Asian Elephants in China: Estimating Population Size and Evaluating Habitat Suitability

We monitored the last remaining Asian elephant populations in China over the past decade. Using DNA tools and repeat genotyping, we estimated the population sizes from 654 dung samples collected from various areas. Combined with morphological individual identifications from over 6,300 elephant photographs taken in the wild, we estimated that the total Asian elephant population size in China is between 221 and 245. Population genetic structure and diversity were examined using a 556-bp fragment of mitochondrial DNA, and 24 unique haplotypes were detected from DNA analysis of 178 individuals. A phylogenetic analysis revealed two highly divergent clades of Asian elephants, α and β, present in Chinese populations. Four populations (Mengla, Shangyong, Mengyang, and Pu’Er) carried mtDNA from the α clade, and only one population (Nangunhe) carried mtDNA belonging to the β clade. Moreover, high genetic divergence was observed between the Nangunhe population and the other four populations; however, genetic diversity among the five populations was low, possibly due to limited gene flow because of habitat fragmentation. The expansion of rubber plantations, crop cultivation, and villages along rivers and roads had caused extensive degradation of natural forest in these areas. This had resulted in the loss and fragmentation of elephant habitats and had formed artificial barriers that inhibited elephant migration. Using Geographic Information System, Global Positioning System, and Remote Sensing technology, we found that the area occupied by rubber plantations, tea farms, and urban settlements had dramatically increased over the past 40 years, resulting in the loss and fragmentation of elephant habitats and forming artificial barriers that inhibit elephant migration. The restoration of ecological corridors to facilitate gene exchange among isolated elephant populations and the establishment of cross-boundary protected areas between China and Laos to secure their natural habitats are critical for the survival of Asian elephants in this region.     

Insights into recently fragmented vole populations from combined genetic and demographic data

We combined demographic and genetic data to evaluate the effects of habitat fragmentation on the population structure of the California red-backed vole (Clethrionomys californicus). We analysed variation in the mitochondrial DNA (mtDNA) control region and five nuclear microsatellite loci in small samples collected from two forest fragments and an unfragmented control site in 1990-91. We intensively sampled the same forest fragments and two different control sites in 1998 and 1999. Vole abundances fluctuated greatly at sizes below 50 individuals per fragment. Fragment populations had significantly lower mtDNA allelic diversity than controls, but not nuclear heterozygosity or numbers of alleles. The use of only trapping and/or mtDNA marker data would imply that fragment populations are at least partially isolated and vulnerable to inbreeding depression. In contrast, the abundance estimates combined with microsatellite data show that small fragment populations must be linked to nearby forests by high rates of migration. These results provide evidence for the usefulness of combining genetic and demographic data to understand nonequilibrium population structure in recently fragmented habitats.     

The power of genetic monitoring for studying demography,ecology and genetics of a reintroduced brown bear population

Genetic monitoring has rarely been used for wildlife translocations despite the potential benefits this approach offers, compared to traditional field‐based methods. We applied genetic monitoring to the reintroduced brown bear population in northern Italy. From 2002 to 2008, 2781 hair and faecal samples collected noninvasively plus 12 samples obtained from captured or dead bears were used to follow the demographic and geographical expansion and changes in genetic composition. Individual genotypes were used to reconstruct the wild pedigree and revealed that the population increased rapidly, from nine founders to >27 individuals in 2008 (λ = 1.17–1.19). Spatial mapping of bear samples indicated that most bears were distributed in the region surrounding the translocation site; however, individual bears were found up to 163 km away. Genetic diversity in the population was high, with expected heterozygosity of 0.74–0.79 and allelic richness of 4.55–5.41. However, multi‐year genetic monitoring data showed that mortality rates were elevated, immigration did not occur, one dominant male sired all cubs born from 2002 to 2005, genetic diversity declined, relatedness increased, inbreeding occurred, and the effective population size was extremely small (Ne = 3.03, ecological method). The comprehensive information collected through genetic monitoring is critical for implementing future conservation plans for the brown bear population in the Italian Alps. This study provides a model for other reintroduction programmes by demonstrating how genetic monitoring can be implemented to uncover aspects of the demography, ecology and genetics of small and reintroduced populations that will advance our understanding of the processes influencing their viability, evolution, and successful restoration.     

Field surveys of capercaillie (<Emphasis Type="Italic">Tetrao urogallus</Emphasis>) in the Swiss Alps underestimated local abundance of the species as revealed by genetic analyses of non-invasive samples

An increasing number of species are becoming threatened by habitat loss and fragmentation. Therefore, solid estimates of the species’ abundance in the remaining populations are required to develop suitable conservation measures and to monitor their effectiveness. The capercaillie (Tetrao urogallus L.) has experienced a dramatic decline in central Europe and has disappeared from large areas of its former natural range. In Switzerland, the species’ distribution, habitat requirements and demographic status were studied and evaluated in an attempt to support appropriate management decisions to conserve the species. National surveys of the capercaillie in Switzerland have traditionally been obtained from male counts at leks. However, individual attendance to the lek is sex- and age-specific. Thus, male counts at leks may provide a biased estimate of local population sizes. In the present study, we compared two alternative indirect methods to estimate the sizes of local populations at eight study sites situated in the Alps and Prealps of Switzerland. We first assessed the sizes of local populations from the observed density and distribution of direct and indirect evidence of the species’ presence during field surveys. Feather and faeces samples collected during field surveys were genotyped at twelve nuclear microsatellite loci and a sex-specific nuclear gene fragment. Individual genotypes were used as genetic tags to estimate the sizes of the eight local populations using an urn model developed for small populations. The index of local population sizes assessed from field surveys was lower than the number of unique genotypes at each study site, which itself underestimated the abundances of populations in most cases. Based on our results, the genetic tagging method appeared to be less biased than the field survey method. However, an alternative faeces sampling scheme, resulting in 2–3 genotypings per individual, could further improve the accuracy of the size estimates of local populations. Our study confirms that genetic tagging methods are a valuable tool to estimate the sizes of local populations and to monitor the response of rare and elusive species to management actions.     

Single‐nucleotide polymorphism discovery and panel characterization in the African forest elephant

The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single‐nucleotide polymorphisms (SNPs) are particularly cost‐effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next‐generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double‐digest restriction‐site‐associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high‐quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step‐change in conservation policies for this elusive species.     

Effective population size and temporal genetic change in stream resident brown trout (Salmo trutta, L.)

Temporal genetic data may be used forestimating effective population size (N _e) and for addressing the `temporal stability' of population structure, two issues of central importance for conservation and management. In this paper we assess the amount of spatio-temporal genetic variation at 17 di-allelic allozyme loci and estimate current N _e in two populations of stream resident brown trout (Salmo trutta) using data collected over 20 years. The amount ofpopulation divergence was found to bereasonably stable over the studied time period.There was significant temporal heterogeneitywithin both populations, however, and N _e was estimated as 19 and 48 for the twopopulations. Empirical estimates of theprobability of detecting statisticallysignificant allele frequency differencesbetween samples from the same populationseparated by different numbers of years wereobtained. This probability was found to befairly small when comparing samples collectedonly a few years apart, even for theseparticular populations that exhibit quiterestricted effective sizes. We discuss someimplications of the present results for browntrout population genetics and conservation, andfor the analysis of temporal genetic change inpopulations with overlapping generations ingeneral.     

Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control region

Forest musk deer ( Moschus berezovskii ) were once distributed widely in China. However, wild populations have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic backgrounds of most captive populations were unclear and the population sizes increased very slowly. To provide useful information for conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 individuals, and the nucleotide and haplotype diversities were relatively high compared with those of other endangered mammals. Of the three investigated populations, the Maerkang population had the highest nucleotide diversity ( π  = 0.0568), haplotype diversity ( h  =   0.836) and average intra-population genetic distance (0.062). The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation of the three populations. Estimates of gene flow indicated that there were few genetic exchanges among the three populations. Building pedigree records and increasing gene flow between populations will be helpful for conserving these populations and this species.     

有性生殖对栗疫病菌群体结构的影响

采用RAPD方法对来源于栗疫病菌8个不同子囊壳的子囊孢子后代和无性生殖的对照群体各23个菌株进行了群体结构的比较。从RAPD随机引物中筛选出扩增多态性丰富的4条引物,共扩增出条带73条,多态性检测率为100%。研究结果表明,在8个子囊壳和无性生殖群体中的基因多样性,64.27%由群体内部引起,只有35.73%的多样性由群体之间的基因差异引起。各子囊壳群体间存在的基因流动很小(Nm=0.8994)。有性群体和无性群体之间的遗传距离为0.1389,基因流动值为3.4212,说明子囊壳群体和无性生殖群体之间存在一定的系统关系。分析表明栗疫病菌子囊孢子后代在自然界的传播对自然界的病菌的多样性起重要的作用。     

Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet

The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long‐term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage.     

Using genetic analysis to estimate population size,sex ratio,and social organization in an Asian elephant population in conflict with humans in Alur,southern India

With growing human and, possibly, elephant populations and a drastic increase in anthropogenic activities, human–elephant conflict in Asia has been on the rise. The Alur area in Karnataka state, southern India, is one such case in point, which has witnessed increasing levels of human–elephant conflict over the last two decades. The tiny, moderately protected habitat available for elephants in this human-dominated landscape does not appear to be able to support elephants over the long term. Options to deal with the escalating conflict include translocation of elephants, bringing elephants into captivity, and culling. We carried out a molecular genetic study of elephants in the Alur area to estimate the minimum number of elephants using the area, the sex ratio, genetic relatedness between individuals, and genetic structure with regard to the larger population in the landscape, so that informed management decisions could be made. Fresh dung samples were collected from the field and genotyped using 12 microsatellite loci. We found 29 unique individuals in the population, comprising 17 females and 12 males of different age classes. Relatedness between females suggested independent colonisations by discrete, small groups rather than by one cohesive clan of related females. This obviates the need for a single solution for dealing with all the females in the area in order to maintain social integrity, and has implications in terms how these elephants can be dealt with. We demonstrate how social organization inferred through molecular data from non-invasive sampling can inform management decisions.     

Genetic variation, genetic structure and effective population size in the tropical holoparasitic endophyteBdallophyton bambusarum (Rafflesiaceae)

The genetic population structure inBdallophyton bambusarum, an endoparasite, was studied in ten subpopulations from a subdeciduous tropical forest in Veracruz Mexico. The sample was analyzed using seven polymorphic loci in cellulose acetate electrophoresis. Isozyme data indicated that the subpopulations ofB. bambusarum contained high genetic variability (H_ep = 0.452 ± 0.045, S.E.). Our analysis suggests that almost each inflorescence ofB. bambusarum is an individual. The subpopulations studied were genetically similar (average Nei's genetic identity 0.941 ± 0.051 and F _st values 0.097 ± 0.026), suggesting that genetic differentiation among subpopulations was small. Direct estimates of effective population size was derived from observations of three fluorescent dyes, and from the genetic neighborhood area derived from these data. The neighborhood area, multiplied by the total density of individuals, gave an N_e = 124.84 plants, and when corrected to consider the proportion of males and females gave an N_e = 118.59 individuals. An indirect estimate of Nm was obtained from the F _st values (mean Nm=2.037), giving an indirect estimate of the effective population size N_b = 12.8 individuals. Both values are relatively high when compared to other plant studies. The gene flow and/or effective populations size of the studied subpopulations ofB. bambusarum are believed to be large enough to prevent differentiation among subpopulations due to genetic drift.     

Plant species diversity and composition of experimental grasslands affect genetic differentiation of Lolium perenne populations

Contrasting hypotheses exist about the relationship between plant species diversity and genetic diversity. However, experimental data of species diversity effects on genetic differentiation among populations are lacking. To address this, Lolium perenne was sown with an equal number of seeds in 78 experimental grasslands (Jena Experiment) varying in species richness (1, 2, 4, 8 to 16) and functional group richness and composition (1-4; grasses, legumes, small herbs, tall herbs). Population sizes were determined 4years after sowing, and single-nucleotide polymorphism (SNP) DNA markers based on bulk samples of up to 100 individuals per population were applied. Genetic distances between the field populations and the initially sown seed population increased with sown species richness. The degree of genetic differentiation from the original seed population was largely explained by actual population sizes, which suggests that genetic drift was the main driver of differentiation. Weak relationships among relative allele frequencies and species diversity or actual population sizes, and a positive correlation between actual population sizes and expected heterozygosity also supported the role of genetic drift. Functional composition had additional effects on genetic differentiation of L. perenne populations, indicating a selection because of genotype-specific interactions with other species. Our study supports that genetic diversity is likely to be lower in plant communities with a higher number of interspecific competitors. Negative effects of species richness on population sizes may increase the probability of genetic drift, and selection because of genotype-specific interactions depending on species and genotypic community composition may modulate this relationship.     

Impact of population bottlenecks on genetic variation and the importance of life-history; a case study of the northern elephant seal

This paper reviews some of the important factors related to the impact of population bottlenecks, using the northern elephant seal (Mirounga angustirostrus) as a case study for illustration. The northern elephant seal was hunted extensively in the 19th century and forced through a bottleneck of approximately 10–20 seals. All measures of molecular genetic variation show current levels for the northern elephant seal to be low. Levels of genetic variation were compared with expectations based on a simulation model that recapitulates demographic growth, based on age-specific data on reproduction and mortality. Predictions from the simulation model are then presented to illustrate the importance of differences in life-history strategy and skewed reproductive success. Either high reproductive skew (e.g. polygyny) or a low growth rate in a population can increase the impact of a bottleneck on molecular variation. Severe population bottlenecks can also disrupt aspects of developmental stability and thereby increase the fluctuating asymmetry and variability of quantitative traits. A comparison of skulls collected before and after the bottleneck showed this to have occurred for some elephant seal quantitative characters.     

Estimates of Gene Flow in Drosophila Pseudoobscura Determined from Nucleotide Sequence Analysis of the Alcohol Dehydrogenase Region

The genetic structure of Drosophila pseudoobscura populations was inferred from a nucleotide sequence analysis of a 3.4-kb segment of the alcohol dehydrogenase (Adh) region. A total of 99 isochromosomal strains collected from 13 populations in North and South America were used to determine if any population departed from a neutral model and to estimate levels of gene flow between populations. This study also included the nucleotide sequences from two sibling species, D. persimilis and D. miranda. We estimated the neutral mutation parameter, 4N mu, in synonymous and noncoding sites for 17 subregions of Adh in each of nine populations with sample sizes greater than three. The nucleotide diversity data in the nine populations was tested for departures from an equilibrium neutral model with two statistical tests. The Tajima and the Hudson, Kreitman, Aguade tests showed that each population fails to reject a neutral model. Tests for genetic differentiation between populations fail to show any population substructure among the North American populations of D. pseudoobscura. The nucleotide diversity data is consistent with direct and indirect measures of gene flow that show extensive dispersal between populations of D. pseudoobscura.     

Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales

Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study, we assess the population genetic structure of the orange coral Astroides calycularis in the Alboran Sea at local and regional scale, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and D(est) statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as 1 km and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.     

基于高密度SNP数据的东亚人群遗传结构研究

目的 东亚疆域辽阔,民族众多,有着广泛多样的语言。中国34个省级行政区可划分为7个地理分区,人群主要分属世界七大语系。已有研究主要集中在东亚人群的起源、迁徙、融合等遗传历史。本文基于5 147份世界人群个体的高密度单核苷酸多态性（SNP）数据,从地域及语言两个角度研究东亚人群尤其是中国人群与世界其他人群的遗传关系,研究中国人群的遗传关系和遗传结构。方法 收集了5 147份世界人群个体的高密度SNP数据,并对其进行质控、合并。通过频率差异分析方法对最终获得的32 789个SNP进行统计学检验,并进一步使用主成分分析、系统发育树、祖先成分分析和D检验统计等方法,对东亚人群与世界其他人群的遗传关系,以及中国人群的遗传关系和遗传结构进行研究。结果 研究发现东亚人群与非洲、美洲和欧洲人群存在显著差异。中国人群可分为7个亚群,不同人群间的遗传聚类与其地理分布、语系语族和族源历史有很强的相关性。结论 本文研究了中国人群与世界人群的遗传关系和差异,并系统研究了中国人群的遗传亚结构。这将丰富东亚人群的群体遗传学、法医遗传学等研究基础,为个体化医疗等工作提供数据支撑。     

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.     

Impact of a population bottleneck on symmetry and genetic diversity in the northern elephant seal

Abstract The northern elephant seal (NES) suffered a severe population bottleneck towards the end of the nineteenth century. Theoretical expectations for the impact of population bottlenecks include the loss of genetic diversity and a loss of fitness (e.g. through a disruption of developmental stability); however, there are few direct demonstrations in natural populations. Here, we report on the comparison of archive samples collected prior to and following the NES population bottleneck. Measures of genetic diversity show a loss of variation consistent with expectations and suggest a strong disruption in the pattern of allele frequencies following the bottleneck. Measures of bilateral characters show an increase in fluctuating asymmetry.     

Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data

Inbreeding depression, which refers to reduced fitness among offspring of related parents, has traditionally been studied using pedigrees. In practice, pedigree information is difficult to obtain, potentially unreliable, and rarely assessed for inbreeding arising from common ancestors who lived more than a few generations ago. Recently, there has been excitement about using SNP data to estimate inbreeding (F) arising from distant common ancestors in apparently "outbred" populations. Statistical power to detect inbreeding depression using SNP data depends on the actual variation in inbreeding in a population, the accuracy of detecting that with marker data, the effect size, and the sample size. No one has yet investigated what variation in F is expected in SNP data as a function of population size, and it is unclear which estimate of F is optimal for detecting inbreeding depression. In the present study, we use theory, simulated genetic data, and real genetic data to find the optimal estimate of F, to quantify the likely variation in F in populations of various sizes, and to estimate the power to detect inbreeding depression. We find that F estimated from runs of homozygosity (Froh), which reflects shared ancestry of genetic haplotypes, retains variation in even large populations (e.g., SD=0.5% when Ne=10,000) and is likely to be the most powerful method of detecting inbreeding effects from among several alternative estimates of F. However, large samples (e.g., 12,000-65,000) will be required to detect inbreeding depression for likely effect sizes, and so studies using Froh to date have probably been underpowered.     

Mitochondrial DNA genealogy of chimpanzees in the Nimba mountains and Bossou, West Africa

The chimpanzee populations of the Bossou and Nimba regions in West Africa were genetically surveyed to 1) reveal the genetic relationship between the Bossou and Nimba populations, and 2) elucidate the evolutionary relationship between the Bossou-Nimba and other West African populations. The chimpanzee group at Bossou is characterized by its small population size, no evidence of contact with neighboring populations, and no female immigration. It is believed that most females and adolescent males emigrate from this population. To reveal the genetic signature of these characteristics, we examined the genetic diversity of Bossou and two neighboring populations (Seringbara and Yealé) in the Nimba Mountains by sequencing approximately 605 bp of the mitochondrial DNA (mtDNA) control region. A total of 20 distinct mtDNA variants were observed from 56 sequences of noninvasively collected, anonymous samples. Nucleotide diversity in the Nimba Mountain populations was 0.03-0.04, and did not differ significantly from that in the Bossou population. Very few mitochondrial variants are shared among the sites sampled, which suggests that there is little gene flow involving mtDNA. Nevertheless, no clear population structures were revealed in either population. A comparison with published sequences from West African chimpanzees (Pan troglodytes verus) indicates that the variants observed in the Bossou and Nimba regions are scattered throughout the subspecies, rather than clustered according to geographic region. This suggests that the Bossou-Nimba populations derived only recently from the common ancestral population of the West African chimpanzees, and did not pass through a bottleneck.