphic characters. (4) Rhinopithecus, with respect to craniofacial features, is a special case among Asian colobines. It combines a high degree of evolutionary specialization with retention of some primitive features thought to have been present in the ancestral Asian colobine.

The lacrimal fossa of cercopithecoidea, with special reference to cladistic analysis of Old World monkey relationships

Re-examination of lacrimal fossa patterns in extant cercopithecoids indicates that the last common ancestor of Cercopithecini and Papionini, and hence of Cercopithecinae, probably retained a maxillary contribution to the lacrimal fossa, as did the common ancestor of Colobinae. Consequently, the presence of a maxilla-lacrimal fossa cannot be used to assess the subfamily affinity of Old World monkeys. In addition to being correlated with general facial lengthening, the derived, exclusively lacrimal pattern of Erythrocebus, Mandrillus, Papio, Theropithecus and some (but not all) guenons, macaques and mangabeys may be associated with extreme narrowing of the interorbital septum. Moreover, the derived condition may have evolved in response to independent exploitation of open country habitats as it enhances protection of the lacrimal sac and serves to reduce eye infection in terrestrial species.

A taxonomic revision of the small catarrhine primates from the early Miocene of East Africa

This paper presents a detailed systematic revision of the small catarrhine primates from the early Miocene of East Africa, recovered from sites in Western Kenya and in Uganda dated at between 22 and 17 m.y. Revised diagnoses and amended hypodigms for each of the species are presented. In addition to the currently identified taxa, Limnopithecus legetet Hopwood, 1933, Dendropithecus macinnesi (Le Gros Clark and Leakey, 1950) and Micropithecus clarki Fleagle and Simons, 1978, two further species are recognized. Limnopithecus evansi (MacInnes, 1943) is resurrected as a valid species, based primarily on previously described material from Songhor, and a new genus, Kalepithecus, is described here for the first time, in order to accommodate distinctive material from Songhor and Koru. The distribution of each species in time and space, and the phylogenetic relationships, are discussed in the light of this taxonomic revision.

Taxonomy and phylogeny of black-and-white colobus monkeys. Inferences from an analysis of loud call variation

Field recordings of male loud calls (or roars) from each major form of black-and-white colobus monkey have been analyzed spectrographically, and features of tempo and pitch measured. Considered together with data on cranial dimensions, coat pattern, and geographical distribution, the results of this analysis suggest that there are five species of black-and-white colobus: Colobus angolensis, C. guereza, C. polykomos, C. satanas, and C. vellerosus. C. guereza and C. vellerosus may have differentiated most recently during a major arid event prior to the last Pleistocene glacial maximum; they have an identical low-pitched roar which we consider to be a shared, derived character. The other species, of which C. satanas has the most distinct roar, may belong to older lineages.

Molar size sequence in Old World monkeys

The molar size sequence is examined in a variety of Old World monkeys. The M3 greater than M2 greater than M1 progression is common in the Papionini and Colobinae and rare in the Cercopithecini. The maxillary molars are much more variable in their size relations than the mandibular molars. The findings indicate necessary caution when using the molar size sequence for taxonomic purposes.

Karyotypic fission theory and the evolution of old world monkeys and apes

The karyotypes of living catarrhines are correlated with the current concepts of their fossil record and systematic classification. A phylogeny, beginning at the base of the Oligocene, for those animals and their chromosome numbers is presented. Todd's (1970) theory of karyotypic fissioning is applied to this case - three fissioning events are hypothesized. A late Eocene event (the primary catarrhine fissioning) is hypothesized to underlie the diversification of the infraorder Catarrhini into its extant families, the second fissioning underlies the radiation of the pongidae/Hominidae in the Miocene and the third accounts for the high chromosome numbers (54 - 72) and the Neogene(Miocene-Pliocene-Pleistocene) radiation of members of the genus Cercopithecus. Published catarrhine chromosome data, including that for "marked" chromosomes (those with a large achromatic region that is the site for ribosomal RNA genes) are tabulated and analysed. The ancestral X chromosome is always retained in the unfissioned metacentric state. The Pongidae/Hominidae have 15 pairs of mediocentric chromosomes that survived the second fissioning whereas the other chromosomes (besides the X) are thought to be fission-derived acrocentrics. Both the detailed karyology and the trend from low to high numbers is best interpreted to support Todd's concept of adaptive radiations correlated with karyotypic fissioning in ancestral populations.