Don J Melnick

Publications of Don J Melnick

• Sex-linked inheritance in macaque monkeys: implications for effective population size and dispersal to Sulawesi.

  Authors: Ben J Evans, Laura Pin, Don J Melnick, Stephen I Wright

  Genetics. 07/2010; 185(3):923-37.

  Sex-specific differences in dispersal, survival, reproductive success, and natural selection differentially affect the effective population size (N(e)) of genomic regions with different modes ofSex-specific differences in dispersal, survival, reproductive success, and natural selection differentially affect the effective population size (N(e)) of genomic regions with different modes of inheritance such as sex chromosomes and mitochondrial DNA. In papionin monkeys (macaques, baboons, geladas, mandrills, drills, and mangabeys), for example, these factors are expected to reduce N(e) of paternally inherited portions of the genome compared to maternally inherited portions. To explore this further, we quantified relative N(e) of autosomal DNA, X and Y chromosomes, and mitochondrial DNA using molecular polymorphism and divergence information from pigtail macaque monkeys (Macaca nemestrina). Consistent with demographic expectations, we found that N(e) of the Y is lower than expected from a Wright-Fisher idealized population with an equal proportion of males and females, whereas N(e) of mitochondrial DNA is higher. However, N(e) of 11 loci on the X chromosome was lower than expected, a finding that could be explained by pervasive hitchhiking effects on this chromosome. We evaluated the fit of these data to various models involving natural selection or sex-biased demography. Significant support was recovered for natural selection acting on the Y chromosome. A demographic model with a skewed sex ratio was more likely than one with sex-biased migration and explained the data about as well as an ideal model without sex-biased demography. We then incorporated these results into an evaluation of macaque divergence and migration on Borneo and Sulawesi islands. One X-linked locus was not monophyletic on Sulawesi, but multilocus data analyzed in a coalescent framework failed to reject a model without migration between these islands after both were colonized.

• Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants.

  Authors: T N C Vidya, Raman Sukumar, Don J Melnick

  Proceedings. Biological sciences / The Royal Society. 12/2008;

  Recent phylogeographic studies of the endangered Asian elephant (Elephas maximus) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understandingRecent phylogeographic studies of the endangered Asian elephant (Elephas maximus) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understanding the species's evolution. Previous explanations for the divergent clades include introgression of mtDNA haplotypes between ancestral species, allopatric divergence of the clades between Sri Lanka or the Sunda region and the mainland, historical trade of elephants, and retention of divergent lineages due to large population sizes. However, these studies lacked data from India and Myanmar, which host approximately 70 per cent of all extant Asian elephants. In this paper, we analyse mtDNA sequence data from 534 Asian elephants across the species's range to explain the current distribution of the two divergent clades. Based on phylogenetic reconstructions, estimates of times of origin of clades, probable ancestral areas of origin inferred from dispersal-vicariance analyses and the available fossil record, we believe both clades originated from Elephas hysudricus. This probably occurred allopatrically in different glacial refugia, the alpha clade in the Myanmar region and the beta clade possibly in southern India-Sri Lanka, 1.6-2.1Myr ago. Results from nested clade and dispersal-vicariance analyses indicate a subsequent isolation and independent diversification of the beta clade in both Sri Lanka and the Sunda region, followed by northward expansion of the clade. We also find more recent population expansions in both clades based on mismatch distributions. We therefore suggest a contraction-expansion scenario during severe climatic oscillations of the Quaternary, with range expansions from different refugia during warmer interglacials leading to the varying geographical overlaps of the two mtDNA clades. We also demonstrate that trade in Asian elephants has not substantially altered the species's mtDNA population genetic structure.

• Resolution of the Hylobates phylogeny: congruence of mitochondrial D-loop sequences with molecular, behavioral, and morphological data sets.

  Authors: Danielle J Whittaker, Juan Carlos Morales, Don J Melnick

  Molecular phylogenetics and evolution. 12/2007; 45(2):620-8.

  Gibbons of the genus Hylobates likely speciated very rapidly following isolation by rising sea levels during the Pleistocene. We sequenced the hypervariable region I (HV-I) of the mitochondrialGibbons of the genus Hylobates likely speciated very rapidly following isolation by rising sea levels during the Pleistocene. We sequenced the hypervariable region I (HV-I) of the mitochondrial D-loop to reconstruct the phylogeny of this group. Although the results clearly supported monophyly of each of the six species, the relationships among them were not clearly resolved by these data alone. A homogeneity test against published data sets of a coding mitochondrial locus (ND3-ND4 region), behavioral characters (vocalizations), and morphological traits (including skeletal and soft tissue anatomy) revealed no significant incongruence, and combining them resulted in a phylogenetic tree with much stronger support. The Kloss's gibbon (H. klossii), long considered a primitive taxon based on morphology, shares many molecular and vocal characteristics with the Javan gibbon (H. moloch), and appear as the most recently derived species. The northernmost species (H. lar and H. pileatus) are the most basal taxa. These data suggest that ancestral gibbons radiated from north to south. Unlike other markers, the HV-I region can accurately identify members of different gibbon species much like a DNA barcode, with potential applications to conservation.

• Molecular phylogenetic affinities of the simakobu monkey (Simias concolor).

  Authors: Danielle J Whittaker, Nelson Ting, Don J Melnick

  Molecular phylogenetics and evolution. 07/2006; 39(3):887-92.

• A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-ND4 gene sequences.

  Authors: Zoltan Takacs, Juan Carlos Morales, Thomas Geissmann, Don J Melnick

  Molecular phylogenetics and evolution. 10/2005; 36(3):456-67.

  The Hylobatidae (gibbons) are among the most endangered primates and their evolutionary history and systematics remain largely unresolved. We have investigated the species-level phylogeneticThe Hylobatidae (gibbons) are among the most endangered primates and their evolutionary history and systematics remain largely unresolved. We have investigated the species-level phylogenetic relationships among hylobatids using 1257 bases representing all species and an expanded data set of up to 2243 bases for select species from the mitochondrial ND3-ND4 region. Sequences were obtained from 34 individuals originating from all 12 recognized extant gibbon species. These data strongly support each of the four previously recognized clades or genera of gibbons, Nomascus, Bunopithecus, Symphalangus, and Hylobates, as monophyletic groups. Among these clades, there is some support for either Bunopithecus or Nomascus as the most basal, while in all analyses Hylobates appears to be the most recently derived. Within Nomascus, Nomascus sp. cf. nasutus is the most basal, followed by N. concolor, and then a clade of N. leucogenys and N. gabriellae. Within Hylobates, H. pileatus is the most basal, while H. moloch and H. klossii clearly, and H. agilis and H. muelleri likely form two more derived monophyletic clades. The segregation of H. klossii from other Hylobates species is not supported by this study. The present data are (1) consistent with the division of Hylobatidae into four distinct clades, (2) provide the first genetic evidence for all the species relationships within Nomascus, and (3) call for a revision of the current relationships among the species within Hylobates. We propose a phylogenetic tree as a working hypothesis against which intergeneric and interspecific relationships can be tested with additional genetic, morphological, and behavioral data.

• Evolution of RAG-1 in polyploid clawed frogs.

  Authors: Ben J Evans, Darcy B Kelley, Don J Melnick, David C Cannatella

  Molecular biology and evolution. 06/2005; 22(5):1193-207.

  Possible genetic fates of a gene duplicate are silencing, redundancy, subfunctionalization, or novel function. These different fates can be realized at the DNA, RNA, or protein level, and theirPossible genetic fates of a gene duplicate are silencing, redundancy, subfunctionalization, or novel function. These different fates can be realized at the DNA, RNA, or protein level, and their genetic determinants are poorly understood. We explored molecular evolution of duplicated RAG-1 genes in African clawed frogs (Xenopus and Silurana) (1) to examine the fate of paralogs of this gene at the DNA level in terms of recombination, positive selection, and gene degeneration and in the absence of extensive recombination among alleles at different paralogs, (2) to test phylogenetic hypotheses about the origins of polyploid species. We found that recombination between different RAG-1 paralogs is infrequent, that degeneration of some paralogs has occurred via stop codons and frameshift mutations, and that this degeneration occurred in paralogs inherited from only one diploid progenitor species. Simulations and phylogenetic analyses of RAG-1 and mitochondrial DNA support one origin of extant tetraploids in Xenopus and at least one origin in Silurana, five allopolyploid origins of extant octoploids, and two allopolyploid origins of extant dodecaploids. In allopolyploid species, which inherit a complete genome from two different ancestors, genes inherited from the same ancestor have a longer period of coevolution than genes inherited from different ancestors. Because of this, gene ancestry could potentially influence gene fate: interacting paralogs derived from the same lower ploidy ancestor might have similar genetic destinies.

• A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution.

  Authors: Ben J Evans, Darcy B Kelley, Richard C Tinsley, Don J Melnick, David C Cannatella

  Molecular phylogenetics and evolution. 11/2004; 33(1):197-213.

  The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid,The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent rainforest refugia probably acted as "lifeboats" that preserved existing species, rather than "species pumps" where many new successful lineages originated. We estimate that polyploidization occurred at least six times in clawed frogs.

• Sex chromosome phylogenetics indicate a single transition to terrestriality in the guenons (tribe Cercopithecini).

  Authors: Anthony J Tosi, Don J Melnick, Todd R Disotell

  Journal of human evolution. 03/2004; 46(2):223-37.

  This is the first molecular study to trace the evolutionary transition in substrate preference across a primate radiation. We surveyed 20 guenons (tribe Cercopithecini) and 4 outgroup taxa for twoThis is the first molecular study to trace the evolutionary transition in substrate preference across a primate radiation. We surveyed 20 guenons (tribe Cercopithecini) and 4 outgroup taxa for two Y-chromosomal genes, TSPY ( approximately 2240 bp) and SRY ( approximately 780 bp), and one X-chromosomal intergenic region ( approximately 1600 bp) homologous to a fragment of human Xq13.3. Parsimony and maximum likelihood analyses of the sex chromosomal datasets consistently cluster the three terrestrial taxa, Cercopithecus aethiops, Cercopithecus lhoesti, and Erythrocebus patas, into a group that is reciprocally monophyletic with a clade of arboreal Cercopithecus spp. Given that the common ancestor of the two clades was most likely an arboreal taxon, this phylogenetic pattern suggests the transition to terrestriality occurred only once among the extant guenons. This pattern also indicates that the genus Cercopithecus is paraphyletic, as presently defined, and calls for taxonomic revision so that the nomen describes a strictly monophyletic group. We outline four acceptable taxonomic schemes and suggest that the most appropriate is to reassign C. aethiops, C. lhoesti, and E. patas to the resurrected genus Chlorocebus. Finally, while the phylogeny and taxonomy of terrestrial guenons were the focus of this study, the X-chromosome sequences presented here represent the first molecular evidence to unambiguously place Allenopithecus nigroviridis as the basal lineage of the tribe Cercopithecini.

• Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the asian and Australian faunal zones.

  Authors: Ben J Evans, Rafe M Brown, Jimmy A McGuire, Jatna Supriatna, Noviar Andayani, Arvin Diesmos, Djoko Iskandar, Don J Melnick, David C Cannatella

  Systematic biology. 01/2004; 52(6):794-819.

  The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas,The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas, and the Moluccas). Studies of this region by Wallace marked the genesis of the field of biogeography, yet few workers have used molecular methods to investigate the biogeography of taxa whose distribution spans this interface. Some taxa, such as the fanged frogs of the ranid genus Limnonectes, have distributions on either side of the zoogeographical lines of Wallace and Huxley, offering an opportunity to ask how frequently these purported barriers were crossed and by what paths. To examine diversification of Limnonectes in Southeast Asia, the Philippines, and Wallacea, we estimated a phylogeny from mitochondrial DNA sequences obtained from a robust geographic sample. Our analyses suggest that these frogs dispersed from Borneo to the Philippines at least twice, from Borneo to Sulawesi once or twice, from Sulawesi to the Philippines once, and from the Philippines to Sulawesi once. Dispersal to the Moluccas occurred from Sulawesi and to the Lesser Sundas from Java/Bali. Species distributions are generally concordant with Pleistocene aggregate island complexes of the Philippines and with areas of endemism on Sulawesi. We conclude that the recognition of zoogeographic lines, though insightful, may oversimplify the biogeography of widespread taxa in this region.

• DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation.

  Authors: Prithiviraj Fernando, T N C Vidya, John Payne, Michael Stuewe, Geoffrey Davison, Raymond J Alfred, P Andau, Edwin Bosi, Annelisa Kilbourn, Don J Melnick

  PLoS biology. 11/2003; 1(1):E6.

  The origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephantsThe origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephants imported in the 16th-18th centuries. Taxonomically, they have either been classified as a unique subspecies or placed under the Indian or Sumatran subspecies. If shown to be a unique indigenous population, this would extend the natural species range of the Asian elephant by 1300 km, and therefore Borneo elephants would have much greater conservation importance than if they were a feral population. We compared DNA of Borneo elephants to that of elephants from across the range of the Asian elephant, using a fragment of mitochondrial DNA, including part of the hypervariable d-loop, and five autosomal microsatellite loci. We find that Borneo's elephants are genetically distinct, with molecular divergence indicative of a Pleistocene colonisation of Borneo and subsequent isolation. We reject the hypothesis that Borneo's elephants were introduced. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionary significant unit. Thus, interbreeding Borneo elephants with those from other populations would be contraindicated in ex situ conservation, and their genetic distinctiveness makes them one of the highest priority populations for Asian elephant conservation.

• Diversification of Sulawesi macaque monkeys: decoupled evolution of mitochondrial and autosomal DNA.

  Authors: Ben J Evans, Jatna Supriatna, Noviar Andayani, Don J Melnick

  Evolution; international journal of organic evolution. 09/2003; 57(8):1931-46.

  In macaque monkeys, females are philopatric and males are obligate dispersers. This social system is expected to differently affect evolution of genetic elements depending on their mode ofIn macaque monkeys, females are philopatric and males are obligate dispersers. This social system is expected to differently affect evolution of genetic elements depending on their mode of inheritance. Because of this, the geographic structure of molecular variation may differ considerably in mitochondrial DNA (mtDNA) and in autosomal DNA (aDNA) in the same individuals, even though these genomes are partially co-inherited. On the Indonesian island of Sulawesi, macaque monkeys underwent an explosive diversification as a result of range fragmentation. Today, barriers to dispersal have receded and fertile hybrid individuals can be found at contact zones between parapatric species. In this study, we examine the impact of range fragmentation on Sulawesi macaque mtDNA and aDNA by comparing evolution, phylogeography, and population subdivision of each genome. Our results suggest that mtDNA is paraphyletic in some species, and that mtDNA phylogeography is largely consistent with a pattern of isolation by distance. Autosomal DNA, however, is suggestive of fragmentation, in that interspecific differentiation across most contact zones is significant but intraspecific differentiation between contact zones is not. Furthermore, in mtDNA, most molecular variation is partitioned between populations within species but in aDNA most variation is partitioned within populations. That mtDNA has a different geographic structure than aDNA (and morphology) in these primates is a probable consequence of (1) a high level of ancestral polymorphism in mtDNA, (2) differences between patterns of ancestral dispersal of matrilines and contemporary dispersal of males, and (3) the fact that female philopatry impedes gene flow of macaque mtDNA.

• Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys.

  Authors: Anthony J Tosi, Juan Carlos Morales, Don J Melnick

  Evolution; international journal of organic evolution. 07/2003; 57(6):1419-35.

  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.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.

• Monkeys and toads define areas of endemism on Sulawesi.

  Authors: Ben J Evans, Jatna Supriatna, Noviar Andayani, Mohammed Iqbal Setiadi, David C Cannatella, Don J Melnick

  Evolution; international journal of organic evolution. 07/2003; 57(6):1436-43.

  Ecological or geological phenomena can impose limits on geographic diversification that cause biogeographical patterns of distantly related but sympatrically occurring taxa to be similar. ConcordantEcological or geological phenomena can impose limits on geographic diversification that cause biogeographical patterns of distantly related but sympatrically occurring taxa to be similar. Concordant patterns of diversity facilitate conservation management because strategic designation of protected areas can capture complementary rather than redundant components of variation. Here we demonstrate that on the biodiverse Indonesian island of Sulawesi, seemingly idiosyncratic distributions of diversity in endemic monkeys (Macaca species) and toads (Bufo celebensis) are actually virtually identical on a fine geographic scale. It appears that range fragmentation has generated seven multi-taxon areas of genetic endemism, each of which should be targeted for conservation. Joint consideration of molecular phylogeography, morphology, and demography helps resolve apparent contradictions in paraphyletic macaque mitochondrial DNA and in undifferentiated toad morphology, and facilitates an understanding of biogeography and conservation genetics of Sulawesi fauna.

• Cercopithecine Y-chromosome data provide a test of competing morphological evolutionary hypotheses.

  Authors: Anthony J Tosi, Todd R Disotell, Juan Carlos Morales, Don J Melnick

  Molecular phylogenetics and evolution. 07/2003; 27(3):510-21.

  We report here the results of the first molecular evolutionary analysis to include members of all 10 extant genera of cercopithecine monkeys. A total of 44 individuals were surveyed for approximatelyWe report here the results of the first molecular evolutionary analysis to include members of all 10 extant genera of cercopithecine monkeys. A total of 44 individuals were surveyed for approximately 2.2 kb of the testis-specific protein, Y-chromosome (TSPY). The TSPY sequences were subjected to parsimony analyses in PAUP 4.0, followed by tree comparison tests designed to assess existing morphological hypotheses of cercopithecine evolution. The results of these tests show that the present Y-chromosome dataset unambiguously supports: (1) monophyly of Macaca, (2) polyphyly of the mangabeys (Cercocebus and Lophocebus), (3) paraphyly of Cercopithecus, and (4) inclusion of Allenopithecus and Miopithecus in the tribe Cercopithecini. A number of unexpected Y-chromosome relationships are also discussed, including a pattern suggesting resurrection of the genus Chlorocebus for the guenons currently identified as Erythrocebus patas, Cercopithecus aethiops, and Cercopithecus lhoesti. Relative rate tests reveal significant difference in the TSPY substitution rate across numerous lineages in the tribe Cercopithecini. Because the rate differences follow no obvious phylogenetic pattern, "local" molecular clocks were not employed and divergence dates were not estimated for this tribe. In contrast, similar analysis of the Papionini reveals rate heterogeneity between a single pair of taxonomic groups: Macaca vs. the "African papionins." Divergence dates were therefore calculated for the tribe by calibrating TSPY clocks specific to each of these two clades.

• Resolution of the Hylobates phylogeny: Congruence of mitochondrial D-loop sequences with molecular, behavioral, and morphological data sets

  Authors: Danielle J. Whittaker, Juan Carlos Morales, Don J. Melnick

  Molecular Phylogenetics and Evolution.

  Gibbons of the genus Hylobates likely speciated very rapidly following isolation by rising sea levels during the Pleistocene. We sequenced the hypervariable region I (HV-I) of the mitochondrialGibbons of the genus Hylobates likely speciated very rapidly following isolation by rising sea levels during the Pleistocene. We sequenced the hypervariable region I (HV-I) of the mitochondrial D-loop to reconstruct the phylogeny of this group. Although the results clearly supported monophyly of each of the six species, the relationships among them were not clearly resolved by these data alone. A homogeneity test against published data sets of a coding mitochondrial locus (ND3–ND4 region), behavioral characters (vocalizations), and morphological traits (including skeletal and soft tissue anatomy) revealed no significant incongruence, and combining them resulted in a phylogenetic tree with much stronger support. The Kloss’s gibbon (H. klossii), long considered a primitive taxon based on morphology, shares many molecular and vocal characteristics with the Javan gibbon (H. moloch), and appear as the most recently derived species. The northernmost species (H. lar and H. pileatus) are the most basal taxa. These data suggest that ancestral gibbons radiated from north to south. Unlike other markers, the HV-I region can accurately identify members of different gibbon species much like a DNA barcode, with potential applications to conservation.

• The Millennium Project: the positive health implications of improved environmental sustainability.

  Authors: Don J Melnick, Yolanda Kakabadse Navarro, Jeffrey McNeely, Guido Schmidt-Traub, Robin R Sears

  Lancet. 365(9460):723-5.

• Phylogenetic relationships of the macaques (Cercopithecidae:Macaca), as revealed by high resolution restriction site mapping of mitochondrial ribosomal genes

  Authors: Juan Carlos Morales, Don J. Melnick

  Journal of Human Evolution.

  Molecular phylogenetic relationships among all recognized species within the genusMacaca, were assessed using high-resolution restriction site mapping of the mitochondrial ribosomal genes. ByMolecular phylogenetic relationships among all recognized species within the genusMacaca, were assessed using high-resolution restriction site mapping of the mitochondrial ribosomal genes. By outgroup comparisons to other members of the cercopithecine subfamily, the macaques appear to be a monophyletic assemblage. Within the genus, the relationships are in general consistent with previous genetic studies, though they are less concordant with the separation of the species into four distinct species groups based on modification of the genitalia. Our data support: (1)Macaca sylvanusas sister clade to all Asian macaques; (2) thesilenusgroup as a monophyletic assemblage, with the Sulawesi macaques diverging and colonizing Sulawesi much earlier than previously thought; (3) thefascicularisgroup as a paraphyletic assemblage, including all non-silenusgroup Asian macaques; (4) thesinicagroup as a monophyletic assemblage, possibly derived from afascicularis-like ancestor; and (5)Macaca arctoidesas a separate lineage from thesinicagroup, also originating from afascicularis-like ancestor. This study supports the notion that species with more specialized genitalia evolved from less derived taxa, and in general are in agreement with the dispersal scenarios proposed by Fooden (1980) and Delson (1980) for the macaques.

• Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

  Authors: TNC Vidya, Raman Sukumar, Don J Melnick

  Recent phylogeographic studies of the endangered Asian elephant (Elephas maximus) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understandingRecent phylogeographic studies of the endangered Asian elephant (Elephas maximus) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understanding the species's evolution. Previous explanations for the divergent clades include introgression of mtDNA haplotypes between ancestral species, allopatric divergence of the clades between Sri Lanka or the Sunda region and the mainland, historical trade of elephants, and retention of divergent lineages due to large population sizes. However, these studies lacked data from India and Myanmar, which host approximately 70 per cent of all extant Asian elephants. In this paper, we analyse mtDNA sequence data from 534 Asian elephants across the species's range to explain the current distribution of the two divergent clades. Based on phylogenetic reconstructions, estimates of times of origin of clades, probable ancestral areas of origin inferred from dispersal-vicariance analyses and the available fossil record, we believe both clades originated from Elephas hysudricus. This probably occurred allopatrically in different glacial refugia, the a clade in the Myanmar region and the beta clade possibly in southern India-Sri Lanka, 1.6-2.1 Myr ago. Results from nested clade and dispersal-vicariance analyses indicate a subsequent isolation and independent diversification of the b clade in both Sri Lanka and the Sunda region, followed by northward expansion of the clade. We also find more recent population expansions in both clades based on mismatch distributions. We therefore suggest a contraction-expansion scenario during severe climatic oscillations of the Quaternary, with range expansions from different refugia during warmer interglacials leading to the varying geographical overlaps of the two mtDNA clades. We also demonstrate that trade in Asian elephants has not substantially altered the species's mtDNA population genetic structure.

• Isolation and characterization of tri- and tetranucleotide microsatellite loci in the Asian elephant, Elephas maximus

  Authors: Prithiviraj Fernando, TNC Vidya, Don J Melnick

  Asian elephants (Elephas maximus) are an endangered species. Their future survival depends on intensive conservation and management, based on in-depth knowledge of particular populations. MolecularAsian elephants (Elephas maximus) are an endangered species. Their future survival depends on intensive conservation and management, based on in-depth knowledge of particular populations. Molecular genetic methods, especially microsatellite analysis through noninvasive sampling, provides an effective means of obtaining such information. The use of tri- and tetranucleotide microsatellite markers is advantageous in noninvasive sampling through dung analysis. Here we describe the isolation and characterization of five tri- and tetranucleotide markers in the Asian elephant. All five loci were found to be polymorphic in a sample of 20 Asian elephants from Sri Lanka.