Conservation genetics in a globally changing environment: present problems,paradoxes and future challenges

Despite recent advances in conservation genetics and related disciplines and the growing impact that conservation genetics is having in conservation biology, our knowledge on several key issues in the field is still insufficient. Here we identify some of these issues together with addressing several paradoxes which have to be solved before conservation genetics can face new challenges that are appearing in the transitory phase from the population genetics into the population genomics era. Most of these issues, paradoxes and challenges, like the central dogma of conservation genetics, the computational, theoretical and laboratory experiment achievements and limitations in the conservation genetics field have been discussed. Further knowledge on the consequences of inbreeding and outbreeding depression in wild populations as well as the capacity of small populations to adapt to local environmental conditions is also urgently needed. The integration of experimental, theoretical and applied conservation genetics will contribute to improve our understanding of methodological and applied aspects of conservation genetics.     

Population genetics of threatened wild plants in Japan

Approximately one-fourth of Japan's native plant species are threatened with extinction. To conserve these species, it is critical to evaluate genetic diversity at species-level and population-level. Some factors, including population size and geographic distribution, are known to influence the population genetic diversity of wild plant species. This article briefly reviews the population genetic studies that have been conducted on wild threatened plants in Japan. A large population size or wide geographic distribution does not always lead to large genetic diversity, suggesting that historical factors such as speciation processes and population expansion often play more important roles in determining genetic diversity than the number of remnant individuals. The mating system of a species also affects genetic diversity; predominantly selfing species tend to have smaller genetic diversity than outcrossing congeners. Another issue of concern in the conservation genetics of wild plants in Japan is the genetic diversity of insular endemics, because Japan consists of many islands, and the insular flora contains many endemic and threatened species. Previous studies on endemic plants on the Bonin and the Ryukyu Islands are reviewed. Compared to the cases of the Bonin Islands or other oceanic islands, there is much larger genetic diversity in plants endemic to the Ryukyu Islands. This difference is probably the result of the differences in the geological history of these islands. Electronic Publication     

金沙江河谷特有植物罂粟莲花的保护遗传学

毛茛科的罂粟莲花(Anemoclema glaucifolium)是中国西南部金沙江河谷地带特有的单种属植物。本研究利用分子生物学手段（SNPs）,对罂粟莲花的遗传多样性和遗传结构进行了研究。三个叶绿体片段(rps16内含子,psbA trnH 基因间隔区以及trnC ycf6基因间隔区)联合分析的结果显示低的遗传多样性和高的遗传分化。这可能是由于居群间长期的地理隔离,狭小的分布区以及生境片段化造成的有限的基因流所引起的。如今在金沙江上修建水电站的位置与罂粟莲花的分布区有部分重叠,这些水电站会淹没罂粟莲花的部分个体和生境,并且改变生态环境,威胁罂粟莲花的生存。本研究对罂粟莲花遗传多样性的研究为制定有效的保护策略提供了信息。     

Genetic composition of the Jadro softmouth trout following translocation into a new habitat

Genetic founder effects of a historical translocation (1965; app. 12 generations ago) of endangered softmouth trout from the only remaining indigenous population to an adjacent uninhabited river were investigated. A comparison of 15 microsatellites from contemporary samples in both the source and re-established populations indicated a very low level of genetic diversity within the two populations. Furthermore, considerable differences in estimates of variability and effective population sizes were detected between populations, but no recent bottlenecks were evident. Our data suggest that the re-established population has lost variation due to genetic drift associated with founder effects following the translocation. Accordingly, in relation to management, we suggest that the re-established population could serve as a secondary source of individuals to buffer possible extinction due to demographic events. Finally, conservation initiatives to enhance the census population size and increase levels of variability in the re-established population are proposed. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

中国濒危兽类保护遗传学研究进展与展望

我国是全球生物多样性大国,拥有包括大熊猫、金丝猴、华南虎、麋鹿、白鱀豚等特有物种和旗舰物种在内的丰富兽类资源。近几十年来,土地利用模式转变、盗猎、环境污染、气候变化等因素使许多兽类物种面临生存威胁,导致物种遗传多样性丧失。而遗传多样性是生物多样性的基本组成部分,决定了物种和种群能否长期生存。保护遗传学作为保护生物学的一大分支学科,旨在通过遗传学分析探明种群遗传变异和物种濒危的遗传学机制。近40年来,随着研究手段和技术的不断发展,我国兽类保护遗传学在遗传多样性和近交水平评估、景观遗传学、生态遗传学和圈养种群遗传管理等方面都取得了重要成果。然而,未来人类社会发展可能为濒危兽类带来的威胁依然存在,高通量测序等新技术的进一步发展则能够帮助我们更加深入地了解濒危物种和种群遗传适应与濒危机制,从而实现对濒危兽类的有效管理与保护。     

Genetic diversity of the endangered Faucaria tigrina (Aizoaceae) through ISSR “fingerprinting” using automated fragment detection

Faucaria tigrina (Haw.) Schwantes is a rare, threatened succulent found exclusively on the outskirts of Grahamstown, Eastern Cape, South Africa. There are three extant populations of the species; two large ones (approximately 300 and 620 adults) separated by under two kilometres, and a third very much smaller one slightly further away. Genetic theory expects that smaller, isolated populations face a loss in genetic variation through inbreeding and genetic drift and that as declining genetic variation is linked to a loss in fitness, this species may face extinction in the long term. This study used the ISSR-PCR genetic methods linked to an automated detection platform to determine if these populations are genetically distinct, and whether they are genetically depauperate. Two ISSR primers were used, and the automated detection system identified a total of 572 ISSR loci. An UPGMA clustering analysis showed each population to be genetically distinct, and that the genetic diversity of each population does not appear to be particularly low. F. tigrina is separable from the related Faucaria britteniae L. Bolus using the ISSR method, suggesting that this method may be appropriate for systematic studies in the Aizoaceae, which comprises many genera with closely related species.     

Restoration of coral populations in light of genetic diversity estimates

Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using microsatellites. The mean number of alleles per locus across 72 surveyed scleractinian coral populations was 8.27 (±0.75 SE). In addition, population genetic datasets from four species (Acropora palmata, Montastraea cavernosa, Montastraea faveolata and Pocillopora damicornis) were analyzed to assess the minimum number of donor colonies required to retain specific proportions of the genetic diversity of the population. Rarefaction analysis of the population genetic datasets indicated that using 10 donor colonies randomly sampled from the original population would retain >50% of the allelic diversity, while 35 colonies would retain >90% of the original diversity. In general, scleractinian coral populations are genetically diverse and restoration methods utilizing few clonal genotypes to re-populate a reef will diminish the genetic integrity of the population. Coral restoration strategies using 10–35 randomly selected local donor colonies will retain at least 50–90% of the genetic diversity of the original population. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

芒属植物野生资源研究及其进展

芒属（Miscanthus）植物（又称芒草）是极具开发潜力的第二代能源作物之一,其生物质产量、抗逆性和生态功能等方面表现优异。我国具有丰富的芒属植物野生种质资源,为芒草资源开发和利用提供了有利条件。近年来,芒属植物的资源价值日益受到重视,其资源的收集、研究以及开发和利用进入了快速发展阶段。本文简要分析了芒属物种的分类现状及其存在的问题,介绍了各物种的地理分布和基本生物学特点;初步概括了迄今对芒属植物资源开展的多方面研究,包括：开花物候和交配系统、群体遗传变异和适应性分化、杂交和多倍化以及在资源利用和遗传改良方面取得的进展。最后,本文展望了芒属植物资源基础研究和产业化发展的前景,并提出了在芒属野生资源研究和利用中存在的问题及其可能的解决办法。     

Genetic diversity of the endangered species Kirengeshoma palmata (Saxifragaceae) in China

In order to investigate the levels of genetic diversity of the endangered species Kirengeshoma palmata (Saxifragaceae), four extant populations were sampled and analyzed using inter-simple sequence repeats (ISSR) markers. We expected a low genetic diversity level, but our results revealed a high level of intraspecific genetic diversity, probably resulting from this species being in a refuge during the last glaciation (at population level: P = 63.25%, A_e = 1.47, H_E = 0.26 and H_O = 0.37; at species level: P = 79.00%, A = 1.5538, H_T = 0.2586 and H_sp = 0.3104). A low level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (16.69%) and AMOVA (19.36%). Populations shared high levels of genetic identity. Insect pollination and seed dispersal by wind may have facilitated extensive gene flow and are likely responsible for this present structure of genetic variation.     

Patterns of genetic variation in anthropogenically impacted populations

Genetic variation is considered critical for allowing natural populations to adapt to their changing environment, and yet the effects of human disturbance on genetic variation in the wild are poorly understood. Different types of human disturbances may genetically impact natural populations in a predictable manner and so the aim of this study was to provide an overview of these changes using a quantitative literature review approach. I examined both allozyme and microsatellite estimates of genetic variation from peer-reviewed journals, using the mean number of alleles per locus and expected heterozygosity as standardized metrics. Populations within each study were categorized according to the type of human disturbance experienced (“hunting/harvest”, “habitat fragmentation”, or “pollution”), and taxon-specific, as well as time- and context-dependent disturbance effects were considered. I found that human disturbances are associated with weak, but consistent changes in neutral genetic variation within natural populations. The direction of change was dependent on the type of human disturbance experienced, with some forms of anthropogenic challenges consistently decreasing genetic variation from background patterns (e.g., habitat fragmentation), whereas others had no effect (e.g., hunting/harvest) or even slightly increased genetic variation (e.g., pollution). These same measures appeared sensitive to both the time of origin and duration of the disturbance as well. This suggests that the presence or absence, strength, type, as well as the spatial and temporal scale of human disturbance experienced may warrant careful consideration when conservation management plans are formulated for natural populations, with particular attention paid to the effects of habitat fragmentation.