Anthony J. Tosi

PATERNAL, MATERNAL, AND BIPARENTAL MOLECULAR MARKERS PROVIDE UNIQUE WINDOWS ONTO THE EVOLUTIONARY HISTORY OF MACAQUE MONKEYS

Abstract.— We report the results of one of the first intrageneric analyses to simultaneously survey mitochondrial, Y‐chromosomal, and autosomal loci from the same individuals representing the same taxa. Phylogenetic trees were constructed for each of these genetic systems from a pool of 63 macaques, representing all 19 recognized species in this genus, and eight outgroup taxa. The mitochondrial locus analyzed here (1.5 Kb) spans the 3′ end of 12S rDNA, tRNA‐VAL, and the 5′ end of 16S rDNA; the Y chromosome dataset (3.1 Kb) consists of the genes SRY and TSPY; the two autosomal datasets include IRBP intron 3 (1.6 Kb) and the 5′ half of C4 “long” intron 9 (3.3 Kb). A total of 1.35 million bases were read, revealing 682 variable sites within the genus Macaca. With regard to earlier unresolved issues of macaque evolution, a comparison of topologies reconstructed from each of the three genetic systems suggests: (1) four monophyletic species groups; (2) an initial bifurcation among Asian macaques between the silenus group progenitor and a M. fascicularis‐like taxon, with the latter representing the probable common ancestor to all non‐silenus group Asian macaques; (3) a possible hybrid origin of M. arctoides from proto‐M. assamensis/thibetana and proto‐ M. fascicularis; and (4) contemporary introgression between M. mulatta and M. fascicularis in Indochina. Inferences 3 and 4 are of particular interest, because episodes of reticulate evolution often go undetected in analyses employing a single genetic system. Finally, divergence calculations suggest that, in female‐philopatric taxa, mitochondrial bifurcations may typically predate Y‐chromosomal divergences at the same node.

Y-Chromosome and mitochondrial markers in Macaca fascicularis indicate introgression with Indochinese M. mulatta and a biogeographic barrier in the isthmus of Kra

This is the first report of Y-chromosome introgression between primate species. We sequenced 3.1 Kb of Y-chromosome DNA and 1.5 Kb of mtDNA for 27 macaques of Foodens (Folia Primatol. [1976] 25: 225–236) fascicularis species group and 5 outgroup taxa (Macaca sylvanus, Papio hamadryas, Theropithecus gelada, Allenopithecus nigroviridis, and Cercopithecus mona). Phylogenies constructed separately for the paternal and maternal data sets show a Y-chromosome paraphyly among lineages of Macacafascicularis, but a mitochondrial monophyly for the same individuals. The Y-chromosome topology depicts Indochinese Macaca fascicularis haplotypes joining with those of M. mulatta, followed by M. cyclopis and M. fuscata, before clustering with a clade of lineages of M. fascicularis from peninsular Malaysia, Indonesia, and the Philippines. These contrasting patterns of mitochondrial and Y-chromosome DNA, evaluated in the context of the evolutionary consequences of macaque sex-biased dispersal, present strong evidence for contemporary hybridization between Macaca fascicularis and M. mulatta in Indochina and a biogeographic barrier in the Isthmus of Kra.

Mitochondrial evidence for the hybrid origin of the kipunji, Rungwecebus kipunji (Primates: Papionini)

Common baboons (Papio), gelada baboons (Theropithecus) and baboon-mangabeys (Lophocebus) are closely related African papionin monkeys. In 2005, the species Lophocebus kipunji was described from relict montane and submontane forests in Tanzania, based upon a single specimen and observations of living animals. Its initial assignment to Lophocebus was based on its overall morphology, but subsequent genetic studies suggesting that it was sister taxon to common baboons (Papio) led to its generic separation, as Rungwecebus. As a mangabey-like sister-taxon to Papio, Rungwecebus could be interpreted either as an arboreal derivative from a more terrestrial, baboon-like ancestor, or as a survivor of a mangabey-like common ancestor of the Lophocebus-Papio-Theropithecus clade. Here, we present a new, strongly-supported, mitochondrial DNA (mtDNA) phylogeny that includes Papio baboons from populations geographically close to the kipunji. Rather than supporting sister-taxon status, the new phylogeny not only situates the kipunjis mtDNA among Papio haplotypes, it clearly assigns it to a mitochondrial clade including geographically adjacent yellow baboons (Papio cynocephalus). This relationship suggests either that the kipunji is descended from a yellow baboon, and has converged on a mangabey-like morphology, or, much more likely, that it originated by hybridization between Papio cf.cynocephalus females and Lophocebus sp. males, about 0.65 Ma. We believe this to be the first case among mammals in which a natural occurrence of inter-generic hybridization can be shown to have resulted in a new, distinct, long-surviving taxon. More such cases can be anticipated as molecular evidence accumulates.

Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys

Evidence of incongruence between mitochondrial and nuclear gene trees is now becoming documented with increasing frequency. Among the Old World monkeys, this discordance has been well demonstrated in the Cercopithecinae, but has not yet been investigated in the Colobinae. The mitochondrial relationships between the colobine genera have recently been clarified and cluster Presbytis and Trachypithecus as sister taxa to the exclusion of Semnopithecus. This is incongruent with previous morphological hypotheses that suggest the latter two are sister taxa, and perhaps even congeneric. In addition to analyzing a previously published 10,896 bp mitochondrial dataset, we sequenced and analyzed a 4297 bp fragment of the X-chromosome in order to test the competing mitochondrial and morphological phylogenetic hypotheses. The results from the mitochondrial dataset again support a Presbytis+Trachypithecus group while the X-chromosomal dataset supported a Semnopithecus+Trachypithecus group. A Shimodaira-Hasegawa test performed on both datasets indicates that the mitochondrial and X-chromosomal trees are significantly better at explaining their respective datasets than alternative topologies (p<0.05). We suggest that differential lineage sorting or ancient hybridization may be the cause of this strong discordance between the mitochondrial and X-chromosomal markers in these taxa.

Lesula: A New Species of Cercopithecus Monkey Endemic to the Democratic Republic of Congo and Implications for Conservation of Congo’s Central Basin

In June 2007, a previously undescribed monkey known locally as “lesula” was found in the forests of the middle Lomami Basin in central Democratic Republic of Congo (DRC). We describe this new species as Cercopithecus lomamiensis sp. nov., and provide data on its distribution, morphology, genetics, ecology and behavior. C. lomamiensis is restricted to the lowland rain forests of central DRC between the middle Lomami and the upper Tshuapa Rivers. Morphological and molecular data confirm that C. lomamiensis is distinct from its nearest congener, C. hamlyni, from which it is separated geographically by both the Congo (Lualaba) and the Lomami Rivers. C. lomamiensis, like C. hamlyni, is semi-terrestrial with a diet containing terrestrial herbaceous vegetation. The discovery of C. lomamiensis highlights the biogeographic significance and importance for conservation of central Congo’s interfluvial TL2 region, defined from the upper Tshuapa River through the Lomami Basin to the Congo (Lualaba) River. The TL2 region has been found to contain a high diversity of anthropoid primates including three forms, in addition to C. lomamiensis, that are endemic to the area. We recommend the common name, lesula, for this new species, as it is the vernacular name used over most of its known range.

The monkey's perspective

The sequencing of the genome of a female rhesus macaque (Macaca mulatta) of Indian origin will provide us with biomedical and evolutionary insights into both humans and Old World monkeys.

Y-chromosomal Window onto the History of Terrestrial Adaptation in the Cercopithecini

Y-chromosomal patterns agree with earlier karyotypic studies in depicting a close relationship among patas, vervets, and l’Hoest’s monkeys distinct from other members of the Cercopithecini. This relationship is suggested to be one of shared ancestry, rather than one due to past hybridization. Thus, on the working assumption that the earliest guenons were arboreal, terrestriality appears to have originated only once among the extant cercopithecins. Consequently, taxonomic revision is necessary as relates to the three terrestrial taxa: Erythrocebus patas, Cercopithecus aethiops, and C. lhoesti.

Y-chromosome Data and Tribal Affiliations of Allenopithecus and Miopithecus

The phylogeny of Old World monkeys has remained unresolved in part because of a lack of resolution in the Cercopithecinae. Competing morphological hypotheses have had Allens swamp monkey (Allenopithecus nigroviridis) and the talapoins (Miopithecus spp.) as basal branches of either the tribe Cercopithecini or the tribe Papionini. Previous molecular analyses have not adequately addressed the issue. To better understand the evolutionary history of these primates, we sequenced and subjected to phylogenetic analysis ∼3.1 kb of 2 loci (TSPY and SRY) from the non-recombining portion of the Y-chromosome. Individuals from the genera Allenopithecus, Miopithecus, Erythrocebus, Chlorocebus, and Cercopithecus were surveyed and their sequences compared with those previously published for the Papionini and Colobinae. The results suggest Allenopithecus and Miopithecus are more closely related to the Cercopithecini than Papionini. Our data also support the hypothesis that within the Cercopithecini, Erythrocebus and Chlorocebus share a close evolutionary relationship, distinct from the other members of the tribe.

Y-chromosomal Markers Suitable for Noninvasive Studies of Guenon Hybridization

We examine previously-published TSPY sequence data to identify synapomorphies useful for tracking Y-chromosomal gene flow between hybridizing guenon species. We then describe a set of PCR primers and protocols that amplify many of these variable sites from feces. Such Y-chromosomal markers are potentially very useful to conservation studies because they may offer an early sign of introgression as a threat to the genetic integrity of a rare species. Moreover, the ability to survey these markers from feces greatly expands the utility of noninvasive studies.

Evolution of Acidic Mammalian Chitinase Genes (CHIA) Is Related to Body Mass and Insectivory in Primates

&NA; Insects are an important food resource for many primates, but the chitinous exoskeletons of arthropods have long been considered to be indigestible by the digestive enzymes of most mammals. However, recently mice and insectivorous bats were found to produce the enzyme acidic mammalian chitinase (AMCase) to digest insect exoskeletons. Here, we report on the gene CHIA and its paralogs, which encode AMCase, in a comparative sample of nonhuman primates. Our results show that early primates likely had three CHIA genes, suggesting that insects were an important component of the ancestral primate diet. With some exceptions, most extant primate species retain only one functional CHIA paralog. The exceptions include two colobine species, in which all CHIA genes have premature stop codons, and several New World monkey species that retain two functional genes. The most insectivorous species in our sample also have the largest number of functional CHIA genes. Tupaia chinensis and Otolemur garnettii retain three functional CHIA paralogs, whereas Tarsius syrichta has a total of five, two of which may be duplications specific to the tarsier lineage. Selection analyses indicate that CHIA genes are under more intense selection in species with higher insect consumption, as well as in smaller‐bodied species (<500 g), providing molecular support for Kays Threshold, a well‐established component of primatological theory which proposes that only small primates can be primarily insectivorous. These findings suggest that primates, like mice and insectivorous bats, may use the enzyme AMCase to digest the chitin in insect exoskeletons, providing potentially significant nutritional benefits.