Feral pig populations are structured at fine spatial scales in tropical Queensland, Australia

Feral pigs occur throughout tropical far north Queensland, Australia and are a significant threat to biodiversity and World Heritage values, agriculture and are a vector of infectious diseases. One of the constraints on long-lasting, local eradication of feral pigs is the process of reinvasion into recently controlled areas. This study examined the population genetic structure of feral pigs in far north Queensland to identify the extent of movement and the scale at which demographically independent management units exist. Genetic analysis of 328 feral pigs from the Innisfail to Tully region of tropical Queensland was undertaken. Seven microsatellite loci were screened and Bayesian clustering methods used to infer population clusters. Sequence variation at the mitochondrial DNA control region was examined to identify pig breed. Significant population structure was identified in the study area at a scale of 25 to 35 km, corresponding to three demographically independent management units (MUs). Distinct natural or anthropogenic barriers were not found, but environmental features such as topography and land use appear to influence patterns of gene flow. Despite the strong, overall pattern of structure, some feral pigs clearly exhibited ancestry from a MU outside of that from which they were sampled indicating isolated long distance dispersal or translocation events. Furthermore, our results suggest that gene flow is restricted among pigs of domestic Asian and European origin and non-random mating influences management unit boundaries. We conclude that the three MUs identified in this study should be considered as operational units for feral pig control in far north Queensland. Within a MU, coordinated and simultaneous control is required across farms, rainforest areas and National Park Estates to prevent recolonisation from adjacent localities.

An assessment of the geographical scale of recurrent gene flow in wild populations of two species of Mekong River carps (Henicorhynchus spp.)

The Mekong is the most productive river fishery in the world, and such as, the Mekong River Basin (MRB) is very important to very large human populations across the region as a source of revenue (through fishing and marketing of aquatic resources products) and as the major source for local animal protein. Threats to biodiversity in the MRB, either to the fishery sector itself or to other sectors are a major concern, even though currently, fisheries across this region are still very productive. If not managed properly however, fish population declines will cause significant economic impact and affect livelihoods of local people and will have a major impact on food security and nutrition. Biodiversity declines will undoubtedly affect food security, income and socio-economic status of people in the MRB that depend on aquatic resources. This is an indicator of unsustainable development and hence should be avoided. Genetic diversity (biodiversity) that can be measured using techniques based on DNA markers; refers to variation within and among populations within the same species or reproductive units. In a population, new genetic variation is generated by sexual recombination contributed by individuals with mutations in genes and chromosomes. Over time, populations of a species that are not reproducing together will diverge as differential impacts of selection and genetic drift change their genetic attributes. For mud carp (Henicorhynchus spp.), understanding the status of breeding units in the MRB will be important for their long term persistence, sustainability and for implementing effective management strategies. Earlier analysis of stock structure in two economically important mud carp species (Henicorhynchus siamensis and H. lobatus) in the MRB completed with mtDNA markers identified a number of populations of both species where gene flow had apparently been interrupted or reduced but applying these data directly to management unit identification is potentially compromised because information was only available about female dispersal patterns. The current study aimed to address this problem and to fully assess the extent of current gene flow (nDNA) and reproductive exchange among selected wild populations of two species of carp (Henicorhynchus spp.) of high economic importance in the MRB using combined mtDNA and nDNA markers. In combination, the data can be used to define effective management units for each species. In general, nDNA diversity for H. lobatus (with average allelic richness (A) 7.56 and average heterozygosity (Ho) 0.61) was very similar to that identified for H. siamensis (A = 6.81 and Ho = 0.75). Both mud carp species show significant but low FST estimates among populations as a result of lower genetic diversity among sampled populations compared with genetic diversity within populations that may potentially mask any 'real' population structure. Overall, population genetic structure patterns from mtDNA and nDNA in both Henicorhynchus species were largely congruent. Different population structures however, were identified for the two Henicorhynchus species across the same geographical area. Apparent co-similarity in morphology and co-distribution of these two relatively closely related species does not apparently imply parallel evolutionary histories. Differences in each species population structure likely reflect historical drainage rearrangement of the Mekong River. The data indicate that H. siamensis is likely to have occupied the Mekong system for much longer than has H. lobatus in the past. Two divergent stocks were identified for H. lobatus in the MRB below the Khone Falls while a single stock had been evident in the earlier mtDNA study. This suggests that the two Henicorhynchus species may possess different life history traits and that different patterns of gene flow has likely influenced modern genetic structure in these close congeners. In combination, results of the earlier mtDNA and the current study have implications for effective management of both Henicorhynchus species across the MRB. Currently, both species are essentially treated as a single management unit in this region. This strategy may be appropriate for H. lobatus as a single stock was evident in the main stream of the MRB, but may not be appropriate for H. siamensis as more than a single stock was identified across the same range for this species. Management strategies should consider this difference to conserve overall biodiversity (local discrete populations) and this will include maintaining natural habitat and migration pathways, provision of fish sanctuaries (refuges) and may also require close monitoring of any stock declines, a signal that may require effective recovery strategies.

Phylogeography of the green turtle, Chelonia mydas, in the Southwest Indian Ocean

Patterns of mitochondrial DNA (mtDNA) variation were used to analyse the population genetic structure of southwestern Indian Ocean green turtle (Chelonia mydas) populations. Analysis of sequence variation over 396 bp of the mtDNA control region revealed seven haplotypes among 288 individuals from 10 nesting sites in the Southwest Indian Ocean. This is the first time that Atlantic Ocean haplotypes have been recorded among any Indo-Pacific nesting populations. Previous studies indicated that the Cape of Good Hope was a major biogeographical barrier between the Atlantic and Indian Oceans because evidence for gene flow in the last 1.5 million years has yet to emerge. This study, by sampling localities adjacent to this barrier, demonstrates that recent gene flow has occurred from the Atlantic Ocean into the Indian Ocean via the Cape of Good Hope. We also found compelling genetic evidence that green turtles nesting at the rookeries of the South Mozambique Channel (SMC) and those nesting in the North Mozambique Channel (NMC) belong to separate genetic stocks. Furthermore, the SMC could be subdivided in two different genetic stocks, one in Europa and the other one in Juan de Nova. We suggest that this particular genetic pattern along the Mozambique Channel is attributable to a recent colonization from the Atlantic Ocean and is maintained by oceanic conditions in the northern and southern Mozambique Channel that influence early stages in the green turtle life cycle.

Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia

We examine the structure and phylogeography of the pig-eye shark (Carcharhinus amboinensis) common in shallow coastal environments in northern Australia using two types of genetic markers, two mitochondrial (control region and NADH hydrogenase 4) and two nuclear (microsatellite and Rag 1) DNA. Two populations were defined within northern Australia on the basis of mitochondrial DNA evidence, but this result was not supported by nuclear microsatellite or Rag 1 markers. One possibility for this structure might be sex-specific behaviours such as female philopatry, although we argue it is doubtful that sufficient time has elapsed for any potential signatures from this behaviour to be expressed in nuclear markers. It is more likely that the observed pattern represents ancient populations repeatedly isolated and connected during episodic sea level changes during the Pleistocene epoch, until current day with restricted contemporary gene flow maintaining population genetic structure. Our results show the need for an understanding of both the history and ecology of a species in order to interpret patterns in genetic structure.

Molecular ecology of european mustelids: Unraveling evolutionary and ecological patterns in Martes and Lutra genera

208 p.

Unveiling the factors shaping the distribution of widely distributed alpine vertebrates, using multi-scale ecological niche modelling of the bat Plecotus macrobullaris

Several alpine vertebrates share a distribution pattern that extends across the South-western Palearctic but is limited to the main mountain massifs. Although they are usually regarded as cold-adapted species, the range of many alpine vertebrates also includes relatively warm areas, suggesting that factors beyond climatic conditions may be driving their distribution. In this work we first recognize the species belonging to the mentioned biogeographic group and, based on the environmental niche analysis of Plecotus macrobullaris, we identify and characterize the environmental factors constraining their ranges. Distribution overlap analysis of 504 European vertebrates was done using the Sorensen Similarity Index, and we identified four birds and one mammal that share the distribution with P. macrobullaris. We generated 135 environmental niche models including different variable combinations and regularization values for P. macrobullaris at two different scales and resolutions. After selecting the best models, we observed that topographic variables outperformed climatic predictors, and the abruptness of the landscape showed better predictive ability than elevation. The best explanatory climatic variable was mean summer temperature, which showed that P. macrobullaris is able to cope with mean temperature ranges spanning up to 16 degrees C. The models showed that the distribution of P. macrobullaris is mainly shaped by topographic factors that provide rock-abundant and open-space habitats rather than climatic determinants, and that the species is not a cold-adapted, but rather a cold-tolerant eurithermic organism. P. macrobullaris shares its distribution pattern as well as several ecological features with five other alpine vertebrates, suggesting that the conclusions obtained from this study might be extensible to them. We concluded that rock-dwelling and open-space foraging vertebrates with broad temperature tolerance are the best candidates to show wide alpine distribution in the Western Palearctic.

Estrutura populacional e filogeografia de Panulirus argus (Latreille, 1804)

Panulirus argus (Latreille, 1804) é uma das principais espécies de lagosta no Atlântico, sendo um dos maiores recursos pesqueiros do Atlântico Ocidental, onde apresenta um alto valor comercial. A forte explotação da espécie resulta em uma grande pressão sobre suas populações. Recentemente, foi descoberto que sob o binômio P. argus estão contidas duas espécies crípticas que ocorrem em alopatria, uma na região do Caribe e outra na costa brasileira. Esta tese tem como objetivo estudar como se estruturam geneticamente as populações dessas duas espécies, com o propósito de fornecer mais informações para a determinação de estoques e um correto manejo das espécies, e analisar os processos históricos evolutivos que moldaram suas histórias demográficas. Para tal, foram estudados dois marcadores mitocondriais (região controle e o gene da Citocromo Oxidase I) e loci de microssatélites de indivíduos de 7 regiões do Caribe (Florida, Bahamas, Turks e Caicos, Porto Rico, Cuba, Colômbia e Venezuela) e 11 estados do Brasil (Pará, Maranhão, Piauí, Ceará, Rio Grande do Norte, Pernambuco, Alagoas, Bahia, Espírito Santo, Rio de Janeiro e São Paulo). Dentro de cada espécie foram observadas duas linhagens mitocondriais diferentes, que co-ocorriam, de maneira homogênea, ao longo de suas distribuições. Hipotetiso que essas linhagens foram formadas a partir de um evento de vicariância com contato secundário ou como consequência de um efeito gargalo seguido de expansão. As duas linhagens são evidentes nas sequências da região controle mitocondrial, mas no gene da COI foram evidentes apenas em P. cf. argus do Caribe. As linhagens do Brasil se separaram há aproximadamente 233 - 288 mil anos e cada uma sofreu expansão em tempos diferentes, a primeira se expandiu há 100 mil anos e a segunda linhagem há 50 mil anos. As linhagens do Caribe se separaram cerca de 1 milhão de anos atrás e possuem o mesmo tempo de expansão, 50 mil anos. Os microssatélites não revelaram subdivisão populacional para nenhuma das duas espécies, porém os marcadores, juntos, sugeriram um fluxo gênico diferenciado entre localidades expostas a diferentes correntes marítimas. Considerando que essas lagostas são intensamente explotadas, é importante ser cuidadoso no momento de definir estoques pesqueiros. Para a espécie do Brasil, dois estoques pesqueiros foram sugeridos, o primeiro do Pará à Bahia e o segundo do sul da Bahia a São Paulo. Para a espécie do Caribe, foi mantida e reforçada a hipótese de quatro estoques sugerida pela FAO (Norte, Sul, Centro-Norte e Centro-Sul).

Filogeografia e evolução molecular de lagostas sapateiras (Scyllarides spp.) da América do Sul

Nos últimos anos, duas espécies de lagostas sapateiras, Scyllarides brasiliensis e S. deceptor, vêm se destacando nos desembarques pesqueiros de lagostas do Atlântico Sul Ocidental. Para espécies comercialmente importantes, o desenvolvimento de estudos que permitam conhecer a variabilidade e entender a dinâmica populacional é fundamental. Assim, o objetivo do primeiro capítulo desta tese foi avaliar a diversidade genética e a estrutura populacional dessas duas lagostas ao longo de aprox. 2.800 km da costa da América do Sul. Para as análises, foram empregados marcadores mitocondriais (citocromo oxidase I: COI; e a região controle: RC) e marcadores nucleares (13 loci de microssatélites desenvolvidos nesta tese). As duas espécies apresentaram altos níveis de variabilidade (S. deceptor: N = 200, mtDNA: h > 0,841, π > 0,005; microssatélites: He = 0,685; S. brasiliensis: N = 211, He = 0,554), distribuídos homogeneamente entre as localidades (S. deceptor: ΦST < -0,004, ΦCT < 0,016, FST global = 0,001, Dest global = 0,003, FCT < 0,002, P > 0,05, K = 1; S. brasiliensis: FST global = 0,004, Dest global = 0,001, FCT < 0,004, P > 0,05, K = 1). A ausência de estruturação nas duas espécies pode estar relacionada a características biológicas que promovem a conectividade entre localidades geograficamente distantes, como alta fecundidade e alto potencial de dispersão das larvas planctônicas. Além disso, os dados mitocondriais sugerem que a história demográfica de S. deceptor foi marcada por eventos de expansão populacionais e geográficos possivelmente relacionados às condições ambientais favoráveis dos episódios interglaciais do Pleistoceno Médio-Tardio. Diversos estudos têm mostrado que os fenômenos de inserção de regiões mitocondriais no DNA nuclear (NuMts) e heteroplasmia limitam a correta amplificação e identificação dos marcadores mitocondriais. Em estudos filogenéticos e de genética de populações, a presença inadvertida de sequências de diversas origens viola o principio de ortologia, o que pode resultar em inferências evolutivas erradas. Assim, o objetivo do segundo capítulo desta tese foi identificar e caracterizar os possíveis NuMts e sequências heteroplásmicas de três regiões mitocondriais (COI, RC e o gene da subunidade maior do RNA ribossomal: 16S) em quatro espécies do gênero Scyllarides (S. aequinoctialis, S. brasiliensis, S. deceptor e S. delfosi). A clonagem e sequenciamento de extratos de DNA genômico e DNA enriquecido com mtDNA revelaram que os genomas destas espécies podem exibir NuMts (que divergem entre 0,6 e 17,6% do mtDNA) e heteroplasmia (que divergem < 0,2% do mtDNA prevalente). Os NuMts surgiram possivelmente de vários eventos independentes de integração ao núcleo ao longo da história evolutiva do gênero Scyllarides. Dependendo do seu grau de similaridade com o mtDNA, a presença de NuMts nas análises filogenéticas no nível de gênero pode causar superestimativa do número de espécies e alterações nos comprimentos dos ramos e nas relações filogenéticas entre espécies.

木根麦冬基因流动与居群遗传变异的时空动态研究

本报告对木根麦冬的生态、遗传与进化等方面进行了综合研究，分析了木根麦冬居群内个体育性变异与基因流的模式与强度，研究了木根麦冬居群遗传变异在时间与空间的动态变化过程，深入探讨了该物种的适应策略、自然选择与进化模式。同时对生物进化中的一些基本问题进行了尝试性探讨。 一、影响有性繁殖生物居群中交配与繁殖成功的行为、生态与遗传现象最终决定等位基因与基因型的相对频率及其在世代间的变化。植物的交配系统不仅决定了居群未来世代的基因型频率，而且还影响到植物居群的有效大小、基因流和选择等其它进化因素。我们利用等位酶多态性，采用似然性方法与计算机模拟为木根麦冬三个居群的种子确定父本。共有90.1%的种子可以在居群中找到唯一的最可能父本。在这些种子中，56.1%在0.95的显著水平上可以确定唯一亲本。并且还发现：1．个体自交越多，产生的种子就越多;2．个体提供 给自己的有效花粉比提供给别的植株的有效花粉多，3．只接受花粉而不提供花粉的植株产生的种子少;4．只接受花粉而不提供花粉的植株产生种子的机会也少，综合我们以前的研究结果，可以认为，木根麦冬的交配系统正在或已经发 生了转变，从以异交为主到以自交为主。 二、点模式分析的结果表明在所研究的三个居群中，木根麦冬个体都表现出相对随机的分布。空间自相关分析却发现开花个体在空间聚集分布，呈斑块状开花。这个结果也表明个体空间分布模式与开花状态没有直接关系，集团性开花可能是一个促进花粉传播的适应特征：开花个体的聚集可能对传粉者形成强有力的吸引。空间自相关分析表明木根麦冬居群中大多数等位基因都聚集成一定大小的斑块。基因的聚集突出的说明了木根麦冬居群内基因流动的状况，花粉与种子的传播受到限制。传粉能力弱的传粉者以及种子的近距离的散布使基因局限于一定的小范围内，从而形成基因斑块，而斑块的大小由传粉者的活动范围及种子的传播距离决定。 三、基因纯合导致有害的隐性基因或部分致死的基因表达，使纯合子适合度降低，因此纯合子频率在世代间的变化将是衡量近交衰退的一个较好的指标。木根麦冬中亲代居群的观察杂合度大大高于子代居群，这个结果表明大量的纯合子在从种子到成株的过程中被淘汰。大量的纯合子被淘汰可能时由于隐性致死或有害等位基因纯合的结果，自交以及有亲缘关系的个体之间交配使有害等位基因与致死等位基因纯合，从而使一个远交种中出现自交衰退，过量的纯合子被淘汰是自交衰退的直接后果。

横断山区紫乌头复合体的物种形成初探

物种形成是生物进化的重要步骤，是进化生物学中的基本问题。研究一些关键地区植物的物种形成，将提高对这些地区植物区系发生与发展的认识，横断山区就是这样一个非常独特与关键的地区。本文通过对主要分布于横断山区的紫乌头A.delavayi复合体进行nrDNA ITS序列、等位酶与RAPD分析，初步探讨了横断山区紫乌头A.delavayi复合体的起源与物种形成。同时对使用RAPD与等位酶数据研究群体遗传结构的方法进行了探讨。主要研究结果如下： 1. ITS序列研究 对乌头属27个类群的ITS序列进行了简约法与邻接法的研究，两种方法得到的系统发育树基本一致。乌头亚属的蔓乌头系 Ser. Volublia不是一个单系起源的类群，显拄乌头系 Ser. Sstylosa 与兴安乌头系Ser. Ambigua各自作为单系起源也没有得到支持。特产于云南西北部横断山区的一些种之间存在非常近的系统发育关系，说明这些种是近期物种形成的产物。紫乌头A.delavayi复合体的不同类群在系统发育树上被分到不同的分支中，含西南乌头A. episcopale的分支最为独特，处于系统发育树靠近基部的位置;松潘乌头 A.sunpanense与四川西北部的弯喙乌头A.campylorrhynchum组成一个分支，另一个分支含土官村乌头A.tuguancunense、紫乌头A.delavayi、玉龙乌头A.stapfianum与黄草乌A.vilmorinianum; 表明紫乌头A.delavayi复合体有3个独立的起源，因而该复合体在遗传上是不成立的。但是为了讨论与叙述的方便，本研究仍使用紫乌头A.delavayi复合体这个名字。 2. 等位酶研究 用10种酶系统14个位点，对紫乌头A.delavayi分布于云南横断山区的4种8个居群进行了等位酶分析。结果表明横断山区紫乌头A.delavayi复合体居群的遗传多样性明显低于北美和欧洲的乌头属植物。呈垂直替代关系的紫乌头A.delavayi与玉龙乌头A.stapfianum居群之间出现有规律的遗传多样性变化，表明冰川对横断山区植物的遗传多样性有重大影响。聚类分析的结果与ITS分析的结果基本一致，西南乌头A. episcopale仍然是较为独特的一类;其余3个种的居群聚为一类，紫乌头A.delavayi与玉龙乌头A.stapfianum之间的遗传一致度非常高，超过0.95。8个居群的主成分分析没有证实西南乌头A. episcopale中存在杂交渗入。Mantel 检验的结果显示8个居群之间的遗传趋异程度与地理距离之间显著相关。基因分化系数GST与近交系数FIS均显示这些居群不是以异交为主。居群间每代迁移个体数Nm显示这些居群间基因流较弱。 3. RAPD研究 用20个随机引物得到117个RAPD位点，对23个居群进行研究。其中19个属于紫乌头A.delavayi复合体，4个属于与之近缘的瓜叶乌头A.hemsleyanum。根据RAPD表型频率与单倍型频率，分别对23个居群进行了聚类分析。结果显示这两种方法所得结果高度一致，而且也与ITS和等位酶的分析结果基本一致。西南乌头A. episco pale仍然是最为独特一个分支，在本文中称为分支1。其余的居群聚成两个关系较近的大分支，一个分支包含所有分布于云南与四川西南部横断山区的居群，称为分支2，另一个包括所有分布于四川西北部与北部横断山区、重庆东北部、湖北西部与陕西的居群。大部分种处于同一分支中，只有弯喙乌头A.campylorrhynchum与瓜叶乌头A.hemsleyanum的居群分别被聚在分支2与分支3中，完全符合居群的地理位置。从3个分支内的聚类关系可以看出居群间遗传趋异等级与地理隔离程度明显相关。在遗传多样性水平上，分支1明显比分支2和分支3低许多，分支2又高于分支3。 在分支2内部，紫乌头A.delavayi与玉龙乌头A.stapfianum之间的遗传多样性变化与等位酶结果相同。在分支3的松潘乌头 A.sunpanense 5个居群中，横断山区海拔最高的2个居群遗传多样性最低。将23个居群划分成不同等级进行AMOVA分析，结果表明总遗传多样性主要分布于地区间，其次是居群间，居群内遗传多样性所占比例很低。 4．群体遗传结构研究中的数据处理方法 本研究结果表明，在使用RAPD表型数据进行AMOVA分析时，最好采用欧氏距离平方系数。本研究还说明，计算GST的两种不同方法将导致结果不同，而要与Hamrick and Godt（1990）的总结进行对比的话，最好使用他们采用的计算方法。 基于以上研究结果，可得出如下结论：⑴ 紫乌头A.delavayi复合体有3个不同的起源。西南乌头A. episcopale是一个古特有种，其余均为近期物种形成的产物。⑵地理隔离在横断山区紫乌头A.delavayi复合体的物种形成过程中影响最大。而地理隔离主要起因于连续分布区的片段化与瓶颈效应，而这两个原因又与横断山区的地质历史与冰川进退密切相关。

银杉的分子谱系地理学研究

银杉（Cathaya argyrophylla）是中国特有的濒危裸子植物，孤立分布于我国亚热带山地。虽然以往等位酶和RAPD标记的研究表明，银杉群体的遗传多样性水平很低而群体间的遗传分化很高，但迄今对该种群体的动态变化以及物种的进化历史仍缺乏了解，包括影响群体遗传结构的因素以及物种可能的避难所等，对如何有效地保护和恢复银杉群体仍缺乏科学依据。本文根据8个核基因片段和2个线粒体片段的序列数据，运用群体遗传学和谱系地理学方法，探讨了银杉在DNA水平上的多样性和群体的动态历史，探讨了影响银杉特殊的群体遗传结构的各种因素，并推测了银杉第四纪冰期的避难所，对银杉花粉活力及其变异进行检测。在此基础上，提出了保护和恢复银杉群体的具体策略和措施。主要研究结果如下： 　　1. 核甘酸多态性和群体遗传结构 　　从101个核基因片段中筛选了8个适用于银杉的片段，对来自四个地区15个群体共86个个体的胚乳总DNA进行了扩增和测序。8个核基因座位的平均核苷酸多态性（θs＝0.0022，πs＝0.0027）显著低于其它松杉植物遗传多态性的多座位估计值。四个地区中，大瑶山（DY）的多态性最高（θs＝0.0026，πs＝0.0027），八面山（BM）最低（θs＝0.0014，πs＝0.0018），大娄山（DL）和越城岭（YC）介于二者之间。大多数座位内的多态位点间紧密连锁，座位间的连锁只在八面山地区检测到。AMOVA分析表明显著性的多态性比例存在于地区间（20.05％）和地区内群体间（9.37％）。FST分析也显示群体间（FST＝0.294）和地区间（FST =0.131-0.319）存在显著的遗传分化。推测伴随着瓶颈效应而出现的遗传漂变及其有限的基因流（Nm=1.2）是导致银杉群体低水平多态性和群体间强烈分化的主要原因。 　　2．谱系地理学分析 　　利用2个线粒体片段（nad1和nad4）序列以及高变异量的核2009片段序列对银杉的谱系地理进行了探讨。2个线粒体片段的多态位点组合成3种单倍型，将银杉分成大娄山（DL）、八面山（BM）以及越城岭（YC）和大瑶山（DY）3个地区，地区间的单倍型完全不同（GST=1.0），结合核基因呈现的群体遗传结构，推测现存银杉群体至少来源于4个冰期避难所，相当于银杉现存的4个相互隔离的地区。2009座位上12个变异位点组合成8种单倍型，位于单倍型谱系内部节点的4种祖先单倍型分布广泛、出现频率最高，其它7个核基因座位具有类似谱系结构。遗传距离和地理距离没有相关性，NST (0.138)与GST (0.134)没有显著性差异，说明现存的银杉群体是相对较近的时间内片断化的产物。2009片段分离位点的失配分布（mismatch distribution）呈双峰和多峰，表明银杉群体没有经历近期的扩张，与古生物学研究证据相吻合。 　　3. 银杉的基因杂合性和花粉生命力 　　利用2009和cad两个核基因片段，采用多胚乳序列法得到总的杂合体比率为64％（2009）和60％（cad），说明银杉群体中存在高比例的杂合体。大娄山地区的杂合体比率是八面山地区的2倍。银杉杂合体比率的高低可能与其遗传多态性有关，也可能是自然选择的结果。采用TTC染色法对银杉的花粉生命力进行了测定，在干燥低温条件下银杉花粉的活力很稳定，保存一年后有活力的花粉数仍高达80％以上。通过对来自两个地区（DY和YC）7个群体共16个银杉个体花粉活力的测定发现，银杉有活力花粉比例高达93.3％，与其它裸子植物相当。花粉活力在地区间和群体间存在显著差异，花坪地区（95.2%）的花粉活力高于大瑶山（91.3%）。花粉活力在群体内个体间差异不显著。 　　4．银杉的进化历史及其保护 　　银杉的低水平的遗传多样性和独特的群体遗传结构对我们推测其冰川期避难所提供了重要依据。本研究在银杉4个孤立分布区发现了彼此不重叠的线粒体单倍型，同时核基因表现出了4个地理群，说明随着第四纪冰期气候的波动和银杉分布范围的片段化，原来广布的群体逐步萎缩，最后被保留在位于西部大娄山（DL），东部八面山(BM)，中南部越城岭(YC)和南部大瑶山(DY) 4个相互隔离的避难所。银杉独特的群体结构和动态历史对进一步制定相应的保护措施具有重要参考价值。由于遗传多态性很低，群体又小，几乎所有现存的银杉群体都面临由于随机事件导致的物种灭绝。更严重的是，当前该物种的适生环境不断恶化和片段化，以及异常低的生殖和存活率导致银杉与其它物种竞争能力很低。因此，除目前采取的原地保护策略外，迁地保护应给予优先考虑。此外，采用传统的控制授粉策略（在遗传上有显著差异的群体间开展人工杂交）是丰富其遗传多态性、恢复衰退群体的可行措施之一。

苍山冷杉复合体的居群遗传变异与谱系地理学

青藏高原为冷杉属(Abies)的多度中心，共分布有10种，9变种和4亚种。其中苍山冷杉复合体(Abies delavayi complex)包括3种，5变种和2亚种。它们的形态性状变异较小，且分布区重叠。迄今对该复合体的遗传多样性水平、分化程度以及进化历史仍缺乏了解。 本研究对苍山冷杉复合体的14个居群、302个个体进行取样，并对193个个体的母系遗传线粒体DNA nad1 intron2区和276个个体的父系遗传的叶绿体DNA trnS-trnG区进行了序列分析。该复合体的线粒体DNA nad1 intron2区的序列为675bp，其中有4个单碱基变异和1个插入/缺失，可分为6种线粒体单倍型。这14个居群的线粒体总核苷酸多态性(π)为0.00114，单倍型多态性(Hd)为0.627，居群间的遗传变异(FST)高达84.034%。叶绿体DNA trnS-trnG区的序列排列后为718bp，共有8个单碱基变异和4个插入/缺失，可分为12种叶绿体单倍型。这14个居群的总核苷酸多态性(π)为0.00116，单倍型多态性(Hd)为0.590，居群间的遗传变异(FST)为65.830%。以上结果显示苍山冷杉复合体居群间已经产生了强烈的遗传分化。叶绿体的3种主导单倍型(H1、H2和 H3)在YLXS、SKXS、GS和WX 4个居群中都有分布;而其它居群则只有主导单倍型(除SJLS外)中的1种或2种。造成边缘居群(如JZS)多样性较低的主要原因是冰期后群体在迁移过程中的遗传漂变和奠基者效应。根据谱系关系线粒体H1型和叶绿体H3型均为较古老的单倍型，线粒体和叶绿体的谱系关系均支持上述分析。 本研究初步推测青藏高原的东南部—横断山区(包括YLXS、SKXS、GS、WX、BMXS、ELS和EMS)可能为苍山冷杉复合体的冰期避难所，群体存在冰期后向西和向南扩张的过程。间冰期群体隔离和扩张过程中的奠基者效应是形成目前居群分化和遗传多样性分布格局的重要因素。

菰的分子谱系地理研究及茭白的起源

近几十年来，栽培作物及其野生近缘（祖先）种的群体遗传结构和进化历史的研究日益受到关注，因为此类研究不仅能加深人们对作物起源和驯化的认识，而且有助于作物野生资源的开发以及作物的遗传改良。分子谱系地理分析（Molecular phylogeography）是此类研究中的重要手段之一，能够有效地了解近缘群体的进化历程以及重建作物的驯化历史。菰（Zizania latifolia Turcz.）是东亚广泛分布、具有重要价值的水生草本植物，其栽培型—茭白是中国第二大水生蔬菜。尽管已有不少涉及此类群的研究，但迄今我们对菰的群体遗传结构和进化历史以及茭白的起源几乎一无所知。本研究从29个基因片段中筛选了2个在菰种内水平上具有显著变异量的核基因片段，进行了分子谱系地理研究，揭示了菰的遗传多样性水平及其地理分布格局，探讨了菰的群体演化历史，并初步探讨了茭白的起源和驯化历史。主要结果如下： 1）基因片段筛选 开展分子谱系地理学研究，需要采用具有显著种内变异的分子标记，为此我们通过预实验对一批备选基因片段进行了筛选。在18个叶绿体和2个线粒体片段中，测序的总长度达17100 bp，但没有发现任何变异位点。在9个核基因片段中，7个片段具有变异位点，但只有2个片段的变异量在1%以上，分别是Adh1a（2.70%）和GPATb（1.25%）基因。所以，本研究最后确定了采用这2个核基因片段来进行菰的分子谱系地理的研究。 2）Adh1a基因谱系地理分析 对来自21个天然群体126个个体，通过Adh1a基因的直接PCR和克隆测序共得到了252条序列，中性检测表明，Adh1a基因符合中性进化模型、没有重组并且有足够的变异量，适合用于进行菰的谱系地理研究和进化历史的推断。在物种水平上，菰的核苷酸多态性水平为θsil = 0.0089，跟一些作物近缘类群相比处于中等偏低的水平;不同群体的核苷酸多态性水平相差明显，多态性最高的群体出现在东北地区，并有从北向南递减的趋势。群体间存在着显著的遗传分化（FST = 0.481）表明群体之间的基因流有限。群体间的遗传距离与地理距离没有相关性，地理邻近的群体并没有共享关系相近的单倍型，整个群体缺乏明显的谱系地理结构。目前的遗传多样性分布格局可能是由于近几十年来的生境退化和丧失造成过去群体的片段化所致。根据群体遗传多样性水平的差异和基因谱系的地理分布格局以及分子钟估算的与北美近缘种的分化时间，我们推断菰的群体经历了从东北向华南逐步扩散的过程。 3）GPATb基因谱系地理分析 为更可靠地推断菰的谱系地理格局，我们选择了GPATb基因作为标记开展了进一步的分析。对相同的采样群体和个体共252条序列的分析表明，在物种水平上，GPATb的核苷酸多态性只相当于Adh1a基因的1/4。综合2个基因的结果，可以认为菰的核苷酸多态性水平是维持在较低的水平上。该位点体现的群体遗传分化也没有Adh1a基因明显。群体之间相近的遗传多样性水平和较低分化程度可能意味着该基因位点受到平衡选择作用的影响，这一推论也得到了中性检测结果的支持。因此，GPATb基因可能受到选择作用的影响，不能用来支持或推翻Adh1a基因的结果。 4）茭白的起源和驯化 对来自13个省份的65个茭白品种的Adh1a和GPATb基因片段进行测序，结果发现，所有的品种在这2个基因上都具有相同的基因型，Adh1a位点上表现为杂合体，而GPATb位点上则是纯合体。这说明在茭白的起源过程中发生了严重的驯化瓶颈效应，也即茭白是单次起源的，是从菰的少数几个甚至单个个体驯化而来。虽然文献考据表明，茭白最早的栽培地区为太湖流域，但我们的分子证据却并不支持其为茭白的驯化起源地点，而可能是在太湖流域以北地区起源的。鉴于采样的局限性，这一结论还有待于进一步的验证。同时2个基因的数据表明来自陕西、四川、云南、湖南和福建的6个菰群体可能是从人为引种的茭白逃逸成为野生的。因此，在以后野生菰群体的采集中，特别是在茭白种植地区，要在详细调查的基础上设计采集方案。

北京地区辽东栎群体遗传结构的研究

本文利用同工酶分析技术测定北京市东灵山区两个辽东栎(Quercus Liaotungensis Koidz)群体的遗传结构。共分析统计了13个酶系统的30位点。结果表明：辽东栎群体具有较高的遗传变异水平，两个小群体的平均多态位点百分率达86. 6%，等位基因平均数为2.25，平均期望杂合度为0.311。固定指数为负值(-0.138)表明群体中杂合体过量。小群体间的分化程度不高，两个小群体间的遗传距离为0.037。同工酶测定的总变异中，5.8%来自小群体间，其余(94.2%)来自小群体内。和具有相似生活特征的其它种类乔木相比，每代迁移率估计值(4.20)偏低。

柠条种子蛋白，同工酶遗传分析与群体遗传结构

本文研究了毛乌素沙地6个不同生态环境的柠条群体和1个锡盟草原站的小叶锦鸡儿群体的同工酶和种子蛋白的遗传变异。利用Brown等(/975)同工酶遗传分析方法对同工酶和种子蛋白的多态性进行了遗传分析。运用Shannon信息指数和Nei指数分析测定了锦鸡儿群体的遗传结构。结果表明： (l) Brown同工酶遗传分析的方法适合于柠条同工酶的遗传分析。 （2用LAP酶对柠条群体进行了精细的遗传结构研究。结果表明毛乌素沙地柠条群体的异交性。GST=D．134，即大部分的变异存在于群体内部，小部分的变异存在于群体之间。柠条群体的繁育系统与水分胁迫有关。随着生境变旱，繁育系统有向近交变化的趋势。 (3) Brown同工酶遗传分析方法也可以运用于种子蛋白遗传分析，柠条种子蛋白各亚基的遗传是孟德尔方式。 (4)由种子蛋白变异所统计测定的柠条群体的遗传分化系数GST=0.l81(Nei指数)或0.179(Shannon指数，Kongkiatngam改进)。群体变异水平按表型多样性依次为人工毛条群体>锡盟群体>滩地群体>硬梁群体>软梁群体>丘下群体>丘上群体。按遗传多样性依次为人工毛条群体>软梁群体>锡盟群体>滩地群体和硬梁群体>丘上群体>丘下群体。群体间基因流水平Nm>/，遗传距离D<0．1。 还试验对玉兰、合欢、紫藤、绿豆几种植物种子蛋白变异的遗传分析。最后对同工酶，种子蛋白遗传分析和群体遗传结构进行了讨论并提出今后工作的一些建议。