Genetic differences between the two remaining wild populations of the endangered Indian rhinoceros (Rhinoceros unicornis)

The management of rare and endangered species in the wild and in captivity requires an understanding of the characterization of the genetic units within each species and their relationships to each other. The Indian rhinoceros (Rhinoceros unicornis) is an endangered species with a current population size of c. 2800 individuals. We analyzed 26 individuals of known origin kept in captivity and 21 wild ranging individuals of the two remnant large wild populations in Assam (India) and Nepal employing mitochondrial and microsatellite markers to determine whether the two geographically isolated populations show distinct patterns of genetic diversity, and whether the genetic diversity of the populations is influenced by past demographic bottlenecks. We identified 10 different mitochondrial D-loop haplotypes, of which 4 were specific to the Assam population (10 sequences examined) and 6 specific to the Nepal population (19 sequences). Similarly, the microsatellite analysis demonstrated a strong genetic differentiation between the Assam and Nepal populations and allowed to assign each individual to its origin with high confidence. Furthermore, our analyses revealed the occurrence of a bottleneck in the Assam population long before the reported bottleneck in 1908, and it revealed that the Nepal population is a recent (probably post-glacial) colonization. In summary, the extent of genetic divergence between the two remnant R. unicornis populations suggests separate conservation programs (even for captive individuals) as long as the persistence of the entire species is not severely threatened. The microsatellite markers can also be used to determine the origin of confiscated material such as horns.     

Genetic consequences of animal translocations: A case study using the field cricket, Gryllus campestris L.

Animal relocations have become a common tool in nature conservation, but the genetic consequences of such projects have rarely been studied in insects. As both natural and artificial formation of new populations may lead to genetic drift (founder effect), decreased genetic diversity and increased rates of inbreeding, genetic analyses can provide valuable information to evaluate the success of a relocation project. The field cricket (Gryllus campestris) has been subjected to reintroduction and translocation projects in England and northern Germany. Here, we present a microsatellite study on the population genetics of one recently established population of this species in comparison with several older populations and some recently colonized sites. Our results show that the translocation did not result in a significant loss of genetic diversity, when compared to source and other natural populations suggesting that translocation of a high number of nymphs from different subpopulations may be a suitable method to decrease the loss of genetic diversity and reduce the risk of inbreeding. Furthermore, the translocation had no negative effect on the source population, which reached a new maximum population size in 2006. An assignment test showed that individuals from the translocated population (F4 generation) were still assigned to the source populations, whereas two young subpopulations that originated by natural colonization from the central population about ten years ago already formed separate genetic clusters. As the strong fragmentation of G. campestris populations in northern Germany hampers natural colonization of newly created potential habitats, translocation projects seem to be an appropriate method to preserve this species.     

Genetic consequences of intensive management in game birds

Introduction of wildlife for game restocking is one major pathway of genetic homogenization. The red-legged partridge (Alectoris rufa, Phasianidae), a small game bird native to south-western Europe, is in high demand by hunters and natural populations are constantly supplemented by commercial stocks of captive-bred individuals. Also, in recent years human-mediated hybridization with congeneric chukar partridges (Alectoris chukar: Greece, Cyprus, from Middle East to East Asia) has been frequently documented in the wild and in captivity. This study attempts to evaluate the genetic consequences of intensive captive breeding and restocking in the A. rufa species. We investigated A. rufa genetic diversity by making comparisons in both a spatial (across the entire species’ range) and a temporal framework. We accomplished this latter by comparing modern vs. ancient partridges resident in museums and collected 1856-1934, well before supplemental stocking became common. Using mtDNA we found significant changes in the haplotype profile of modern vs. ancient A. rufa, and widespread introgression with chukar genes across the entire species range only in modern representatives, with the relevant exception of Corsican populations. However, Random Amplified Polymorphic DNA (RAPD), as opposed to microsatellite DNA markers, showed also modern Corsican populations to harbour many A. rufa × A. chukar hybrids. We conclude that captive breeding programs should make strict use of time-saving and comparatively low cost DNA barcodes to minimize genetic pollution, such as those provided by diagnostic RAPD markers. We also recommend that the active ban on import of exotics and/or hybrids be extended to non-local populations. Altogether this would represent a substantial step forward to preserve A. rufa as well as other game species subjected to similar intensive management.     

Identifying unique populations in long-dispersal marine species: Gulfs as priority conservation areas

Identification of areas which should be a subject of protection is crucial for safeguarding the marine ecosystems. Amongst the reasons for protecting a region or location, the existence of unique populations or evolutionary significant units for one or more key species is a priority. The North American silver hake, Merluccius bilinearis, is currently managed as two stocks (northern and southern) without considering gulf areas separately. Employing microsatellite and mitochondrial markers we have detected significant F_ST values between hake individuals inhabiting gulfs and those distributed in the open sea, and asymmetric gene flow, higher from the gulf to the open sea than in the opposite direction. These differences can be interpreted as signals of separate populations in gulfs which may act as sources of variability for hake species. Occurrence of similar phenomena in Atlantic waters in both the northern and the southern Hemisphere, for these two pelagic–demersal hake species, suggests that gulfs may constitute a target for designing marine protected areas and confirms the adequacy of gulf-specific management already employed in Argentina.     

中华鳖5个群体遗传多样性的微卫星分析

利用微卫星分子标记技术对洞庭（DT）、黄河（HH）、黄沙（HS）、日本（RB）以及洞庭（DT）与黄河（HH）的杂交子代（DT♀×HH♂）绿卡（LK）5个中华鳖群体的150个个体进行遗传多样性分析。11对微卫星引物扩增出的等位基因数为3～6个,平均等位基因数为4.1818。5个种群相比,绿卡（LK）的平均有效等位基因数、平均期望杂合度、平均观测杂合度和平均多态信息含量最高,分别是2.3969、0.5274、0.5545和0.4660。对种群间的遗传分化分析表明,黄河（HH）和洞庭（DT）之间的遗传分化最小,为0.0233,而洞庭（DT）和日本（RB）之间的遗传分化最大,为0.0969。基于Nei＇s遗传距离构建的UPGMA系统进化树显示黄河（HH）和洞庭（DT）及其子代绿卡（LK）亲缘关系较近,而与黄沙（HS）和日本（RB）的亲缘关系较远,最远的为日本（RB）群体。     

Linking the gaps between conservation research and conservation management of rare dipterocarps: A case study of Shorea lumutensis

To conserve a rare plant, conservation programs must be guided by the biological attributes of the species. What constitutes the most critical biological information for plant conservation has been the issue of discussion for the last 30 years. Most scientists promote an approach that is either ecological or genetic in emphasis. Ecological and genetic processes will often interact synergistically to influence the population viability and to determine the persistence of populations in the long run. Consequently, conservation management of plant species, in addition to ecological information, requires a robust understanding of underlying genetic processes as well as the variation within and between populations. Conservation has a cost and the resources available for conservation programs are always limited. Therefore, conservation management strategies should not only be scientifically justified but also practical in terms of resource availability. Shorea lumutensis is a rare and endemic dipterocarp in Peninsular Malaysia. A comprehensive research activity was initiated to assess the population ecology and population genetics of S. lumutensis to elucidate specific ecological and genetic requirements and subsequently to set conservation strategies and priorities. This paper is apparently the first attempt at applying both the ecological and genetic approaches into conservation management of a rare dipterocarp. In addition, this paper also attempts to link the gaps between conservation research and conservation management in a realistic manner. It is our hope that this study will serve as a model for the study of other rare dipterocarps which should be given priority for conservation.     

DNA barcoding for conservation and management of Amazonian commercial fish

DNA barcoding is used to assign a biological specimen to a species. DNA-based procedure has become the preferred forensic tool for criminal prosecution in cases involving the sale of incorrectly identified food. The aim of this work was to develop a DNA-based marker for allowing an accurate and reliable identification of Amazonian fish species of commercial interest. For this purpose, we extracted DNA from fish directly purchased in local markets and identified de visu by local experts. We PCR amplified the mitochondrial 12S rRNA and cytochrome oxidase I (COI) genes. Twenty-nine commercial species accounting for most commercial landings in the River Amazon markets were unambiguously identified based on their DNA for the first time. Phylogenetic trees reconstructed based on the sequences of the two mitochondrial genes clustered species in concordance with their taxonomic classification. We illustrated the utility of DNA barcoding demonstrating that the group of fish generically sold as “Acará” includes seven different species, which are being exploited together as a single species, thus estimation of exploitation rates was not possible until now. Application of genetic markers for species authentication in markets and control of commercial landings will contribute to recognition of the real fishing targets and to the conservation of fish resources in the Amazon basin.     

Genetic structure, population dynamics, and conservation of Black caiman (Melanosuchus niger)

Microsatellite DNA polymorphisms were screened in seven populations of the largest Neotropical predator, the Black caiman Melanosuchus niger (n = 169), originating from Brazil, French Guiana and Ecuador. Eight loci were used, for a total of 62 alleles. The Ecuadorian population had the lowest number of alleles, heterozygosity and gene diversity; populations of the Guianas region exhibited intermediate diversities; highest values were recorded in the two populations of the Amazon and Rio Negro. During the last century Melanosuchus populations have been reduced to 1-10% of their initial levels because of hunting pressure, but no strong loss of genetic diversity was observed. Both the inter-locus g-test and the Pk distribution suggested no recent important recovery and/or expansion of current populations. On a global scale, the inter-population variation of alleles indicated strong differentiation (F_ST = 0.137).Populations were significantly isolated from each other, with rather limited gene flow; however, these gene flow levels are sufficiently high for recolonization processes to effectively act at regional scales. In French Guiana, genetic structuring is observed between populations of two geographically close but ecologically distinct habitats, an estuary and a swamp. Similar divergence is observed in Brazil between geographically proximate “black water” and “white water” populations. As a consequence, the conservation strategy of the Black caiman should include adequate ecosystem management, with strong attention to preservation of habitat integrity. Distribution of genetic diversity suggests that current populations originated from the central Amazonian region. Dispersal of the species may thus have been deeply influenced by major climatic changes during the Holocene/Pleistocene period, when the Amazonian hydrographic networks were altered. Major ecological changes such as glaciations, marine transgressions and a hypothesized presence of an Amazonian Lake could have resulted in extension of Black caiman habitats followed by isolation.     

What genetics tell us about the conservation of the critically endangered Balearic Shearwater?

The Balearic shearwater Puffinus mauretanicus is one of the most critically endangered seabirds in the world. The species is endemic to the Balearic archipelago, and conservation concerns are the low number of breeding pairs, the low adult survival, and the possible hybridization with a sibling species, the morphologically smaller Yelkouan shearwater (P. yelkouan). We sampled almost the entire breeding range of the species and analyzed the genetic variation at two mitochondrial DNA regions. No genetic evidence of population decline was found. Despite the observed philopatry, we detected a weak population structure mainly due to connectivity among colonies higher than expected, but also to a Pleistocene demographic expansion. Some colonies showed a high imbalance between immigration and emigration rates, suggesting spatial heterogeneity in patch quality. Genetic evidence of maternal introgression from the sibling species was reinforced, but almost only in a peripheral colony and not followed, at least to date, by the spread of the introgressed mtDNA lineages. Morphometric differences were not correlated with mtDNA haplotypes and introgression is probably due to a secondary contact between the two species several generations ago. Overall, results suggested that the very recent demographic decline in this critically endangered species has not yet decreased its genetic variability, and connectivity found among most colonies should help to reduce species extinction risk. Spreading of introgression should be monitored, but the species is not jeopardized at the moment by genetic factors and the major conservation actions should concentrate at enhancing adult survival.     

Challenges and opportunities of genetic approaches to biological conservation

I discuss future challenges and opportunities in genetic approaches to biodiversity conservation. Resolving taxonomy uncertainties and identifying diverged evolutionary units within species are both bedevilled by a plethora of definitions: the challenge for the conservation community is to come to an agreed definition of species and for a unit within species for conservation purposes. For genetic management in the wild, the main challenge is to apply well-established genetic principles to management, especially of fragmented populations. Fears about outbreeding depression are preventing rational use of gene flow for genetic rescue; predicting the risk of outbreeding depression is the most important unmet scientific challenge in the field. The major challenge in genetic management of captive populations of threatened animal species is to institute explicit management to minimize genetic adaptation to captivity, so that reintroduction success is maximized. The development of low cost genome sequencing offers many research opportunities and challenges. For example, there are opportunities to identify genes involved in speciation and a major challenge is to devise molecular tests to predict reproductive isolation between populations. Genomics offers opportunities to provide higher precision estimate for many parameters of importance to conservation. A major challenge is to devise means to assess, on a genome-wide basis, genetic diversity that is important to adaptive evolution. There is a challenge to develop simple inexpensive means to monitor genetic diversity of species on a global scale. Many of the most important practical challenges concern application of current genetic knowledge to the management of threatened species.     

Genetic diversity and relatedness of boreal caribou populations in western Canada

We studied genetic diversity within and gene flow among six ‘threatened’ populations of boreal caribou (Rangifer tarandus caribou) inhabiting Alberta and British Columbia, Canada. Mean expected heterozygosity (H_E) across 11 loci spanned a narrow range between 0.74 and 0.79. Estimates of H_E were in the mid to high range of those typically observed in natural populations of large mammals, including caribou, and were not suggestive of any immediate threat to survival. We concluded that recent anthropogenic fragmentation of caribou range in western Canada has yet to affect genetic diversity of populations. Analysis of population structure identified a region of relatively low gene flow corresponding with the valley of the Peace River. The highest value of F_ST observed between populations on the same side of the river was 0.025, whereas the lowest value that spanned the river was 0.044. Confirming this result, an assignment test demonstrated that 96.5% of animals could be assigned to the correct side of the Peace River, though only 66.0% of animals could, on average, be assigned to populations of actual origin. Taken as a whole, our results support the existence of two discrete metapopulations bisected by the Peace River, within each of which there exist multiple populations, or at least multiple regions, which experience considerably higher levels of interchange. For caribou inhabiting the boreal plains, large rivers such as the Peace and Mackenzie may serve as biologically meaningful boundaries for managing metapopulations.     

秦巴山区黄牛群体的微卫星DNA遗传多样性

为分析秦巴山区西镇牛、赤崖牛、陨巴牛和宣汉牛4个黄牛(Bos taurus)品种的遗传多样性,本研究以蜀宣花牛和郏县红牛作对照,利用12对微卫星引物对6个黄牛品种的289头黄牛个体进行了遗传多样性检测,统计了各品种的等位基因及频率、有效等位基因数、遗传杂合度、多态信息含量及各群体间遗传距离,并对其进行聚类分析.结果表明,6个黄牛品种在12个微卫星位点共发现110个等位基因,等位基因频率为0.001 6～0.517 3,总群体各位点平均有效等位基因数为2.787 7～7.132 6;各位点多态信息含量为0.5192～0.895 3;平均杂合度为0.667 2～0.724 1.群体间发现特有等位基因11个,基因频率为0.008 1～0.381 6;优势等位基因(P＞0.4) 19个,基因频率为0.403 2～0.820 0;共有等位基因41个,占全部等位基因的37.27％,仅有13个共有等位基因为优势等位基因(P＞0.4),占37.71％.群体间Nei's遗传一致度为0.596 5～0.840 8,标准遗传距离(Ds)为0.173 5～0.524 7.聚类分析结果显示,6个黄牛品种聚为3类,陨巴牛与宣汉牛首先聚在一起,然后同西镇牛聚在一类;赤崖牛与郏县红牛聚为一类;蜀宣花牛自成一类.研究结果表明,12对微卫星标记可用于秦巴山区黄牛遗传多样性的分析,秦巴山区各黄牛品种遗传多样性丰富,选育程度不同,4个黄牛品种虽然地理分布格局相近,自然环境相似,但亲缘关系并非相近,应为来源不同的品种.因此,西镇牛、赤崖牛、陨巴牛和宣汉牛不宜合并为1个品种.本研究所揭示的秦巴山区黄牛品种的遗传分化特点及亲缘关系,为研究品种的遗传共适应特点,预测杂交优势,制定育种战略等提供了科学依据.     

Relationship between population size and genetic diversity in endangered populations of the European bullhead (Cottus gobio): implications for conservation

This study investigated the relationship between the current size of endangered bullhead (Cottus gobio) populations and microsatellite genetic variability. Additionally, the microsatellite data were used to evaluate whether a genetic test for population bottlenecks was able to provide evidence of recent severe population declines. Finally, our results were used to develop conservation priorities and measures. Population size appears to be a crucial parameter in determining the amount of genetic diversity that can be preserved in bullheads, since a significant positive correlation was observed between both variables. Furthermore, in some populations we were able to detect genetic signatures of the documented decline in population size. We suggest that the most immediate goal for bullhead conservation should be to increase the size and the range of the populations, and in doing so minimise or even reverse further genetic erosion. Potential management actions like habitat quality improvement, reduction of river fragmentation and supplementation programmes (translocation, supportive breeding) are discussed.     

RFLP analysis of the mitochondrial DNA of otters (Lutra lutra) from Europe—implications for conservation of a flagship species

The distribution of otters (Lutra lutra) in Europe is largely fragmented, mainly due to historic anthropogenic causes. Nevertheless, in eastern Germany a large coherent area is inhabited by a viable otter population. In this paper, the mitochondrial genome of 81 otters is studied by RFLP analysis of PCR-amplified 1.5 and 2.5 kb long fragments, particularly to estimate the amount of genetic variability of European otters, and to identify possible geographical population subsets for conservation management. No restriction site polymorphism was detected within the control region (1.5 kb), but polymorphism of cleaving sites in the 2.5 kb fragment could be assigned to three haplotypes. Two occurred exclusively in a comparatively small area northwest and west of Berlin, which may be considered a region of increased genetic variability in otters. The low level of mtDNA variability in European otters might be due to genetic drift in postglacial founder populations with long-term low densities, and continuous historical overhunting.     

Conservation genetics and ecology of Angiopteris chauliodonta Copel. (Marattiaceae), a critically endangered fern from Pitcairn Island, South Central Pacific Ocean

Angiopteris chauliodonta, endemic to remote Pitcairn Island, was until recently thought to occur in only two small populations. Survey work carried out on the island in 1997 increased the number of populations to six, but as the total number of plants found was 774 (of which only 147 were mature adults) the species should be regarded as critically endangered. The species occurred in native fern-rich Homalium taypau and Metrosideros collina forest that was in many areas heavily invaded by Syzygium jambos and Lantana camara. RAPD analysis identified related populations but there was no correlation between genetic and geographical distance. The highest levels of genetic diversity was partitioned within populations (H_S=0.154; D_ST=0.116), although the larger populations were not necessarily the most diverse. Threats are primarily due to forest clearance, invasive species and erosion. Conservation management for this species will be through reinforcement of existing populations to maximise their genetic diversity and translocation of new populations to suitable habitats.     

RAPD-based Analysis of Genetic Diversity and Selection of Lingonberry (<Emphasis Type="Italic">Vaccinium vitis-idaea</Emphasis> L.) Material for <Emphasis Type="Italic">ex situ</Emphasis> Conservation

Random amplified polymorphic DNA markers were used to assess relatedness and genetic diversity for 15 lingonberry (Vaccinium vitis-idaea) populations. Seven primers yielding 59 polymorphic bands were used to analyse 13 populations, representing ssp. vitis-idaea from Sweden, Finland, Norway, Estonia and Russia, and two populations, representing ssp. minus from Japan and Canada. A cluster analysis and a multidimensional scaling analysis (MDS) showed similar phenetic patterns among populations, with a pronounced geographic grouping in most cases. Significant correlations were obtained between geographic and genetic distances for the entire set of populations as well as for the 13 ssp. vitis-idaea populations. Mean within-population diversity was 0.206 when estimated with Lynch and Milligan's index, and 0.431 when estimated with Shannon's index, which is in agreement with the mixed mating system reported for lingonberry. Within-population variability accounted for 68.6% of the total variance when all populations were included, and for 78.8% when only populations of ssp. vitis-idaea were analysed. Two different approaches were applied to the selection of plant material for a potential gene bank: (1) a hierarchical sampling strategy based on a cluster analysis and (2) the Maximum genetic diversity program, developed for the establishment of core collections. Random sampling was undertaken for comparisons with the selected data sets. The most diverse and representative set of lingonberry specimens was obtained when samples were selected with the Maximum diversity program.     

Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation

The endangered fish species Anaecypris hispanica is restricted to eight disjunct populations in the Portuguese Guadiana drainage. The genetic structure of these populations was studied in order to determine levels of genetic variation within and among populations and suggest implications for conservation of the species. Based on five microsatellite loci, the null hypothesis of population homogeneity was tested. Tests for genetic differentiation revealed highly significant differences for pairwise comparisons between all populations, and substantial overall population subdivision (F_ST=0.112). All sampled populations contained unique alleles. Our findings indicate marked genetic structuring and emphasise limited dispersal ability. The high levels of genetic diversity detected within and among A. hispanica populations suggest, however, that the observed fragmentation and reduction in population size of some populations during the last two decades, has impacted little on levels of genetic variability. Data imply that most A. hispanica populations should be managed as distinct units and that each has a high conservation value containing unique genetic variation. It is argued that geographic patterns of genetic structuring indicate the existence of eight management units.     

Extreme population divergence and conservation implications for the rare endangered Atlantic Forest sloth, Bradypus torquatus (Pilosa: Bradypodidae)

The maned sloth (Bradypus torquatus) is an endangered species endemic to the Atlantic Forest of eastern Brazil. This biome has been reduced to 7% of its original extent and the remaining forests are highly fragmented. We analyzed 70 samples from the largest remnant populations in the states of Bahia, Espírito Santo and Rio de Janeiro to characterize their geographic structure and to produce estimates of genetic diversity. The analysis indicated that the remnant populations are reproductively isolated and extremely divergent. The populations present a very discontinuous distribution, with divergent genetic clusters specific to different geographical regions, probably caused by allopatric fragmentation. This pattern is likely related to Pleistocenic climatic and vegetation changes, and indicates the presence of at least two independent evolutionary units. The analyses also indicate that populations separated by more than 100 km should be considered different management units. Thus, devastation of the Atlantic Forest leads to an unrecoverable loss of genetic diversity in this species. These conclusions should direct conservation actions aimed at preserving the distinctiveness of each evolutionary unit, as well as to preserve the demographic isolation of different management units.     

The potential contribution of ecotourism to African wild dog Lycaon pictus conservation in South Africa

African wild dogs are endangered, and in South Africa as elsewhere, they inhabit a fraction of their former range. In this study, we assessed the potential for economic benefits derived from ecotourism to offset the costs of three wild dog conservation options using a contingent valuation study of the willingness of visitors to four protected areas to pay to see wild dogs at the den - within a viable population in a large protected area (Kruger National Park), through reintroduction into nature reserves, and through the conservation of wild dogs occurring on ranchland in situ. Results indicated that tourism revenue from wild dogs in large protected areas is more than sufficient to offset the costs and could potentially be used to subsidise wild dog reintroductions or the conservation of wild dogs in situ on ranchland. On ranchland and for reintroductions, tourism revenue was generally predicted to offset most of the costs of conserving wild dogs where predation costs are low, and to exceed the costs where willingness to pay is high, and/or where the costs of predation by wild dogs are zero. Conservation efforts should facilitate the derivation of eco-tourism-related benefits from wild dogs on ranchland and in private reserves to create incentives for wild dog conservation. Ecotourism should be part of a multifaceted approach to wild dog conservation which also includes education and awareness campaigns, and efforts to encourage landowners to cooperate to form conservancies.     

Flock size and human disturbance affect vigilance of endangered red-crowned cranes (Grus japonensis)

Vigilance is used to detect predators and monitor rivals. We studied red-crowned cranes (Grus japonensis) in Yancheng Biosphere Reserve, China, to examine changes in the allocation of time to vigilance as a function of flock size in areas with different levels of human disturbance. There was low level of human activity in the core area of the reserve whereas more human activity occurred in the buffer zone. Vigilance decreased linearly with flock size but to significantly different extent in the two areas, with a more pronounced decrease in the more disturbed area. In smaller crane flocks, vigilance was higher in the more disturbed area. Vigilance also varied in a non-linear fashion with flock size first decreasing and then increasing in larger flocks. Increase in vigilance in larger flocks was accompanied by an increase in fighting suggesting that vigilance in large flocks was aimed partly at monitoring rivals. The effect of human disturbance on vigilance suggests that less time is available for foraging in more disturbed areas. Nevertheless, moving to less disturbed areas may not be an option for the cranes given the increase in vigilance that would probably occur in areas with more cranes.