Genetic Variation of Major Histocompatibility Complex and Microsatellite Loci: A Comparison in Bighorn Sheep

Examining and comparing genetic variation for major histocompatibility complex (MHC) and microsatellite (MS) loci in the same individuals provides an opportunity to understand the forces influencing genetic variation. We examined five MHC and three MS loci in 235 bighorn sheep (Ovis canadensis) from 14 populations and found that both types of loci were highly variable and were in Hardy-Weinberg proportions. Mean F(ST) values for both markers were very similar and MHC and MS genetic variability was predominantly distributed within rather than among populations. However, analyses of genetic distances and tree topologies revealed different spatial patterns of variation for the two types of loci. Collectively, these results indicated that neutral forces substantially influenced MS and MHC variation, and they provided limited evidence for selection acting on the MHC.     

Evidence for Variation in the Effective Population Size of Animal Mitochondrial DNA

Background

It has recently been shown that levels of diversity in mitochondrial DNA are remarkably constant across animals of diverse census population sizes and ecologies, which has led to the suggestion that the effective population of mitochondrial DNA may be relatively constant.

Results

Here we present several lines of evidence that suggest, to the contrary, that the effective population size of mtDNA does vary, and that the variation can be substantial. First, we show that levels of mitochondrial and nuclear diversity are correlated within all groups of animals we surveyed. Second, we show that the effectiveness of selection on non-synonymous mutations, as measured by the ratio of the numbers of non-synonymous and synonymous polymorphisms, is negatively correlated to levels of mitochondrial diversity. Finally, we estimate the effective population size of mitochondrial DNA in selected mammalian groups and show that it varies by at least an order of magnitude.

Conclusions

We conclude that there is variation in the effective population size of mitochondria. Furthermore we suggest that the relative constancy of DNA diversity may be due to a negative correlation between the effective population size and the mutation rate per generation.     

Conservation Genetics of the Philippine Tarsier: Cryptic Genetic Variation Restructures Conservation Priorities for an Island Archipelago Primate

Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier.     

Genetic and Morphological Variation of Two Rare Species of Lepidium (Brassicaceae) on Mangere Island,Chatham Islands,and Implications for Their Conservation Management

The genus Lepidium in New Zealand comprises a number of threatened and endemic species. Two recently described species, Lepidium panniforme and L. oblitum, have a restricted distribution on the remote and difficult to access Mangere Island, Chatham Islands. We examined the genetic and morphological variation of L. panniforme and L. oblitum on Mangere Island to assess the best conservation management options. Amplified fragment length polymorphism (AFLP) data and morphological data were used to detect finer scale variation in L. panniforme and L. oblitum. Bayesian analysis of AFLP genotypes detected up to four genetic clusters on Mangere Island. The morphological data were also variable, although better reflected the taxonomic treatment of the Mangere Island plants. The conservation implications of such high genetic and morphological variation over such a small spatial scale are discussed, to propose the best method for ensuring the ongoing survival of these island endemics.     

Reduced Genetic Diversity and Effective Population Size in an Endangered Atlantic Salmon (Salmo Salar) Population from Maine, USA

Atlantic salmon (Salmo salar) populations in Maine, USA, are listed as a Distinct Population Segment under the U.S. Endangered Species Act due to reduced spawning runs and juvenile densities. Whenever possible, optimal conservation strategies for endangered populations should incorporate both present and historical knowledge of genetic variation. We assayed genetic diversity at seven microsatellite loci and at the mitochondrial ND1 gene in an endangered wild population of Atlantic salmon captured from the Dennys River from 1963 to 2001 using DNA’s extracted from archival scale and tissue samples. We examined temporal trends of genetic diversity, population structure, and effective population size (Ne). Overall temporal trends of diversity and Ne show significant reductions from 1963 to 2001 raising the possibility that current restoration efforts may be impacted by historical loss of diversity potentially critical to adaptation. Although our results suggest genetic stability in this population from 1963 to 1981, significant differentiation was observed for both the 1995 and 2001 samples compared with all other temporal samples. The presence of an ND1 mtDNA haplotype in this population, historically observed only in European and Newfoundland stocks, may represent previously unrecognized local wild diversity or, alternatively, may represent introgression from non-native fish.     

Reconciling Genetic and Demographic Estimators of Effective Population Size in the Anuran Amphibian Bufo Calamita

We used genetic and demographic methods to estimate the variance effective population sizes (N _e) of three populations of natterjack toads Bufo calamita in Britain. This amphibian breeds in temporary pools where survival rates can vary among families. Census population sizes (N) were derived from spawn string counts. Point and coalescent-based maximum likelihood estimates of N _e based on microsatellite allele distributions were similar. N _e/N ratios based on genetic estimates of N _e ranged between 0.02 and 0.20. Mean demographic estimates of N _e were consistently higher (2.7–8.0-fold) than genetic estimates for all three populations when variance in breeding success was evaluated at the point where females no longer influence their progeny. However, discrepancies between genetic and demographic estimators could be removed by using a model that included extra variance in survivorship (above to Poisson expectations) among families. The implications of these results for the estimation of N _e in wild populations are discussed.     

The Genetic Basis of Natural Variation in Kernel Size and Related Traits Using a Four-Way Cross Population in Maize

Kernel size is an important component of grain yield in maize breeding programs. To extend the understanding on the genetic basis of kernel size traits (i.e., kernel length, kernel width and kernel thickness), we developed a set of four-way cross mapping population derived from four maize inbred lines with varied kernel sizes. In the present study, we investigated the genetic basis of natural variation in seed size and other components of maize yield (e.g., hundred kernel weight, number of rows per ear, number of kernels per row). In total, ten QTL affecting kernel size were identified, three of which (two for kernel length and one for kernel width) had stable expression in other components of maize yield. The possible genetic mechanism behind the trade-off of kernel size and yield components was discussed.     

Genome-Wide Estimates of Coancestry,Inbreeding and Effective Population Size in the Spanish Holstein Population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.     

Extensive Variation and Sub-Structuring in Lineage A mtDNA in Indian Sheep: Genetic Evidence for Domestication of Sheep in India

Previous studies on mitochondrial DNA analysis of sheep from different regions of the world have revealed the presence of two major- A and B, and three minor- C, D and E maternal lineages. Lineage A is more frequent in Asia and lineage B is more abundant in regions other than Asia. We have analyzed mitochondrial DNA sequences of 330 sheep from 12 different breeds of India. Neighbor-joining analysis revealed lineage A, B and C in Indian sheep. Surprisingly, multidimensional scaling plot based on F_ST values of control region of mtDNA sequences showed significant breed differentiation in contrast to poor geographical structuring reported earlier in this species. The breed differentiation in Indian sheep was essentially due to variable contribution of two major lineages to different breeds, and sub- structuring of lineage A, possibly the latter resulting from genetic drift. Nucleotide diversity of this lineage was higher in Indian sheep (0.014 ± 0.007) as compared to that of sheep from other regions of the world (0.009 ± 0.005 to 0.01 ± 0.005). Reduced median network analysis of control region and cytochrome b gene sequences of Indian sheep when analyzed along with available published sequences of sheep from other regions of the world showed that several haplotypes of lineage A were exclusive to Indian sheep. Given the high nucleotide diversity in Indian sheep and the poor sharing of lineage A haplotypes between Indian and non-Indian sheep, we propose that lineage A sheep has also been domesticated in the east of Near East, possibly in Indian sub-continent. Finally, our data provide support that lineage B and additional lineage A haplotypes of sheep might have been introduced to Indian sub-continent from Near East, probably by ancient sea trade route.     

A Genetic Framework for Grain Size and Shape Variation in Wheat

Grain morphology in wheat (Triticum aestivum) has been selected and manipulated even in very early agrarian societies and remains a major breeding target. We undertook a large-scale quantitative analysis to determine the genetic basis of the phenotypic diversity in wheat grain morphology. A high-throughput method was used to capture grain size and shape variation in multiple mapping populations, elite varieties, and a broad collection of ancestral wheat species. This analysis reveals that grain size and shape are largely independent traits in both primitive wheat and in modern varieties. This phenotypic structure was retained across the mapping populations studied, suggesting that these traits are under the control of a limited number of discrete genetic components. We identified the underlying genes as quantitative trait loci that are distinct for grain size and shape and are largely shared between the different mapping populations. Moreover, our results show a significant reduction of phenotypic variation in grain shape in the modern germplasm pool compared with the ancestral wheat species, probably as a result of a relatively recent bottleneck. Therefore, this study provides the genetic underpinnings of an emerging phenotypic model where wheat domestication has transformed a long thin primitive grain to a wider and shorter modern grain.     

Sex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi

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 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.THE effective size of a population (N_e) determines the relative impact of genetic drift and natural selection on mutations with mild effects on fitness (Charlesworth 2009). Differences in N_e are hypothesized to affect virtually every aspect of genome evolution, including rates of molecular evolution, abundance of introns and transposable elements, and persistence of duplicate genes, and this has important implications for the evolution of complexity via both adaptive and degenerative processes (Lynch 2007). Of relevance are not only the number of different individuals in a population, but also the number of copies of a gene within each individual. In diploid species with separate sexes, sex chromosomes and mitochondrial DNA (mtDNA) differ in copy number from autosomal DNA (aDNA): both sexes have two alleles at autosomal loci whereas in species with male heterogamy, males have one X and one Y chromosome, females have two Xs, and a female/male pair has effectively only one copy of mtDNA due to maternal inheritance. Sex-specific differences in demographic parameters such as migration, adult sex ratio, and variance in reproductive success also affect relative copy number and associated levels of neutral polymorphism at mtDNA, aDNA, the X chromosome (xDNA), and the Y chromosome (yDNA) (Hedrick 2007).The effective population size is the number of individuals in a Wright–Fisher idealized population (Fisher 1930; Wright 1931) that have the same magnitude of genetic drift as an observed population, where ideal individuals are diploid, and have discrete (nonoverlapping) generations, constant population size, and random mating. N_e can be quantified in terms of variance in allele frequency over generations (variance N_e) or variance in inbreeding over time (inbreeding N_e). If population size is constant with random mating, these approaches for quantifying N_e produce identical results (Kimura and Crow 1963; Whitlock and Barton 1997). At mutation–drift equilibrium with an equal number of males and females and a Poisson distributed number of offspring with a mean of two offspring per individual, N_e-aDNA and N_e-xDNA are expected to be four and three times as large, respectively, as N_e-yDNA and N_e-mtDNA; we refer to this as the “ideal expectation with an equal proportion of males and females.”Demography can alter relationships between N_e of different parts of the genome. For example, extreme skew in adult sex ratio can cause N_e of uniparentally inherited portions of the genome to exceed N_e of biparentally inherited portions (Figure 1A; Nunney 1993; Caballero 1994; Hoelzer 1997; Hedrick 2007). With a skewed sex ratio, the more common sex has a higher variance in reproductive success than the rare one, and this causes the overall variance in reproductive success to increase as the sex-ratio bias increases (Nunney 1993). Sex-biased dispersal such as female philopatry also alters relationships between N_e-aDNA, N_e-xDNA, N_e-yDNA, and N_e-mtDNA (Figure 1B), causing N_e of portions of the genome that disperse less to increase (Nei and Takahata 1993; Hoelzer 1997; Wang and Caballero 1999).Open in a separate windowFigure 1.—N_e of aDNA, xDNA, mtDNA, and yDNA as a function of (A) sex ratio skew and (B) the probability of female dispersal. In B, a finite island model of subdivided populations of constant size is assumed with a population size of 10,000 individuals, 10 subpopulations, and a male probability of migration equal to 0.1.At least five factors related to natural selection also can cause the relative N_e of aDNA, xDNA, yDNA, and mtDNA to depart from expectations: (1) very low or absent recombination in mtDNA and a portion of yDNA, (2) haploidy of mtDNA and yDNA, (3) hemizygosity of xDNA in males, (4) sexual selection and differences in gene content, and (5) differences in the rate and variance of mutation. “Selective sweeps” in which an advantageous mutation is fixed by natural selection, reduces N_e of linked sites (Maynard Smith and Haigh 1974) and this can affect the entire mitochondrial genome and nonrecombining portion of the Y chromosome. Nonrecombining portions of yDNA and mtDNA are also affected by stochastic loss of alleles containing the fewest deleterious mutations (“Muller''s ratchet”; Muller 1964; Felsenstein 1974), which results in a gradual decline of fitness of these chromosomes over time. N_e of nonrecombining DNA is further reduced by elimination of variation linked to substantially deleterious mutations (“background selection”; Charlesworth et al. 1993), by interference between linked polymorphisms that impedes fixation of advantageous alleles and extinction of deleterious ones (the “Hill–Robertson effect”; Hill and Robertson 1966; McVean and Charlesworth 2000), and by increased frequency of deleterious mutations linked to advantageous ones during a selective sweep (“genetic hitchhiking”; Rice 1987). Hemizygous X-linked and haploid Y-linked loci in males and mtDNA loci in both sexes are more vulnerable to recessive deleterious mutations because they are not masked by a second allele (Otto and Goldstein 1992). Hemizygosity on the X chromosome can also increase the rate of selective sweeps when advantageous mutations are recessive (Charlesworth et al. 1987). Similarly, these loci are also susceptible to recessive species incompatibilities—a factor that at least partially accounts for Haldane''s rule for hybrid sterility (Haldane 1922; Orr 1997). Sexual selection differentially influences the probability of fixation of mutations depending on mode of inheritance (Wade and Shuster 2004), especially mutations with antagonistic fitness effects between the sexes (Gibson et al. 2002). Additionally, the rate of evolution of animal mtDNA is much higher than aDNA, xDNA, and yDNA (Haag-Liautard et al. 2008) and this presumably contributes to variation in the frequency of nonneutral mutations in different parts of the genome.Differences among N_e of mtDNA, yDNA, xDNA, and aDNA are thought to be particularly pronounced in papionin monkeys (macaques, baboons, geladas, mandrills, drills, and mangabeys). These monkeys have a highly sex-biased adult demography; females form stable philopatric groups of close relatives, whereas males generally change social groups and disperse more widely (Dittus 1975). Often adult sex ratio of papionins is female biased (Dittus 1975; Melnick and Pearl 1987; O''Brien and Kinnard 1997; Okamoto and Matsumura 2001), and males have higher variance in reproductive success than females (Dittus 1975; de Ruiter et al. 1992; Keane et al. 1997; Van Noordwijk and Van Schaik 2002; Widdig et al. 2004). These sex differences predict strong population subdivision of mtDNA with little or no subdivision of aDNA, deep mtDNA coalescence times, and frequent mtDNA paraphyly among species, and discordant genealogical relationships between mtDNA and yDNA—and this has been observed in multiple studies (Melnick and Pearl 1987; Melnick 1988; Melnick and Hoelzer 1992; Melnick et al. 1993; Hoelzer et al. 1994; Evans et al. 1999, 2001, 2003; Tosi et al. 2000, 2002, 2003; Newman et al. 2004). Female philopatry and obligate male migration is a common social system in mammals (Greenwood 1980; Dobson 1982; Johnson 1986), though less so in humans (Seielstad et al. 1998), and molecular variation provides an effective tool for exploring the impact of natural selection and demography on aDNA, the sex chromosomes, and mtDNA (Nachman 1997; Bachtrog and Charlesworth 2002; Stone et al. 2002; Berlin and Ellegren 2004; Hellborg and Ellegren 2004; Wilder et al. 2004; Hammer et al. 2008).We explored the genetic effects of demography and linked selection in structuring sequence polymorphism of a papionin monkey—the macaques—at two levels. We first tested whether levels of polymorphism in aDNA, xDNA, yDNA, and mtDNA in a Bornean population of the pigtail macaque, Macaca nemestrina, match expectations under scenarios involving natural selection and also whether the data might be explained by simple demographic models with sex-specific dispersal or a biased sex ratio. We then explored demography on a larger, inter-island scale by estimating the time of divergence between macaques on Borneo and Sulawesi islands and by testing for evidence of ongoing migration between these islands.     

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Offspring number and size are key traits determining an individual’s fitness and a crop’s yield. Yet, extensive natural variation within species is observed for these traits. Such variation is typically explained by trade-offs between fecundity and quality, for which an optimal solution is environmentally dependent. Understanding the genetic basis of seed size and number, as well as any possible genetic constraints preventing the maximization of both, is crucial from both an evolutionary and applied perspective. We investigated the genetic basis of natural variation in seed size and number using a set of Arabidopsis thaliana multiparent advanced generation intercross (MAGIC) lines. We also tested whether life history affects seed size, number, and their trade-off. We found that both seed size and seed number are affected by a large number of mostly nonoverlapping QTL, suggesting that seed size and seed number can evolve independently. The allele that increases seed size at most identified QTL is from the same natural accession, indicating past occurrence of directional selection for seed size. Although a significant trade-off between seed size and number is observed, its expression depends on life-history characteristics, and generally explains little variance. We conclude that the trade-off between seed size and number might have a minor role in explaining the maintenance of variation in seed size and number, and that seed size could be a valid target for selection.     

Population Structure in Daphnia Obtusa: Quantitative Genetic and Allozymic Variation

Quantitative genetic analyses for body size and for life history characters within and among populations of Daphnia obtusa reveal substantial genetic variance at both hierarchical levels for all traits measured. Simultaneous allozymic analysis on the same population samples indicate a moderate degree of differentiation: G(ST) = 0.28. No associations between electrophoretic genotype and phenotypic characters were found, providing support for the null hypothesis that the allozymic variants are effectively neutral. Therefore, G(ST) can be used as the null hypothesis that neutral phenotypic evolution within populations led to the observed differentiation for the quantitative traits, which I call Q(ST). The results of this study provide evidence that natural selection has promoted diversification for body size among populations, and has impeded diversification for relative fitness. Analyses of population differentiation for clutch size, age at reproduction, and growth rate indicate that neutral phenotypic evolution cannot be excluded as the cause.     

Habitat Suitability and Population Size Estimates for the Mongoose Lemurs (Eulemur mongoz) of Madagascar and the Comoro Islands,and Implications for Their Conservation

International Journal of Primatology - Tropical forests face an alarming rate of loss driven by anthropogenic pressures, exposing forest-dwelling species such as primates to extinction risks....     

Effect of Extra-Pair Paternity on Effective Population Size in a Reintroduced Population of the Endangered Hihi, and Potential for Behavioural Management

We collected genetic and behavioural data on hihi (Notiomysts cincta, an endangered New Zealand bird) after reintroduction to Mokoia Island to assess the effect of extrapair copulation on effective population size (N_e), and investigate the potential for increasing N_e through behavioural management. DNA fingerprinting revealed that 46% of chicks (n = 188) resulted from extra-pair paternity, and 82% of broods (n = 56) had at least one extra-pair chick. Of the extra-pair young, 34%(n = 89) were from unpaired males, and the remainder were from paired males. Variance in reproductive success (VRS) among individuals changed between years, and the relative variance among males and females depended on the sex ratio. VRS increased when measured over longer time scales, the variance in recruits being three times higher than the variance in the number of hatchlings. Extra-pair copulation increased VRS by 150% in 1 year and decreased it by 30% in another year, but this only caused a 4% decrease and 8% increase, respectively, to N_e/N. Although there is potential to manage VRS in this species through behavioural management, a more important factor is adult lifespan, which is the main correlate of lifetime reproductive success as well as the determinant of generation time. The high annual mortality rate in Mokoia hihi (females = 64%, males = 52%) has prevented the population from growing, so the key factors limiting N and N_e/N are the same.     

The Roles of Spatial Pattern and Size Variation in Shaping Height Inequality of Plant Population

Game-theoretic models predict that there is an ESS height for the plant population to which all individual plants should converge. To attain this conclusion, the neighborhood factors were assumed to be equal for all the individual plants, and the spatial pattern and size variation of population were left without consideration, which is clearly not right for the scenario of plant competition. We constructed a spatially-explicit, individual-based model to explore the impacts of spatial structure and size variation on individual plant’s height and population’s height hierarchies under the light competition. The monomorphic equilibrium of height that all the individual plants will converge to only exists for a population growing in a strictly uniform spatial pattern with no size variation. When the spatial pattern of the population is non-uniform or there’s size variation among individual plants, the critical heights that individual plants will finally reach are different from each other, and the height inequality at the end of population growth will increase when the population’s spatial pattern’s degree of deviation from uniform and population’s size variation increase. Our results argue strongly for the importance of spatial pattern and neighborhood effects in generating the diversity of population’s height growth pattern.     

Microsatellite Analysis of Genetic Variation and Population Subdivision for the Black Muntjac, Muntiacus crinifrons

The black muntjac (Muntiacus crinifrons) is a rare deer found only in a restricted region in east China. Recent studies of mitochondrial DNA diversity have shown a markedly low level of nucleotide diversity for the species, and the Suichang population was genetically differentiated from the two other populations, in Huangshan and Tianmushan mountains. In this study, we extended the analysis of genetic diversity and population subdivision for the black muntjac using data from 11 highly polymorphic nuclear DNA microsatellite loci. Contrary to the results based on mtDNA data, the microsatellite loci revealed that the black muntjac retained a rather high nuclear genetic diversity (overall average H (E) = 0.78). Nevertheless, both types of markers supported the idea that the extant black muntjac population is genetically disrupted (overall phi (ST) = 0.16 for mtDNA and overall F (ST) = 0.053 for microsatellite, both P < 0.001). The correlation between genetic differentiation and geographic distance was not significant (Mantel test; P > 0.05), implying that the patterns of genetic differentiation observed in this study might result from recent habitat fragmentation or loss. Based on the results from the mtDNA and nuclear DNA data sets, two management units were defined for the species, Huangshan/Tianmushan and Suichang. We also recommend that a new captive population be established with individuals from the Suichang region as a founder source.