Search

Subspecies were traditionally defined by identifying gaps between phenotypes across the geographic range of a species, and may represent important units in the development of conservation strategies focused on preserving genetic diversity. Previous taxonomic research proposed that phenotypic variation between scattered Indri indri populations warranted the naming of two distinct subspecies, I. i. indri and I. i. variegatus. We tested these subspecific designations using mitochondrial sequence data generated from the control region or D-loop (569 bp) and a large section (2362 bp) of multiple genes and tRNAs known as Pastorini’s fragment and nuclear microsatellite markers. This study used 114 samples of I. indri from 12 rainforest sites in eastern Madagascar, encompassing the entire range of the species. These genetic samples represent multiple populations from low- and high-elevation forests from both putative subspecies. Molecular analyses of the mitochondrial sequence data did not support the two proposed subspecies. Furthermore, the microsatellite analyses showed no significant differences across the range beyond population level differentiation. This study demonstrates the utility of incorporating multiple lines of evidence in addition to phenotypic traits to define species or subspecies.

Limited information is available on the Philippine Crocodile, Crocodylus mindorensis, concerning levels of genetic diversity either relative to other crocodilian species or among populations of the species itself. With only two known extant populations of C. mindorensis remaining, potentially low levels of genetic diversity are a conservation concern. Here, we evaluated 619 putative Philippine Crocodiles using a suite of 11 microsatellite markers, and compared them to four other crocodilian species sample sets. The two remaining populations from the island of Luzon and the island of Mindanao, representing the extremes of the former species’ distribution, appear to be differentiated as a result of genetic drift rather than selection. Both extant populations demonstrate lower genetic diversity and effective population sizes relative to other studied crocodilian species. The 57 C. mindorensis and C. porosus, Saltwater Crocodile, hybrids identified earlier from the Palawan Wildlife Rescue and Conservation Center were revalidated with a suite of 20 microsatellite loci; however, the timing of the event and the prevalence of hybridization in the species had yet to be fully determined. We defined the hybrids as one first cross from a C. porosus female and a C. mindorensis male and 56 C. mindorensis backcross individuals. This hybridization event appears to be confined to the PWRCC collection.

Studies of hybrid zones can inform our understanding of reproductive isolation and speciation. Two species of brown lemur (Eulemur rufifrons and E. cinereiceps) form an apparently stable hybrid zone in the Andringitra region of south-eastern Madagascar. The aim of this study was to identify factors that contribute to this stability. We sampled animals at 11 sites along a 90-km transect through the hybrid zone and examined variation in 26 microsatellites, the D-loop region of mitochondrial DNA, six pelage and nine morphological traits; we also included samples collected in more distant allopatric sites. Clines in these traits were noncoincident, and there was no increase in either inbreeding coefficients or linkage disequilibrium at the centre of the zone. These results could suggest that the hybrid zone is maintained by weak selection against hybrids, conforming to either the tension zone or geographical selection-gradient model. However, a closer examination of clines in pelage and microsatellites indicates that these clines are not sigmoid or stepped in shape but instead plateau at their centre. Sites within the hybrid zone also occur in a distinct habitat, characterized by greater seasonality in precipitation and lower seasonality in temperature. Together, these findings suggest that the hybrid zone may follow the bounded superiority model, with exogenous selection favouring hybrids within the transitional zone. These findings are noteworthy, as examples supporting the bounded superiority model are rare and may indicate a process of ecologically driven speciation without geographical isolation.

Thornicroft's giraffe, Giraffa camelopardalis thornicrofti, is a geographically isolated subspecies of giraffe found only in north-east Zambia. The population only occurs in Zambia's South Luangwa Valley, an area which interestingly places it between the current distribution of Masai (G.c.tippelskirchi) giraffe to the north, and the Angolan (G.c.angolensis) and South African (G.c.giraffa) giraffe in the south-west and south, respectively. Specific studies have been undertaken on the ecology of this subspecies, but their population genetics remains unknown. We studied 34 individuals from the South Luangwa National Park and adjacent Lupande Game Management Area and seven individuals from northern Botswana. The complete cytochrome b and control region sequences of the mitochondrial genome were sequenced and analysed together with database data by maximum likelihood tree reconstruction and maximum parsimony network analyses. The giraffe from Zambia's South Luangwa Valley are most closely related to the subspecies G.c.tippelskirchi and part of their radiation. However, they form a unique population that would benefit from increased research and conservation management. Resume La girafe de Thornicroft, Giraffa camelopardalis thornicrofti, est une sous-espece isolee geographiquement que l'on ne trouve qu'au nord-est de la Zambie. Cette population ne vit que dans le sud zambien de la Vallee de la Luangwa, une zone qui la situe entre la distribution actuelle de la girafe masai (G.c.tippelskirchi) au nord, celle de la girafe d'Angola (G.c.angolensis) et celle d'Afrique du Sud (G.c.giraffa), respectivement au sud-ouest et au sud. Des etudes specifiques ont ete entreprises sur l'ecologie de cette sous-espece, mais la genetique de cette population reste inconnue. Nous avons etudie 34 individus du Parc National de South Luangwa et de l'Aire de gestion de la faune de Lupande qui lui est proche et sept individus du nord du Botswana. Les sequences completes du cytochromeb et d'une region de reference du genome mitochondrial ont ete realisees et analysees en regard des donnees de reference par des analyses par reconstruction de l'arbre selon le principe du maximum de vraisemblance et par la methode de parcimonie maximale. Les girafes de la Vallee de South Luangwa en Zambie sont plus etroitement apparentees a la sous-espece G.c.tippelskirchi et font partie de leur radiation. Cependant, elles constituent une population unique qui aurait tout interet a faire l'objet de nouvelles recherches et d'une meilleure gestion de conservation.

Land use in Madagascar has resulted in extensive deforestation and forest fragmentation. Endemic species, such as the black-and-white ruffed lemur (Varecia variegata), may be vulnerable to habitat fragmentation due to patchy geographic distributions and sensitivities to forest disturbance. We tested for genetic differentiation among black-and-white ruffed lemur groups in two sites in a large forest patch and three sites in smaller patches. We also investigated the relationship between the genetic diversity of populations and patch configuration (size and isolation), as well as the presence or absence of past genetic bottlenecks. We collected blood (n = 22 individuals) or fecal (n = 33) samples from lemurs and genotyped the extracted DNA for 16 polymorphic microsatellites. Bayesian cluster analysis and FST assigned individuals to three populations: Ranomafana (two sites in continuous forest), Kianjavato (two fragments separated by 60 m of non-forest), and Vatovavy (a single fragment, more isolated in time and space). Vatovavy showed significantly lower allelic richness than Ranomafana. Kianjavato also appeared to have lower allelic richness than Ranomafana, though the difference was not significant. Vatovavy was also the only population with a genetic bottleneck indicated under more than one mutation model and a significant FIS value, showing excess heterozygosity. These results indicate that a small geographic separation may not be sufficient for genetic differentiation of black-and-white ruffed lemur populations and that patch size may influence the rapidity with which genetic diversity is lost following patch isolation.

Knowledge of both population size and genetic diversity is critical for assessing extinction risk but few studies include concurrent estimates of these two components of population biology. We conducted an investigation of population density and size, and genetic variation and past demographic events, of the Endangered grey-headed lemurEulemur cinereicepsin south-east Madagascar. We estimated lemur density using line-transect surveys and used satellite imagery to calculate forest fragment area in three localities. We collected tissue samples from 53 individuals and used 26 polymorphic microsatellite loci to obtain measures of population structure (divergence and diversity) across these localities. We tested the probability of past bottleneck events using three models. Contrary to expectation, there were no significant differences in population density across localities. Genetic diversity decreased, but not significantly, with decreasing habitat area and population size. We found a higher likelihood of past bottleneck events in the fragmented coastal populations. The low population size and prior decline in diversity in coastal patches are consistent with their isolation, anthropogenic disturbance, and exposure to cyclone activity. The similarities in the estimates of density between continuous and fragmented sites may indicate recent population growth in the fragments but these populations nevertheless remain at risk from reduced levels of genetic variation. These patterns should be confirmed with more extensive sampling across the limited range ofE. cinereiceps.

To assess genetic diversity in North American captive Asian elephants Elephas maximus, one mitochondrial DNA (mtDNA) segment was sequenced in combination with multilocus genotypes generated from 20 nuclear microsatellite loci for 201 individuals. The analysis of 627 bp of the C-terminal of cyt b and the hypervariable left domain of the noncoding control region (labeled as MDL fragment) sequences revealed the existence of two mtDNA lineages (α and β clade). Analysis of the MDL confirmed that North American captive Asian elephants belong to either the previously characterized α or β clade. An average nucleotide diversity of 0.017 was observed for the Asian elephant mtDNA MDL fragment sequences. Regardless whether an individual possessed mtDNA α or β clade haplotype, all individuals belonged to one nuclear gene lineage for the two X-linked (BGN and PHKA2) and one Y-linked (AMELY) genes sequenced. Analysis of multilocus genotypes indicated an average observed and expected heterozygosities were 0.543 and 0.539 in wild-sourced and 0.579 and 0.547 in the captive-born Asian elephants, respectively. No subdivision among the sampled individuals was detected, including data partitioned by mtDNA clades. Aside from parent–offspring dyads, no further relationships were detected among wild-sourced and captive-born Asian elephants (average relatedness value

Two geographically distinct populations of giraffe (Giraffa camelopardalis) were sampled for this study, the northern Namib Desert and Etosha National Park. Population genetic parameters and relationships within subpopulations were estimated to better understand the genetic architecture of this isolated subspecies. Gene flow between the geographically separated populations can be attributed to recent translocation of giraffe between the two populations. Inbreeding estimates in the six subpopulations studied were low though we found evidence that genetic drift may be affecting the genetic diversity of the isolated populations in northern Namibia. Population dynamics of the sampling locations was inferred with relationship coefficient analyses. Recent molecular systematics of the Namibian giraffe populations indicates that they are distinct from the subspecies Giraffa camelopardalis giraffa and classified as G. c. angolensis. Based on genetic analyses, these giraffe populations of northern Namibia, the desert-dwelling giraffe and those protected in Etosha National Park, are a distinct subspecies from that previously assumed; thus we add data on G. c. angolensis to our scientific knowledge of this giraffe of southern Africa.

Giraffe were historically free-ranging across most of sub-Saharan Africa but are now most often confined to national parks, conservation areas, or private ranches. Five viable populations of Rothschild’s giraffe (Giraffa camelopardalis rothschildi) remain in protected areas in Kenya and Uganda. The viable population in Uganda is Murchison Falls National Park and the four populations in Kenya are Lake Nakuru National Park (LNNP), Ruma National Park, Giraffe Manor, and Mwea Natural Reserve. The Kenya Wildlife Service queried a rapid decline in LNNP giraffe numbers falling from 153 individuals (1995) to 62 individuals (2002) and the failure of that population to recruit young in those years. Significantly reduced browse options, inbreeding depression and preferential lion predation were considered as potential reasons for this trend. Population genetic parameter estimates derived from multilocus genotype analyses suggest that the LNNP population was in good genetic health with respect to the likelihood of inbreeding depression. The population decline coincided with the drought attributed to the 1994 El Nino. Possible dietary complications from highly concentrated tannin levels because of forced over consumption of the park’s declining acacia trees may have compromised young giraffe, making them easy and opportunistic prey for the park’s lion population.

A total of 114 captive elephants (6 Asian; 108 African) from 43 private institutions or North American zoos accredited by the Association of Zoos and Aquariums were sampled and evaluated to investigate genetic status. Because previous analyses of the captive collection indicated potential cytonuclear dissociation between mitochondrial DNA (mtDNA) sequence and microsatellite nuclear DNA genotype data, we investigated this phenomenon within the captive collection with 2 X-linked genes (BGN and PHKA2) and 1 Y-linked gene (AMELY). These data reveal that individuals with forest-derived elephant mtDNA lineages carried only savannah elephant nuclear gene haplotypes. These results are concordant with a previous study of wild populations sampled across Africa, indicating that cytonuclear genomic dissociation was captured in the founders of the North American African elephant collection. These results are important for resolving questions that can potentially impact future management and breeding programs related to the collection.

The white-collared lemur (Eulemur cinereiceps) is found in southeastern Madagascar. This species is endangered due to the loss and fragmentation of its natural habitat and hunting. Eighteen nuclear microsatellite loci were isolated from genomic DNA derived from an animal from Mahabo Forest in Madagascar. Population genetic parameters were estimated from a population of white-collared lemur sampled at Vevembe Forest 7 years apart to evaluate the potential utility of this marker suite.

The plowshare tortoise, Astrochelys yniphora, or Angonoka is one of Madagascar’s land tortoises, living in the vicinity of Baly Bay bamboo scrub in northwest Madagascar. Primary threats to this endangered species are due to poaching for pet trade and the loss and fragmentation of its natural habitat. The number of wild Angonoka is estimated to be ~400. Twenty polymorphic nuclear microsatellite loci were isolated from a genomic DNA on individuals from Andrafiafaly in Baly Bay National Park, Madagascar. Results from this study will help for future studies of the social structure and population dynamics of this species as well as identification of confiscated individuals from the illegal pet trade.

This study presents the first detailed morphometric measurements of wild caught black-and-white ruffed lemurs (Varecia variegata) from the eastern rainforests of Madagascar and aims to quantify the morphological variation present throughout their recognized range. One hundred and forty-four adult and juvenile individuals from 15 sites were sampled for 20 cranial, dental and postcranial morphometric and body mass measurements. Data were collected from an equal number of male and female individuals sampled across seasons over a 7-year period (1999–2002, 2004–2006). Results indicate that adult body mass and morphometric measurements varied between sexes across sites; however, the only significant intersexual difference found was that females possessed, on average, longer tails than males. Contrary to previous studies, significant seasonal variation could not be detected in either male or female body mass or testicular volume (i.e., breeding vs. nonbreeding, food-scarce vs. food-abundant seasons). Measurements did, however, vary significantly by site and subspecies, though clinal variation could not explain these differences. The introduced population from Nosy Mangabe exhibited significantly lower body mass and overall body length than all other populations; however, this distinction may not have been attributable to natural variation, and may have instead resulted from the ecologically restrictive habitat (e.g., unusually high lemur population densities, limited food resources, ecological isolation) of this introduced population. Finally, although fore-to-hindlimb, brachium-to-thigh and hindlimb indices were comparable to previous values, forelimb indices calculated here deviate significantly from previous reports, placing V. variegata within the upper range of lemurid taxa. It is currently unknown whether this is an artifact of sampling methods (i.e., live vs. skeletal specimens) or whether this is an avenue that warrants further investigation. Am. J. Primatol. 70:913–926, 2008. © 2008 Wiley-Liss, Inc.

Twenty-two nuclear microsatellite loci were isolated from a genomic DNA library derived from Madagascar’s Rousettus madagascariensis. Marker characteristics were determined from a single population (37 individuals) from Fort Dauphin (southeastern Madagascar). Sixteen of the 22 loci were within Hardy–Weinberg expectations. These loci are highly informative with polymorphic information content values ranging between 0.757 and 0.916. These loci will provide valuable information for the study of population genetics and gene flow within this species of bats. Due to the dramatic reduction and alteration of their habitat, data generated utilizing this marker suite will potentially provide additional information for the effective long-term management of this near-threatened bat species.

Decken's sifaka (Propithecus deckeni deckeni) is found between the Mahavavy and Manambolo Rivers, in western Madagascar. Twenty-one polymorphic nuclear microsatellite loci were isolated from genomic DNA derived from a P. d. deckeni, from Tsingy de Bemaraha National Park. Population genetic parameters were estimated on 10 individuals each, sampled from Tsingy de Bemaraha National Park and Tsiombikibo Classified Forests. Significant null alleles were detected in seven loci which were dropped before population genetic parameters were re-estimated and compared to the full marker suite.

Diademed sifaka (Propithecus diadema) distributed throughout Madagascar’s eastern rain forests from the Mangoro and Onive Rivers north to the Mananara River. Twenty-one polymorphic nuclear microsatellite loci were isolated from genomic DNA derived from a P. diadema, from Mantadia National Park. Population genetic parameters were estimated on 10 individuals each, sampled from Mantadia National Park and Maromizaha Unprotected Forest. Allele sizes ranged from 4 to 14 and observed heterozygosities ranged from 0.200 to 0.900 per locus. This marker suite will be informative in further population genetic studies.

Twenty nuclear microsatellite loci were isolated from a genomic DNA library derived from a free-ranging red-bellied brown lemur (Eulemur rubriventer), from the Ranomafana National Park, Madagascar. Population genetic parameters were estimated as baseline values from samples collected from populations harboured in the Ranomafana and Andringitra National Parks. The marker suite will be used in a future study on the population dynamics of this species.

The golden-crowned sifaka (Propithecus tattersalli) is one of the most critically endangered species of Propithecus endemic to a limited area in the Daraina region of north-eastern Madagascar. This species is endangered due to habitat loss and fragmentation, a consequence of deforestation. Twenty nuclear microsatellite loci were isolated from genomic DNA derived from a Propithecus tattersalli from the Daraina area in north-eastern Madagascar. Population genetic parameters were estimated on 20 individuals from two Daraina forest fragments to determine the potential utility of this marker suite for future studies on the golden-crowned sifaka.

Ring-tailed lemur (Lemur catta) is the only species in the Genus Lemur, distributed in the deciduous and spiny forests of southwestern Madagascar. This species is listed as endangered due to the loss and fragmentation of its natural habitat, a consequence of deforestation. Twenty-one nuclear microsatellite loci were isolated from a genomic DNA derived from a free-ranging ring-tailed lemur population from the Tsimanampetsotsa National Park, Madagascar. We report various parameter estimates and measures to establish the utility of this marker suite as screened among individuals this single forest fragment.

The Komodo monitor (Varanus komodoensis) is a classic example of a species that has been fragmented into small isolated populations over a limited range. This species, classified as endangered under Appendix I of the Convention on the International Trade of Endangered Species. We describe 10 novel species-specific microsatellite loci characterized in representatives from three of the endemic island populations. One locus, 12HDZ820 appears to be fixed in one population at an allele size not found in the other two. This microsatellite suite should be helpful in augmenting the marker selection currently available for Komodo Monitor population studies.

Twenty novel polymorphic microsatellite loci were isolated and characterized from the Indri, Indri indri, genome. Along with sequence data, this marker suite will be used in future studies to establish population structure throughout its range and to verify the proposed subspecific nomenclature. Gene diversity (0.760 and 0.783) and allelic richness (5.8 and 6.43) were estimated in the Betampona and Andasibe populations, respectively.

The radiated tortoise (Geochelone radiata) is an endangered species endemic to Madagascar. It inhabits the semiarid spiny forest of the southern part of the island, an ecosystem heavily affected by habitat destruction. Furthermore, illegal harvesting greatly threatens this species. The main objective of our study was to acquire better knowledge of its genetic structure, in order to take appropriate management decisions concerning, for instance, the reintroduction of confiscated individuals. Our hypothesis was that rivers represent effective barriers to tortoise dispersal despite the fact that they are dry most of the year. We used 13 polymorphic microsatellite markers to compare samples from six populations across the range of the species. All analyses (Fisher’s exact tests, FST values, AMOVA) indicated that the radiated tortoise exhibits moderate levels of genetic structure throughout its range. In addition, we used a multiple regression approach that revealed the importance of rivers to explain the observed structure. This analysis supported the role of the Menarandra and Manambovo Rivers as major barriers to the dispersal of most radiated tortoises, but Markov chain Monte Carlo simulations revealed that low levels of recurrent gene flow may explain why FST values were not higher. We identified three distinct conservation units with relatively high assignments rates (87%), which should be valuable for the management of the species. This is the first study to report the genetic structure of a species sampled throughout the Malagasy spiny forest.

The Verreaux's sifaka (Propithecus verreauxi) is one of the species of Propithecus, living in the dry forest of southwest Madagascar. This species is endangered due to the loss and fragmentation of its natural habitat, a consequence of deforestation. Thirteen novel nuclear microsatellite loci were isolated and characterized in three populations of Verreaux's sifaka. The marker suite proved informative with an average of 8.9 alleles per locus and observed heterozygosity across the three populations of 0.675.

Phylogenetic analysis of ca. 4500 base pairs of mitochondrial DNA sequence data reveals further genetic diversity in mouse lemurs (Microcebus) on the eastern and western coasts of Madagascar. Molecular data and phylogenetic analyses revise the previously monotypic species of eastern Madagascar, Microcebus rufus, with the description of 3 new species. Three additional Microcebus species are proposed in eastern Madagascar, along with another Microcebus species in western Madagascar. Correlating the molecular data with previously generated sequence data, we present a tentative pattern of distribution along the east coast. We show that the general distribution of Microcebus is based on a traditional eastern/western division. The preliminary model appears strongly influenced by both rivers and altitudinal differences acting independently as barriers.

The black and white ruffed lemur, Varecia variegata , which is endemic to Madagascar, is under the threat of extinction due to the loss and fragmentation of its natural habitat, a consequence of deforestation. Behavioural researchers studying a population of V. variegata inhabiting the Manombo Special Reserve, noted that over a 4-year period, none of the family groups within the reserve produced offspring while those in neighbouring populations had been reproductively successful. Inbreeding depression was postulated as the trigger for this occurrence. However, another explanation exists. A cyclone, striking the region in 1997, destroyed a large percentage of the mature fruit-producing trees that V. variegata relied upon as a food source, which is likely to have produced a nutritional deficit. A panel of 25 simple sequence repeat (SSR) markers was utilised to assess the genetic diversity within four V. variegata populations, including individuals from Manombo and three other populations in southeastern Madagascar. The data revealed that the level of genetic diversity apparent within the Manombo population is comparable to the other groups studied. Therefore, it seems probable that genetic factors are not responsible for the recent lack of reproductive success on the part of the V. variegata at Manombo Special Reserve.

Twenty-two polymorphic microsatellite loci were isolated and characterized from the Avahi laniger genome. All were polymorphic in both the Eastern Woolly Lemur (A. laniger) and the Western Woolly Lemur (A. occidentalis). One locus, WOOL157, harboured allele structures that were species-specific. This marker suite will be used in future studies to establish the ranges and population structures of the two Avahi species on the island of Madagascar.

We developed microsatellite markers for the recently described forest rodent, Eliurus carletoni, from an enriched genomic library. Nine loci composed of four dinucleotide, one trinucleotide, one tetranucleotide and three compound repeats were isolated and characterized using two wild populations. One locus was found to be monomorphic. For the polymorphic loci, the average number of alleles per locus was 7.13 and 8.38 for each population. Mean expected and observed heterozygosities were high (i.e. 0.76 and 0.80). Tests for linkage disequilibrium were not significant across all locus pairs. One locus tested significant for null alleles, but only one population exhibited a significant deviation from the Hardy–Weinberg Equilibrium (HWE) at this locus. All remaining loci show no evidence of departure from HWE. Overall, we identified eight polymorphic loci that may be used in conservation and population genetics studies of E. carletoni.

Twenty-one polymorphic microsatellite loci were isolated and characterized from the genome of the prehensile-tailed skink (Corucia zebrata). The markers were screened using a set of 16 individuals from the collection of the Philadelphia Zoo. The corresponding characterization indicated significant levels of heterozygosity and information potential for use in future studies. These markers will be a valuable tool in analysing the paternal contributions in twin birth questions and for population genetic studies in wild populations.

The Malagasy big-headed turtle (Erymnochelys madagascariensis) is the only Erymnochelys species living in lakes, rivers and watersheds of western Madagascar. This species is endangered due to over harvesting of natural populations for human consumption. Eleven nuclear microsatellite loci were isolated from a genomic DNA library derived from a free-ranging Malagasy big-headed turtle from the Beroboka Classified Forest, Madagascar. Population genetic parameters were estimated on 10 individuals sampled from Ampijoroa and Andranohobaka River, Madagascar, to determine marker utility and as preliminary baseline values to study future populations in these locations.

The Coquerel's sifaka (Propithecus coquereli) is one of the species of Propithecus, living in the dry forest of northwest Madagascar. This species is endangered due to the loss and fragmentation of its natural habitat, consequential of deforestation. Twenty nuclear microsatellite loci were isolated from genomic DNA derived from a free ranging Coquerel's sifaka from the Mariarano Classified Forest, Madagascar. Population genetic parameters were estimated as baseline values from samples collected in that forest.

Sixteen polymorphic microsatellite markers with an average allele size of k = 4.3 are identified from a genomic plasmid library constructed for giraffe (Giraffa camelopardalis ssp.). Primer sequences and marker data are reported in tabular form. The markers were screened in a population of 25 Maasai giraffe (G. c. tippelskirchi) collected near the Athi River, Kenya. The average observed heterozygosity for each marker was 0.36 with an average expected heterozygosity of 0.535. Hardy–Weinberg deviations are reported from this population, which is suspected to be inbred. The markers will be used to screen the captive giraffe population for subspecific or hybrid classification.

Decken's sifaka (Propithecus deckeni deckeni) is found between the Mahavavy and Manambolo Rivers, in western Madagascar. Twenty-one polymorphic nuclear microsatellite loci were isolated from genomic DNA derived from a P. d. deckeni, from Tsingy de Bemaraha National Park. Population genetic parameters were estimated on 10 individuals each, sampled from Tsingy de Bemaraha National Park and Tsiombikibo Classified Forests. Significant null alleles were detected in seven loci which were dropped before population genetic parameters were re-estimated and compared to the full marker suite.

In order to screen microsatellites for conservation genetics studies of the species, a total of 23 microsatellite loci from Korean goral (Naemorhedus caudatus), including 15 previously developed loci and 8 new loci in this study, were tested. Eleven microsatellites were screened and subjected to cross-species amplification using a test panel of four Caprinae species, Japanese serows (Capricornis crispus), Chinese gorals (Naemorhedus goral), Northern chamois (Rupicapra rupicapra) and domestic goats (Capra hircus). In addition, all eleven microsatellites (SY3A, SY12A, SY12B, SY48, SY58, SY71, SY76, SY84, SY84B, SY112, and SY129) satisfied the criteria to be a core set of microsatellites. This core set of microsatellites and cross-species amplification of Korean goral microsatellites were found to be helpful for high-resolution studies for conservation and management of Korean goral and other endangered Caprinae species.

The complete mitochondrial DNA (mtDNA) genome of Hubbard's or Zombitse sportive lemur (Lepilemur hubbardorum) was generated by polymerase chain reaction (PCR) amplification, primer-walking sequencing and fragment cloning. Comparative analyses of Hubbard's sportive lemur were conducted with available complete mitochondrial genome sequences from eight other lemur species. The mitochondrial genome of Hubbard's sportive lemur is 16,854 base pairs (bp) and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. Three rare start codons were found, in which GTG is the start codon for the ATPase 6 subunit gene (ATP), ATC for the NADH dehydrogenase (ND) 2 subunit gene, and ATT for the ND5 subunit gene. In the control region, sequence analysis found one repetitive unit between conserved sequence blocks (CSB)-1 and CSB-2 for L. hubbardorum. Comparative analysis of eight other lemur species showed different repetitive units between and outside of these two blocks. According to the phylogenetic analysis of the 12 heavy-strand encoded protein-coding genes, all nine lemur species representative of four lemuriformes families were monophyletic. This template and the newly designed primers described in this study will allow scientists to generate comparative sequences for all sportive lemurs to validate phylogenetic discrepancies in the genus Lepilemur and to evaluate evolutionary and biogeographic models.

The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed forBos taurus taurusto rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to amplify and screen genomic information from extinct species, and placeBison priscuswithin the Bovidae. The quality of genotype calls and the placement of samples within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.

The Madagascar tree boa, Sanzinia madagascariensis madagascariensis, is one of four snakes in the family Boidae living in Madagascar. This species is considered ‘vulnerable’ due to habitat loss and utilization as a food source by locals. Twenty species-specific microsatellite loci were isolated and characterized from Sanzinia m. madagascariensis to assess population genetic parameters. Individuals were collected from two populations in the east and the northeastern coast of Madagascar: Torotofotsy wetlands and Mananara-Nord Biosphere Reserve, respectively. This marker suite will provide a useful tool for future research to determine and validate the taxonomic status of the tree boa with samples collected extensively throughout the island.

The current range of the red ruffed lemur (Varecia rubra) population is primarily restricted to forests of the Masoala Peninsula on the northeastern coast of Madagascar. Whereas much of the peninsula is protected as Masoala National Park, parts of the forest are at risk from anthropogenic pressures and habitat fragmentation. We sampled 32 individual red ruffed lemur from two sites: Ambatoledama (DAMA), a narrow forest corridor across an area of degraded habitat connecting larger blocks of forest in the northwestern reaches of the park, and Masiaposa (MAS) forest, a largely pristine forest on the lower western side of the peninsula. Population genetic parameters were estimated for these two populations employing 15 microsatellite loci derived from the V. variegata genome. We found that by exceeding the expected heterozygosity at mutation-drift equilibrium, the DAMA population has undergone a recent population bottleneck. Population structure analysis detected individuals harboring genotypic admixture of the DAMA genetic cluster in the MAS population, suggesting a possibility of unilateral gene flow or movement between these populations.

The silky sifaka, Propithecus candidus, considered one of the rarest and most endangered primates in the world, exists in only a few fragmented forests in northeastern Madagascar. This species faces increasing pressures as a direct result from loss of habitat in the form of tavy (slash and burn agriculture), illegal logging and mining along with hunting for subsistence, even within protected areas. We report a marker suite of 21 loci developed from genomic DNA from a silky sifaka collected in 2003 from Anjanaharibe-Sud Special Reserve. Polymorphism of each locus evaluated in 18 individuals pooled from Marojejy National Park and Anjanaharibe-Sud Special Reserve. The number of observed alleles per locus ranges from 2 to 7. The observed and expected heterozygosity were 0.389–0.889 and 0.322–0.789, respectively. The information revealed in this study will provide useful tools for further study of the social structure and population dynamics of the silky sifaka to facilitate conservation management in the imminent future.

BackgroundA central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation.ResultsBy analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations.ConclusionSuch extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separatein situandex situmanagement, not only of pelage morphs, but also of local populations.

The Philippine crocodile (Crocodylus mindorensis) is considered one of the most endangered of the crocodilian species.Rumors or anecdotal concerns have existed for some time as to the possibility of hybrid individuals existing in a captivecollection under consideration for providing reintroduction candidates; however, visual observations failed to identify sus-pected hybrids. Samples were collected from 619 Philippine crocodiles from several captive facilities and two free-rang-ing populations. Mitochondrial DNA D-loop (601 bp) fragments were sequenced for each crocodile and compared to 28individuals representing ten crocodile species. Among Philippine crocodiles, 48 variable sites (47 parsimony informativesites) were identified, which defined six C. mindorensis haplotypes and one C. porosus-derived haplotype. Data were alsogenerated for a 965 bp fragment of the ND4 subunit gene fragment for two samples of each D-loop haplotype. Amongthem, 91 variable sites (90 parsimony informative site) were identified, which defined three C. mindorensis haplotypesand one C. porosus-derived haplotype. From the nuclear genome, the C-mos gene was successfully amplified for the 388bp partial fragment for all Philippine crocodile samples. Only two variable sites were identified. These sequences werecompared to GenBank sequences for C. porosus. Of the 619 Philippine crocodile samples, 57 samples were found to har-bor D-loop haplotypes identified as C. porosus and 31 of those harbored C-mos mutational sites diagnostic for C. porosus introgression. All individuals indicating C. mindorensis x C. porosus hybridization were sampled from the Palawan Wildlife Rescue and Conservation Center.