基于RAPD标记的丽江云杉遗传多样性及谱系地理

由于青藏高于独特的地理环境,第四纪冰期反复的退缩和扩展对目前该地区生物物种的地理分布及居群结构产生重要的影响。本文对这一地区特有分布物种丽江云杉(Picea likiangnsis)3个变种丽江云杉变种(var. likiangensis)、川西云杉变种(var. rubescens)和林芝云杉变种(var. linzhiensis)共11个种群228个个体进行RAPD分析,研究其遗传多样性及谱系地理。结果表明,该种具有较高的总体遗传多样性,多态位点达85.42%;然而在群体水平上却保持了相对低的多态性,种群间差异不显著,种群平均多态条带百分率为62.31%,Nei’s平均遗传多样性指数(H_E)为0.250,Shannon’s多样性指数(H_pop)从0.267到0.421 1。Nei’s基因多样性(G_ST=0.256)和AMOVE分析(Phi_st=0.236)表明,群体间有较高的遗传分化,群体间基因流有限(N_m=1.453 2),远远低于已报道的其它松科植物。UPGMA聚类分析表明3个形态上分离的变种没有单个聚成一枝,形成单系群。本研究认为,在第四纪冰期丽江云杉这一种在南部可能存在至少3个不同的避难所,北边和西边的居群应该是南方避难所里的居群经过不同的回迁路线而产生的,有可能是由于种内亚种间的反复杂交造成了目前的种群分布模式。     

基于叶绿体微卫星研究鄂报春谱系遗传结构

鄂报春Primula obconica作为一种广泛栽培的园艺植物,其野生居群的遗传多样性及遗传结构的研究还少见报道。本文通过叶绿体微卫星分析了17个鄂报春野生居群(共278个个体),共发现4个多态性位点(16个等位基因),得到14个单倍型。结果表明鄂报春具有很高的总基因多样性(HT=0.971)和极低的居群内基因多样性(HS=0.028);分子方差分析(AMOVA)显示98%的变异存在于居群间。这些结果说明早期的生境片断化及有限的种子传播能力是造成当前遗传结构的重要原因。Nst值显著大于Gst值,表明关系相近的单倍型会出现在相同的地区内,同时最小生成树(MST)的分析结果证实了这样的结论。我们在最小生成树的两个组中推断出一些古老单倍型,并推测在冰期时湖北和我国的西南地区可能是该物种的避难所。     

滇魔芋中国种群的谱系地理研究

中国西南山区是重要的生物多样性热点地区, 复杂的地形地貌促进了种群的隔离分化, 形成了丰富的物种。魔芋属(Amorphophallus)植物是原产中国南方地区和中南半岛的重要经济作物, 物种和种群呈间断分布。魔芋属物种自然种群的种群动态历史和遗传分化机制有待深入研究。该研究以中国境内的滇魔芋(A. yunnanensis)自然种群为对象, 通过5个叶绿体DNA片段对16个种群进行了谱系地理学研究, 并分析了其遗传分化格局的形成机制。遗传变异分析表明, 滇魔芋各种群的遗传多样性较低(核苷酸多样性: 0.000 07-0.001 82), 且种群之间存在高水平的遗传分化(平均遗传分化指数为0.363)。系统发育分析结果显示, 滇魔芋呈显著的东西分化格局, 东部支系主要由贵州高原及邻近的湘西、桂北的种群组成, 而西部支系则由云南高原的种群组成。此外, 在东部支系发现了近期的种群扩张以及与西部种群的基因交流现象。基于滇魔芋的种群动态历史和显著的地理隔离模式, 推测山地与河流导致的隔离生境和冰期气候波动可能对滇魔芋的种群遗传分化具有重要作用。     

基于核基因和叶绿体基因的台湾水韭遗传多样性和遗传结构的分析

利用核基因和叶绿体基因对台湾水韭（Isoetes taiwanensis Devol）2个居群20个样本的遗传多样性和遗传结构进行了分析,并对台湾水韭的保育提出了建议。核基因的检测结果显示,2个居群共存在18个单倍型,单倍型多样性为0.9842,核苷酸多样性为0.00215,居群间基因流N_m为4.26,居群间分化系数G_st值为0.05543;叶绿体DNA的检测结果显示,单倍型数目为6,单倍型多样性为0.6211,核苷酸多样性为0.00326。其中台北居群的单倍型多样性和核苷酸多样性均比金门居群高。核基因和叶绿体基因的AMOVA分析显示,居群内的遗传差异远高于居群间。台湾水韭的核苷酸多样性相对其他水韭属植物较低,可能与台湾水韭的染色体倍型以及狭域分布有关。居群结构的形成可能和基因流以及奠基者效应有关。宜采用原地和迁地保护的方法对居群进行保护。     

西南地区野生刺梨的遗传多样性和遗传结构研究

为了探究西南地区野生刺梨(Rosa roxburghii)的遗传多样性和起源演化,该研究基于 2 段单拷贝核基因(GAPDH和ncpGS)和 3 段叶绿体基因(atp F-trn H、trn L-trn F和trn G-trn S)的拼接序列,对刺梨 27 个野生居群共 320 个个体进行PCR扩增和测序,并用相关软件对测序结果进行分析.结果表明:(1)在单拷贝核基因和叶绿体基因水平上刺梨均表现出较低的遗传多样性(scnDNA:Hd = 0.469 2,π = 0.000 49;cpDNA:Hd=0.653 4,π=0.000 65),并且不同居群间存在较大差异.(2)分子方差分析(AMOVA)结果均显示,遗传变异主要发生在居群内,表明居群内的变异是野生刺梨遗传变异的主要来源,居群间存在明显的遗传分化(cpDNA:FST=0.336 47,GST =0.273,NST= 0.308;scnDNA:FST =0.094 87,NST =0.076,GST =0.056),刺梨的分布不具有明显的谱系地理结构(P＞0.05).(3)中性检验 Tajima's D值均为不显著负值,符合中性进化模型.Fu's Fs值均为显著负值,结合失配分析曲线,推测刺梨种群在小范围内经历过扩张,但总体上维持稳定状态.(4)根据单倍型多样性得出,毕节地区的居群遗传多样性水平较高并且拥有丰富的单倍型,推测可能为冰期避难所,因此应对其实施就地保护,对于拥有特殊性状和特有单倍型的居群也应采取优先保护措施.该文为野生刺梨资源保护和遗传育种提供了一定的参考价值.     

毛茛叶报春高分化的谱系地理结构

毛茛叶报春（Primula ranunculoides Chen）是我国特有的珍稀濒危花卉,其野生种质资源已十分稀少。为了揭示其谱系地理结构,本文对11个居群114个个体的叶绿体trnL-F和trnS-G基因片段进行了测序分析。结果共检测到10个单倍型,除YJPA和YJPB两居群共享一个单倍型（H9）外,其余各居群均仅有一个特有单倍型,居群内不存在单倍型多样性。毛茛叶报春具高分化的谱系地理结构,居群间的总平均遗传距离达0.015,单倍型间的平均突变次数高达31.2步,两者均显著高于同属的近缘种。其种子散布能力弱、生境片断化和地理隔离明显及两年生的生活史可能是导致其高分化谱系地理结构产生的主要原因。Samova、Structure以及TCS分析均支持将毛茛叶报春11个居群的遗传结构分为6组,它们与地形（山脉）关系密切对应,彼此间分化明显,因此建议不同山体的居群应视为不同的保护单元进行遗传管理。     

基于线粒体COⅡ基因序列的中华蜜蜂地理种群的遗传多样性研究

通过分析我国20个不同地理种群中蜂线粒体COⅡ序列的变异,对中华蜜蜂群体遗传分化程度遗传多样性进行全面研究。结果表明:COⅡ基因部分序列中共发现16个变异位点和18个单倍型,核苷酸差异数的平均值为0.939,核苷酸分歧度(Dxy)在0.1%~0.965%之间变化,核苷酸遗传距离为-0.007%~1.489%。总种群的Fst为0.4978,差异均极显著(P0.001)。研究结果显示种群总体单倍型多样性较为丰富,种群间核苷酸分歧度差异很大。20个东方蜜蜂不同地理种群间存在显著的遗传分化。     

基于叶绿体DNA非编码序列的蒙古扁桃谱系地理学研究

该研究选取中国西北干旱区第三纪孑遗植物蒙古扁桃（Amygdalus mongolica）,基于叶绿体DNA非编码trnH psbA序列对蒙古扁桃17个居群324个个体进行了谱系地理学研究。结果表明：（1）蒙古扁桃trnH psbA序列长度350 bp,变异位点63个,共有9种单倍型,居群间总遗传多样性为（H_t）为0.758,居群内平均遗传多样性为（H_s）为0.203,贺兰山东麓及阴山南麓边缘的居群具有较高的单倍型多样性及核苷酸多样性并固定较多特有单倍型,推测这2个地区是蒙古扁桃在第四纪冰期时的重要避难所。（2）AMOVA分析表明,居群间的遗传变异为83.84%,居群内的遗传变异为16.16%,居群间遗传分化系数N_st>G_st（N_st=0.733, G_st=0.655, P>0.05）,表明蒙古扁桃不存在明显的谱系地理结构;根据单倍型地理分布及网络关系图,把蒙古扁桃自然地理居群分为东、西两大地理组群,而且东、西地理组群没有共享单倍型;居群遗传结构分析表明,两大地理组群遗传分化较大。（3）蒙古扁桃居群在间冰期或冰期后经历了近期的居群扩张,由于奠基者效应使得多数居群只固定了单一的单倍型。     

梵净山冷杉和元宝山冷杉的叶绿体微卫星遗传多样性分析

梵净山冷杉和元宝山冷杉是极度濒危的国家一级重点保护植物.应用叶绿体微卫星标记(cpSSR)研究它们的遗传多样性,并与同属的广布种岷江冷杉的一个种群进行比较.结果表明：3对 cpSSR 引物(Pt63718、Pt30204和Pt71936)在这3种冷杉的249个个体中共检测到21个等位基因,组成35种单倍型;它们的单倍型数和有效单倍型数分别为梵净山冷杉(No＝12,Ne＝3．92),元宝山冷杉(No＝9,Ne＝3．28),两者均低于广布种岷江冷杉(No＝14,Ne＝11．57);梵净山冷杉和元宝山冷杉的稀有单倍型较少,其频率最高的单倍型分别出现在该种群的46．0％和44．1％的个体中;梵净山冷杉(He＝0．75)和元宝山冷杉(He＝0．70)的单倍型多样性也低于岷江冷杉(He＝0．97).梵净山冷杉和元宝山冷杉的叶绿体微卫星遗传多样性水平低.     

基于叶绿体DNA变异的湖北梨属种质系统进化及遗传多样性分析

利用trnL intron、trnL-trnF、trnS-psbC和accD-psa I等4个叶绿体DNA片段对来自湖北省的88份梨属种质资源进行系统进化和遗传多样性分析。结果表明,4个cpDNA片段共检测到变异位点11个,其中单一突变位点6个,插入/缺失(Indel)位点5个。acc D-psa I多态性最高,其变异位点数、核苷酸多态性和单倍型多样性均为最高。供试梨种质的核苷酸多样性和单倍型多样性分别为0.00112和0.769;Tajima's D检验值在P0.10水平上均不显著,表明所检测的4个区域以及合并后的片段均遵循中性进化模型;4个序列合并共检测到叶绿体单倍型10个,其中兴山梨种质中检测到的单倍型最多,荆门其次;Hap2和Hap5是2个主要单倍型,分别占总样本数的31.82%和30.68%;中介邻接网络图显示东方梨和西洋梨独立进化,而较为原始的稀有单倍型Hap8和Hap9均位于荆门,暗示该地区可能为砂梨的起源中心或多样性中心之一。     

根据cpDNA trnL-F非编码区序列变异分析黑桫椤海南和广东种群的遗传结构与系统地理

以黑桫椤分布在海南和广东 9个种群为材料 ,通过 PCR产物直接测序和克隆后再测序的方法测定了叶绿体 DNA(cp DNA) trn L- F非编码区序列。序列长度介于 10 17bp至 10 2 1bp;碱基组成 A T含量较高 ,百分比值为 6 0 .4 3%～ 6 2 .2 6 %。根据序列的核苷酸变异共鉴定出 15个单倍型。黑桫椤具高水平单倍型多样性 (h=0 .880 )和较高水平核苷酸多样性 (Dij=0 .0 0 342 ) ,其悠长的进化历史可能增加了遗传变异在谱系内的积累。单倍型最小生成网图和邻接树、种群间分化度 (FST=0 .12 6 4 5 )和基因流 (N m=3.4 9)、AMOVA分析 (地区间遗传变异占 11.91% ,p>0 .0 5 )以及 DNA歧义度结果一致显示 ,黑桫椤分布在海南和广东的种群彼此间不存在遗传分化。黑桫椤单倍型的系统发育地理式样具“星状”特征 ,提示种群在历史上曾经发生过扩张 ,扩张后的种群还未能获得足够时间去建立更加复杂的结构     

Low levels of intraspecific genetic variation at a rapidly evolving chloroplast dna locus in North American duckweeds (Lemnaceae)

Although most previous studies on chloroplast (cp) DNA variation in plants have concentrated on systematics and evolution above the species level, intraspecific variation in cpDNA is common and has provided useful insights into population-level evolutionary processes. Polymerase chain reaction methods were used to examine restriction site and sequence variation in the chloroplast rpLI6 gene within and among populations of duckweed species (Spirodela and Lemna) from the southern and eastern United States. To our knowledge, the rpL16 region has not previously been used to investigate cpDNA variation in nature. While considerable restriction site and sequence variation were detected among species, no variation was found within populations of either of the two species (S. punctata and L. minor) selected for sequence analysis, and S. punctata showed no interpopulational variation. Two cpDNA haplotypes were identified in L. minor, with one haplotype restricted to three sites in Louisiana and the other found in all other populations sampled. This paucity of variation cannot be readily explained as the result of a low mutation rate. In general, group II introns appear to be subject to very little functional constraint, and extensive sequence differences have been found between species in the chloroplast rpL16 intron in particular. However, factors such as historical range expansions and contractions, founding effects, fluctuations in local population size, and natural selection may play a role in reducing cpDNA sequence variability in these species.     

Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.)

Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat‐bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo–P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.     

Phylogeographic structure of Hippophae tibetana (Elaeagnaceae) highlights the highest microrefugia and the rapid uplift of the Qinghai‐Tibetan Plateau

The uplift of the Qinghai‐Tibetan Plateau (QTP) dramatically changed the topography and climate of Asia and affected the biodiversity of the plateau and its adjacent areas. However, the effects of the uplift on the dispersal, differentiation and adaptation of plants remain a puzzle when the date and processes of the uplift cannot be determined with certainty and the impacts of the Quaternary glaciations on plants on the QTP are unknown. To clarify the relationships among plants on the QTP with the plateau uplift and the Quaternary glaciations, the cpDNA trnT‐trnF regions of 891 individuals from 37 populations of Hippophae tibetana, endemic to the QTP, were sequenced in the present study. A total of 50 haplotypes were found and a strong phylogeographic structure was revealed (N_ST = 0.854, G_ST = 0.611, N_ST > G_ST, P < 0.01). The results show that three main lineages of the present populations of H. tibetana occupy the western, the middle, and the eastern geographical range, respectively, and their divergence time dates back to 3.15 Ma before present. Of 50 haplotypes, 33 (66%) are private haplotypes, which are restricted to single populations. These private haplotypes are scattered throughout the present geographical range of H. tibetana and originated from multiple differentiations in many lineages during more than 1.0 Ma period, strongly suggesting that multiple microrefugia of H. tibetana existed throughout the present geographical range during the last glacial maximum (LGM) and even earlier glaciations. Additionally, the average elevation of present populations is over 4500 m in the west and the equilibrium‐line of glaciers in the LGM was 500–300 m lower than present in the major interior part of the plateau suggesting that at most sites in the west, LGM microrefugia of H. tibetana may have been above 4000 m above sea level, the highest of all known refugia. Moreover, the divergence times among and within the three lineages and their distinct distributions as well as dispersal barriers support the theory of the recent and rapid uplift of the QTP. The rapid uplift of the plateau within the last 3.4 Ma and the associated environmental changes may have affected the dispersal and differentiation of H .tibetana and shaped its phylogeographic structure.     

Phylogeography of Iris missouriensis (Iridaceae) based on nuclear and chloroplast markers

We investigated the phylogeography of Iris missouriensis (Iridaceae), which is widely distributed in western North America. We utilized transposon display and DNA sequencing to quantify nuclear and chloroplast genetic structure. Our objectives were (i) to characterize the geographic structure of genetic variation throughout the species range, (ii) to test whether both margins of the range show reduced genetic diversity as predicted by north-south expansion and contraction associated with climate change, and (iii) to determine whether the subspecies Iris missouriensis ssp. longipetala is genetically distinct. We found that genetic diversity was significantly lower in the northern part of the range but was not significantly different between the central and southern regions, indicating greater stability of the southern margin vs. the northern. Among-population differentiation was high (PhiPT=0.52). The largest divisions in each marker set were concordant and separated the southern Rocky Mountains and Basin and Range provinces from the remainder of the range. The boundaries of this phylogeographic break do not coincide with gaps in present-day distributions or phylogeographic breaks identified in other species, and may indicate a measure of reproductive isolation. Consistent with current treatments, we did not find support for the taxonomic placement of I. missourienis ssp. longipetala as a distinct species. Although transposon display has been used to investigate relationships among crop accessions and their wild relatives, to our knowledge, this is the first use of these markers for population-level phylogeography of a nonmodel species and further demonstrates their utility in species recalcitrant to amplified fragment length polymorphism protocols.