Juan Carlos Morales

Asian Primate Classification

In the foreseeable future there is little likelihood of achieving consensus on the number of Asian primate genera and species, and their subspecific composition. There is a more realistic hope of reaching agreement on the number of recognizable subspecies. The latter objective is more urgent because in order to reliably assess generic and specific numbers, it is essential that effective conservation measures are implemented for as many subspecies as possible. This cannot be comprehensively accomplished until their validity is assessed and they are satisfactorily established and defined. The Asian primate classification that we present is the outcome of electronic communication among the co-authors after a workshop, which was especially convened to attempt to determine the number of recognizable primate subspecies and to identify potentially recognizable subspecies. The generic and specific arrangement is a compromise that does not necessarily reflect the individual views of the co-authors: 183 subspecies in 77 species in 16 genera. The 31 subspecies allotted a low credibility rating are almost balanced by the 22 scientifically unnamed populations that may warrant subspecific status.

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.

A new west African chimpanzee subspecies

We have sequenced a portion of the mitochondrial DNA control region from the hairs of Nigerian chimpanzees living on both sides of the Niger River, which is proposed as a biogeographic boundary. Our data suggest that a previously unrecognized type of chimpanzee may be present in Nigeria and adjacent parts of Cameroon, and that the zoogeographic barriers separating chimpanzees are different from those previously proposed.

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.

The mitochondrial and nuclear genetic structure of Myotis capaccinii (Chiroptera: Vespertilionidae) in the Eurasian transition, and its taxonomic implications

Allopatric isolation in glacial refugia has caused differentiation and speciation in many taxa globally. In this study, we investigated the nuclear and mitochondrial genetic differentiation of the long fingered bat, Myotis capaccinii during the ice ages in south‐eastern Europe and Anatolia. The mitochondrial DNA (mtDNA) analyses indicated a suture zone similar to those recorded in other animal species, including bats, suggesting the association of more than one refugium with the region. Contrary to most of the other species where a suture zone was seen in Anatolia, for M. capaccinii the geographical location of the genetic break was in south‐eastern Europe. This mitochondrial differentiation was not reflected in the nuclear microsatellites, however, suggesting that the lack of contact during the ice ages did not result in reproductive isolation. Hence taxonomically, the two mitochondrial clades cannot be treated as separate species.

Phylogeography of the Greater Horseshoe Bat, Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae), in Southeastern Europe and Anatolia, with a Specific Focus on Whether the Sea of Marmara is a Barrier to Gene Flow

Population differentiation during the ice ages, followed by range expansions has significantly contributed to the geographic distribution patterns of the genetic diversity in Europe. In this regard, the Iberian, Italian, Balkan peninsulas and Anatolia comprise important glacial refugia. In different parts of Anatolia, suture zones, where lineages that diverged in the different glacial refugia met again, were observed for several species. In this study, we investigated the mitochondrial genetic differentiation of the greater horseshoe bat, Rhinolophus ferrumequinum in southeastern Europe and Anatolia. The mitochondrial DNA analyses indicated a suture zone in central Anatolia, similar to those recorded in other animal species, showing the presence of more than one refugium within the region. The time of the split of these lineages that diverged in allopatry was dated to the Pleistocene. However, the location of this suture zone did not coincide with the Sea of Marmara, not supporting a recent hypothesis, based on microsatellite data, which states that this water body might be an impediment to post glacial gene flow in this species.

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia

BackgroundPopulation-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date.MethodsWe collected a total of 125 bat flies from three Pteropus species (Pteropus vampyrus, P. hypomelanus, and P. lylei) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (FST), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities.ResultsAll flies were identified as Cyclopodia horsfieldi with the exception of two individuals of Eucampsipoda sundaica. Low levels of population genetic structure were detected between populations of Cyclopodia horsfieldi from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise FST values from flies collected from island populations of Pteropus hypomelanus in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure.ConclusionsThe lack of population genetic structure and morphological variation observed in Cyclopodia horsfieldi is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that Pteropus vampyrus may facilitate movement of bat flies between the three Pteropus species in the region. We demonstrate the utility of parasite genetics as an additional layer of information to measure host movement and interspecific host contact. These approaches may have wide implications for understanding zoonotic, epizootic, and enzootic disease dynamics. Bat flies may play a role as vectors of disease in bats, and their competence as vectors of bacterial and/or viral pathogens is in need of further investigation.

EVOLUTIONARY RELATIONSHIPS AMONG GENERA OF PHALANGERIDAE (METATHERIA: DIPROTODONTIA) INFERRED FROM MITOCHONDRIAL DNA

Abstract We sequenced the 12S rRNA gene of 2 elusive and morphologically plesiomorphic species of phalanger: the small Sulawesi cuscus (Strigocuscus celebensis—Gray, 1858) and the Sulawesi bear cuscus (Ailurops ursinus—Temminck, 1824). The sequences were integrated with previously existing data on the same gene in other species of phalangerids, as well as newly derived data from Wyulda Alexander, 1918. In contrast to current wisdom, we resolve S. celebensis not as a member of the tribe Trichosurini, but rather as a taxon sister to Ailurops in a reconstituted Ailuropinae in turn successively sister to Phalangerinae. Examination of our data supports an evolutionary origin for the family approximately 34 million years ago (mya), in the northwestern region of the Sahul Shelf, the continental mass underlying Australia and New Guinea. The radiation of the most plesiomorphic genera in the family, Trichosurus and Wyulda, is restricted to that region. S. celebensis, resolved as sister to A. ursinus in a clade ingroup to trichosurines, diverged from remaining ingroup lineages between 21.1 and 23.3 mya, a time when Sulawesi was available for colonization and sea currents would have enhanced the colonization potential from the east of Sulawesi and neighboring islands. We recommend Trichosurinae as a subfamilial level entity on par with Ailuropinae and Phalangerinae, circumscription of Trichosurinae to Trichosurus and Wyulda, and removal of Strigocuscus into Ailuropinae, leaving only Phalanger and Spilocuscus in Phalangerinae.

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.