High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis

Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (F(ST) = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories.     

Genetic population structure of the large blue butterfly Maculinea alcon in Denmark

We have investigated the genetic population structure within and the genetic differentiation between local populations of the large blue butterfly Maculinea alcon throughout the Jutland peninsula. Samples were collected as eggs on foodplants (Gentiana pneumonanthe), and reared to 4th instar caterpillars in the laboratory. A significant excess of homozygotes was found for all the investigated allozyme loci in most of the populations. A North-South cline was observed for the allele frequencies at some of the loci and for several linkage groups. Because some of the allele frequency clines were parallel to clines in adult morphological variation, we interpret our results as evidence for the co-existence of at least two gene pools within the Danish Maculinea alcon populations. Multilocus electrophoretic data revealed highly positive but variable FST values, which under this scenario would reflect varying frequencies of the Maculinea gene pools across the local populations. The significantly positive FIS values indicate that these gene pools are at least partly reproductively isolated (Wahlund effect). The co-occurrence of several Maculinea alcon gene pools on many local sites in Jutland is of great importance for conservation of the fragmented Maculinea populations. Our results show that there is probably more Maculinea biodiversity to conserve than was previously thought, and suggests that extant populations are more fragmented and vulnerable than counts of flying adults or eggs on foodplants indicate.     

Genetic Differentiation and Conservation of 14 Surviving Individuals of Euryodendron excelsum Endemic to China

Random amplification polymorphic DNA (RAPD)markers were used to assess the genetic variations and the evolutionary relationships among all 14 individuals of a critically endangered Euryodendron excelsum (Theaceae)population distributed in Ba Jia Zhen,Yangchun,Guangdong,China.Twenty-three random primers detected 156 sites,out of which 95 (60.26%) were polymorphic loci.The number of the observed alleles was 1.6090,and the number of the effective alleles was 1.3471.Nei's gene diversity was 0.1993,and Shannon index was 0.1534.A relatively high level of genetic variation was identified in E.excelsum.An unweighted pair group method with arithmetic mean (UPGMA) tree established from Jaccard similarity coefficients suggested that 14 individuals were clustered into two subgroups and that the No.2 plant was genetically distant from the rest of the individuals.The UPGMA clustering was also supported by a principle components analysis of RAPD phenotypic data.The management and conservation strategy of E.excelsum was proposed based on our results.     

Development of polymorphic microsatellite markers for Dalbergia nigra (Papilionoideae), an endangered tree from the Brazilian Atlantic Forest

Dalbergia nigra is an endangered tree restricted to the Brazilian Atlantic Forest. Ten polymorphic microsatellite loci were isolated and characterized in 47 trees from two populations. The total number of alleles per locus ranged from three to 12 alleles. The levels of observed and expected heterozygosities ranged from 0.304 to 0.740 and from 0.278 to 0.872, respectively. Significant deviations from Hardy-Weinberg were detected for only three loci in each population. No pair of loci exhibited significant linkage disequilibrium. These microsatellites provide an efficient tool to investigate genetic structure in forest remnants with the purpose of conservation of this species.     

Genetic differentiation and diversity of Acacia koa populations in the Hawaiian Islands

Acacia koa A. Gray (koa) is a leguminous tree endemic to the Hawaiian Islands and can be divided into morphologically distinguishable groups of A. koaia Hillebrand, A. koa and populations that are intermediate between these extremes. The objectives of this investigation were to distinguish among divergent groups of koa at molecular levels, and to determine genetic diversity within and among the groups. Phylogenetic analyses using the ITS/5.8S rDNA and trnK intron sequences did not separate the representative koa types into distinct clusters. An unweighted pair group method with arithmetic mean cluster analysis and principal coordinate analysis, based on allele profiles of 12 microsatellite loci for 215 individual koa samples, separated the population into three distinct clusters consistent with their morphology, A. koaia, A. koa and intermediate forms. There was an average of 8.8 alleles per polymorphic locus (AP) among all koa and koaia individuals. The intermediate populations had the highest genetic diversity (H′ = 1.599), AP (7.9) and total number of unique alleles (21), whereas A. koaia and A. koa showed similar levels of genetic diversity (H′ = 0.965 and 0.943, respectively). No correlation was observed between geographic distance and genetic distance as determined by a Mantel test (r = 0.027, P = 0.91). The data presented here support previous recommendations that morphological variation within koa should be recognized at the subspecific level rather than as distinct species.     

遗传标记及其在林木研究中的应用

遗传标记经历了形态标记、细胞学标记、生化标记和分子标记等4个阶段,其中分子标记的发展最为迅猛和有效。本文比较了几种主要分子标记方法的特点,为更好地利用分子标记提供了理论依据,并对分子标记在林木遗传多样性研究、遗传育种、DNA指纹图谱的构建、亲缘关系鉴定及分类研究等方面的应用做了介绍。     

Isolation and characterization of microsatellite markers for Acacia senegal (L.) Willd., a multipurpose arid and semi-arid tree

Acacia senegal is a multipurpose African tree that improves the soil fertility of degraded areas. The species is exploited mainly for gum arabic, but it also supplies fuel wood and fodder for animals. Despite its wide distribution in Africa, no microsatellite markers have yet been characterized for this species. In this study, we characterized 11 polymorphic microsatellite loci specifically designed for A. senegal and analysed 247 individuals from three populations from Niger. On average, 10.9 alleles per locus were detected and expected heterozygosity ranged from 0.160 to 0.794, showing the ability of the markers to detect genetic diversity in this species.     

Genetic viability and population history of the giant panda, putting an end to the "evolutionary dead end"?

The giant panda (Ailuropoda melanoleuca) is currently threatened by habitat loss, fragmentation, and human persecution. Its dietary specialization, habitat isolation, and reproductive constraints have led to a perception that this is a species at an "evolutionary dead end," destined for deterministic extinction in the modern world. Here we examine this perception by a comprehensive investigation of its genetic diversity, population structure, and demographic history across its geographic range. We present analysis of 655 base pairs of mitochondrial (mt) control region (CR) DNA and 10 microsatellite loci for samples from its 5 extant mountain populations (Qinling, Minshan, Qionglai, Liangshan, and Lesser Xiangling). Surprisingly, extant populations display average to high levels of CR and microsatellite diversity compared with other bear species. Genetic differentiation among populations was significant in most cases but was markedly higher between Qinling and the other mountain ranges, suggesting, minimally, that the Qinling population should comprise a separate management unit for conservation purposes. Recent demographic inference using microsatellite markers demonstrated a clear genetic signature for population decline starting several thousands years ago or even further back in the past, and being accelerated and enhanced by the expansion of human populations. Importantly, these data suggest that the panda is not a species at an evolutionary "dead end," but in common with other large carnivores, has suffered demographically at the hands of human pressure. Conservation strategies should therefore focus on the restoration and protection of wild habitat and the maintenance of the currently substantial regional genetic diversity, through active management of disconnected populations.     

利用ISSR标记研究野大豆居群内遗传变异及其取样策略

为了有效地保护野大豆(Glycine soja Sieb.et Zucc.)并制定合理的居群取样策略,对上海江湾机场的一个人然野大豆居群进行了 100个单株(个体)的随机取样,并用ISSR分子标记对其进行了遗传多样性分析.利用筛选出的15条ISSR引物在这个居群中检测到较高的遗传变异,样本内个体间的相似系数变化在0.17～0.89之间.居群内平均每个位点的平均预期杂合度(He)为0.171 4,香农指数(I)为0.271 4.PCA分析显示,江湾野大豆居群内的遗传变异不是呈均匀分布,而是呈从状分布.该野大豆居群遗传多样性和样本内个体数量间的相关性分析显示:在个体数少于40的情况下,遗传多样性随个体数的增加而迅速增加;当样本中的个体数大于40时,遗传多样性的增加减慢并很快趋于饱和.研究表明:对野大豆居群进行异地保护时,对各居群的采样植株数不应当低于35～45;在居群内采样时,所采集的个体之间最好相隔一定的空间距离.     

利用ISSR标记研究野大豆居群内遗传变异及其取样策略

为了有效地保护野大豆(Glycine soja Sieb.et Zucc.)并制定合理的居群取样策略,对上海江湾机场的一个天然野大豆居群进行了100个单株(个体)的随机取样,并用ISSR分子标记对其进行了遗传多样性分析。利用筛选出的15条ISSR引物在这个居群中检测到较高的遗传变异,样本内个体间的相似系数变化在0．17～0．89之间。居群内平均每个位点的平均预期杂合度(He)为0．1714,香农指数(I)为0．2714。PCA分析显示,江湾野大豆居群内的遗传变异不是呈均匀分布,而是呈丛状分布。该野大豆居群遗传多样性和样本内个体数量间的相关性分析显示：在个体数少于40的情况下,遗传多样性随个体数的增加而迅速增加：当样本中的个体数大于40时,遗传多样性的增加减慢并很快趋于饱和。研究表明：对野大豆居群进行异地保护时,对各居群的采样植株数不应当低于35～45;在居群内采样时,所采集的个体之间最好相隔一定的空间距离。     

Genetic diversity and fitness in Scabiosa columbaria in the Swiss Jura in relation to population size

Due to changes in land use, remnants ofunfertilised, nutrient-poor calcareousgrassland in the Swiss Jura are small in areaand are highly fragmented. We selected 89 seedfamilies from eleven populations of varioussizes of Scabiosa columbaria for a studyof molecular diversity, and used the samematerial in a greenhouse experiment to measurevariation in fitness-related traits and theability of populations to cope withcompetition. Using RAPD-PCR we detected 71RAPD-phenotypes among 87 genotypes. Moleculardiversity within populations was variable andrelatively high, with an expectedheterozygosity H _e ranging from 0.09 to0.24. H _e, the Shannon index (SI) and thepercentage of polymorphic bands were notcorrelated with population size, but thesmallest populations had the lowest moleculardiversity (H _e, SI). Populationdifferentiation was moderate with 12% of themolecular diversity among populations. Measuresof fitness in the greenhouse differed amongseed families (P < 0.001), but not amongpopulations. Mean above-ground biomass waslargely reduced when plants had to compete withBromus. Mean fitness of populationsdecreased when molecular diversity (H _e)was low, but only when plants had to competewith Bromus (P = 0.02). Accordingly, therelative competition ability of Scabiosaplants decreased when molecular diversity(H _e) was low (P = 0.01). Our resultssuggest an increased risk of local extinctionof Scabiosa columbaria in the Swiss Juracaused by a decreased viability and reducedphenotypic plasticity due to genetic erosion insmall populations.