滇牡丹遗传多样性的ISSR分析

应用ISSR标记对中国西南地区特有植物滇牡丹(Paeonia delavayi)的遗传多样性进行了研究。从100个引物中筛选出10个用于正式扩增,在取自16个自然居群和1个迁地保护居群的511个个体中,检测到92个多态位点。在居群水平上,多态位点百分率（PPB）为44.61%,Nei′s基因多样性指数（H）和Shannon信息指数（I）分别为0.1657和0.2448。在物种水平上,多态位点百分率（PPB）为79.31%,Nei′s基因多样性指数（H）和Shannon信息指数（I）分别为0.2947和0.4355。居群间的遗传分化系数(G_ST)达0.4349。结果表明：滇牡丹遗传多样性水平较高,居群间遗传分化较大。结合以前的研究结果,对滇牡丹的现状进行评估的结果显示,滇牡丹并不濒危。     

昌化江河谷隔离对海南岛特有植物盾叶苣苔遗传多样性的影响

为评估盾叶苣苔的遗传多样性与遗传分化格局,探索影响盾叶苣苔遗传变异地理分布的因素,该研究采集盾叶苣苔(Metapetrocosmea peltata)11个种群172份材料,通过PCR扩增和测序分析核糖体转录间隔区(ITS)序列的变异式样。结果表明:(1)盾叶苣苔物种水平的遗传多样性很高(H_T=0.998, π=0.023 5),种群间基因流很弱(N_m=0.04)且存在强烈的遗传分化(G_ST=0.375)。(2)单倍型分析显示,盾叶苣苔的单倍型大多是种群特异的,仅白马岭与南茂岭种群有共享单倍型。(3)Mantel test表明,遗传距离和地理距离存在一定相关性(相关系数r=0.322,P=0.010)。(4)Structure聚类分析将盾叶苣苔划分为6种遗传成分,其地理分布与昌化江河谷导致的隔离样式基本一致,基于Nei遗传距离的种群聚类分析支持这一结果,显示盾叶苣苔遗传多样性的分布受到昌化江河谷的隔离作用。(5)AMOVA分析确定67%的变异来自地区间,表明地理隔离是盾叶苣苔种群分化的重要因素。这表明昌化江及其支流所引起的海南岛山地内部隔离是盾叶苣苔种群发生强烈遗传分化的重要原因,从而导致盾叶苣苔在物种水平具有较高的遗传多样性。上述研究结果为海南特有苦苣苔资源盾叶苣苔的保护和可持续利用提供了理论指导,将有助于理解海南岛特有植物和其他海岛植物遗传变异的地理分布及其影响因素。     

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(atpF-trnH、trnL-trnF和trnG-trnS)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:F_ST=0.336 47,G_ST=0.273,N_ST= 0.308; scnDNA:F_ST=0.094 87,N_ST=0.076,G_ST=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。     

基于SSR标记的新疆野杏群体遗传多样性及遗传结构

利用27对SSR分子标记对新疆4个野杏群体遗传多样性和遗传结构进行分析,评价新疆野杏遗传多样性水平和分化程度,为新疆野杏合理保护与利用提供科学依据。结果显示：（1）27对SSR引物共检测到431个等位基因（N_a）,各位点平均等位基因数（N_a）和多态性信息含量（PIC）分别为15.96和0.84;物种水平上Shannons信息指数（I）和期望杂合度（H_e）分别为2.21和0.78。（2）群体水平上等位基因数（N_a）、有效等位基因（N_e）、Shannons信息指数（I）、期望杂合度（H_e）和观察杂合度（H_o）分别为10.98、5.85、1.92、0.79和0.55;其中新源县野杏群体遗传多样性最丰富,巩留县群体遗传多样性最低。（3）基于F统计量分析的遗传分化系数（F_st）为0.05,基因流（N_m）为5.26;分子方差分析显示新疆野杏群体大部分遗传变异来自群体内（95.4%）,群体间的遗传变异仅占4.6%。（4）新疆野杏群体遗传距离为0.06~0.49,平均为0.24;遗传相似度为0.61~0.94,平均为0.80;遗传相似度的聚类分析和遗传距离的主坐标分析结果一致,均将供试4个群体划分为两组;Mantel检测显示,新疆野杏群体遗传距离与地理距离无显著相关（r=0.332,P＝0.16）。研究表明,新疆野杏资源具有丰富的遗传多样性,群体遗传分化程度较低,群体间遗传距离较小,这与新疆野杏群体的大小和悠久的演化历史以及群体间频繁的基因交流相关。     

山茶科3种中国特有濒危植物的遗传多样性研究

猪血木(Euryodendron excelsum)、圆籽荷(Apterosperma oblata)和杜鹃红山茶(Camellia changii)均为我国特有的山茶科珍稀濒危植物。本研究应用随机扩增多态性DNA(RAPD)检测方法,比较了这3个物种的遗传多样性。利用20－24个随机引物从猪血木、圆籽荷和杜鹃红山茶居群中分别获得206－305条RAPD谱带,多态位点百分率(PPL)分别为51.80％、80.26％和38.83％;居群间遗传分化指数G_ST分别为0.3566、0.1713、0.1242。结果显示：自然分布较广的圆籽荷的遗传多样性高于另外两种自然分布区狭窄的种类。3个物种的遗传变异均主要存在于居群内,但猪血木居群间的遗传分化明显高于圆籽荷和杜鹃红山茶,这可能与其生境的严重片断化有关。根据3个物种不同的遗传结构特点,建议加强现有自然居群的就地 保护,促进居群自然更新;收集不同分布点的种源,尽快建立广东山茶科珍稀濒危植物的保育中心,深入开展人工快繁研究,扩大这些种群的数量。     

基于SSR分子标记的草果栽培起源分析

为探索草果（Amomum tsaoko）的遗传多样性和栽培起源,对草果和拟草果（A. paratsaoko）在8个SSR位点上的遗传变异进行了分析。结果表明,8个SSR位点在20个草果居群和5个拟草果居群分别检测到149和101个等位基因,特有等位基因分别为44和59个。方差分析（AMOVA）表明,仅10.43%的遗传变异存在于2物种间,8.66%于种内居群间,80.91%于居群内（P<0.01）。拟草果居群总的遗传分化程度较大（0.15≤F_st≤0.25）,草果的为中度（0.05≤F_st≤0.15）。SMM模式下2物种的遗传分化均加大（F_st<P_st）。因此,草果和拟草果共享祖先的遗传多样性,可能通过随机遗传漂变完成谱系分选后基因突变的积累形成了现有遗传分化模式;围绕大围山的马关、屏边地区可能是草果栽培起源地理中心。     

滇北球花报春天然群体表型变异研究

滇北球花报春(Primula denticulata ssp. sinodenticulata)的早春蓝紫色球状花序具有独特的观赏价值, 但由于多种因素的影响, 其天然群体正在逐渐减少。为评价其遗传多样性水平, 我们对滇北球花报春10个天然群体进行了表型性状变异研究。结果表明: 滇北球花报春8个表型性状在群体间和群体内均存在极显著差异, 变异系数(CV)在4.73–9.90%之间, 表型分化系数(V_st)在0.1541–0.4069之间, 平均值为0.2854, 群体内的变异是表型变异的主要来源。根据8个表型性状的UPGMA聚类分析将10个天然群体划分为3类。依本研究结果, 在对滇北球花报春种质资源保护时进行就地保护是十分必要的, 并且应该优先保护表型变异较为丰富的天然群体。     

濒危物种巴东木莲的等位酶遗传多样性及其保护策略

为了确定中国特有濒危植物巴东木莲(Manglietia patungensis)的就地保护优先单元和制定迁地保护的取样策略,采用超薄平板聚丙烯酰胺等电聚焦电泳技术对巴东木莲的7个野生居群的等位酶遗传多样性及遗传结构进行了分析。通过对8个酶系统19个酶位点的分析结果来看,巴东木莲具有较高的遗传多样性和一定程度的遗传分化。每位点平均等位基因数（A）为1.57,多态位点百分率（P）为48.1%,平均预期杂合度（H_e）为0.192。巴东木莲居群间的遗传分化系数（G_ST）为0.165,说明其16.5％的遗传变异存在于居群间;基于遗传分化系数计算的基因流（N_m）为1.27,说明居群间存在适度的基因流;固定指数(F)为-0.191,显示巴东木莲居群杂合体轻微过量,纯合体略显不足。本研究表明,目前巴东木莲仍具有较高的遗传多样性并且在其适宜生境中可以完成自然更新,因此应采取以就地保护为主的综合保育策略。     

中华鳖阴茎头的组织学观察

2021年8月,在安徽省合肥市庐江县牛王寨采集到东亚腹链蛇属(Hebius)蛇类标本1号。经形态比较发现,该蛇明显不同于大别山地区已有的东亚腹链蛇属物种——棕黑腹链蛇(H. sauteri)和绣链腹链蛇(H. craspedogaster)。分子系统学分析显示,该标本与东亚腹链蛇(H. vibakari)遗传关系最近,且形态上符合东亚腹链蛇特征,提示该标本应为东亚腹链蛇。东亚腹链蛇是安徽省和大别山地区爬行动物分布新记录种,这也是该物种在中国东北地区之外首次被报道。该分布新记录扩大了对东亚腹链蛇的分布范围的认知,对东亚腹链蛇的种群分化和生物地理学研究具有重要意义。     

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。     

Phylogeography of two East Asian species in Croomia (Stemonaceae) inferred from chloroplast DNA and ISSR fingerprinting variation

The genus Croomia (Stemonaceae) comprises three herbaceous perennial species that are distributed in temperate-deciduous forests in Southeastern North America (C. pauciflora) and East Asia (C. japonica, C. heterosepala). The two Asian species have abutting ranges in South Japan, but C. japonica also occurs disjunctively on the adjacent Asiatic mainland in East China. In our phylogenetic analysis of Croomia, based on chloroplast (cp) DNA sequence variation of the trnL-F region, and rooted with Stemona spp., the two Asian species are identified as sister that likely diverged in the Mid-to-Late Pleistocene (0.84–0.13 mya), whereas the divergence of C. pauciflora dates back to the Late Plio-/Pleistocene (<2.6 mya). Phylogeographical analysis of the two East Asian species detected seven cpDNA (trnL-F) haplotypes across 16 populations surveyed, and all of those were fixed for a particular cpDNA haplotype (H_E = 0.0, G_ST = 1). A survey of inter-simple sequence repeats (ISSRs) markers also detected remarkably low levels of within-population diversity (C. japonica: H_E = 0.085; C. heterosepala: H_E = 0.125), and high levels of inter-population differentiation (C. japonica: Φ_ST = 0.736; C. heterosepala: Φ_ST = 0.550), at least partly due to pronounced regional genetic substructure within both species. Non-overlapping distributions of cpDNA haplotypes and strong genetic (cpDNA/ISSR) differentiation among populations and/or regions accord with findings of a nested clade analysis, which inferred allopatric fragmentation as the major process influencing the spatial haplotype distribution of the two species. Based on mismatch distribution analysis and neutrality tests, we do not find evidence of population expansion in both species. Overall, we conclude that components of temperate-deciduous forest types in South Japan and East China are particularly sensitive to range fragmentation, isolation, and enhanced (incipient) species formation through climate-induced expansions of other forest types over glacial and interglacial periods of the (Late) Quaternary.     

Divergence and gene flow between the East Sea and the Southeast Atlantic populations of North Pacific light fish Maurolicus japonicus Ishikawa

In the present study, we examined the divergence time and the magnitude of gene flow between two distantly separated populations of North Pacific light fish Maurolicus japonicus, one in the southern part of the East Sea (off Korea) and the other in the Southeast Atlantic Ocean (off Namibia). The mitochondrial 16SrDNA sequences (524 base pairs) obtained from the two populations were analyzed using the isolation with migration (IM) coalescent method as well as the conventional F _ST statistic and a phylogeographic method. A significant nonzero F _ST value (0.176, P<0.05) indicated genetic differentiation between the two populations. The low level of nucleotide diversity compared to the moderately high level of haplotype diversity implied that the populations have experienced a bottleneck followed by rapid growth in both populations. IM analysis suggested that these two populations most likely split approximately 500?C800 K years ago during the Pleistocene climatic oscillations and that gene flow has occurred unidirectionally from the Southeast Atlantic population to the East Sea population. Nested clade phylogeographic analysis supports restricted gene flow between the two populations.     

Genetic diversity of mitochondrial cytochrome b gene in swamp buffalo

The swamp buffalo (Bubalus carabanensis) is mainly bred for meat, transport and rice cultivation in China and Southeast Asian countries. In the current study, we investigated the genetic diversity, maternal origin and phylogenetic relationship of swamp buffalo by analyzing 1,786 mitochondrial cytochrome b (cytb) sequences from China, Vietnam, Laos, Thailand, India and Bangladesh. Our results indicated that the swamp buffalo can be divided into two major lineages (SA and SB with the sublineages) and three rare lineages (SC, SD and SE), which showed strong geographic differentiation. The SA1 lineage represented a major domestication event, which involved population expansion. Regions III and V showed higher haplotype diversity than the other regions, indicating that the regions of Southwest China and IndoChina are potential domestication centers for the swamp buffalo. In addition, the swamp buffalo showed a closer phylogenetic relationship to tamaraw. In conclusion, our findings revealed a high level of genetic diversity and the phylogenetic pattern of the swamp buffalo.     

Cryptic diversification of the swamp eel Monopterus albus in East and Southeast Asia, with special reference to the Ryukyuan populations

The swamp eel Monopterus albus is widely distributed in tropical and subtropical freshwaters ranging from Southeast Asia to East Asia, and is unique in its ability to breathe air through the buccal mucosa. To examine the genetic structure of this widespread species, molecular phylogenetic analyses of mitochondrial 16S rRNA sequence (514 bp) were conducted for 84 specimens from 13 localities in Southeast and East Asia. The analyses showed clearly that this species can be genetically delineated into three clades based on geographical populations [China–Japan (Honshu + Kyushu), Ryukyu Islands, and Southeast Asia clades], with each clade exhibiting its own reproductive behavior. Therefore, “M. albus” is believed to be composed of at least three species. The Southeast Asia clade with the highest genetic diversity may include more species. The Ryukyu clade was estimated to have diverged more than 5.7 million years ago, suggesting that the Ryukyuan “M. albus” is native. In contrast, in the China–Japan clade, all haplotypes from Japan were closely related to those from China, suggesting artificial introduction(s).     

Microsatellite DNA markers indicate three genetic lineages in East Asian indigenous goat populations

The genetic differentiation and phylogenetic relationships of 18 indigenous goat populations from seven East Asian countries were analysed based on data obtained from 26 microsatellite DNA markers. The mean number of alleles (MNA) per population ranged from 2.5 to 7.6, with an average of 5.8. Genetic variability estimated from MNA and heterozygosity (H_E and H_O) were relatively low in coastal and island populations. A heterozygous deficiency within populations (F_IS = 0.054, P < 0.001) and total inbreeding (F_IT = 0.181, P < 0.01) were observed, and genetic differentiation in the populations (F_ST) was 13.4%. The results of Bayesian model‐based clustering and a neighbour‐joining tree based on Nei's genetic distance showed that Asian goat populations could be subdivided into at least the following three genetic clusters: East Asian, Southeast Asian and Mongolian. These results are in close accordance with conventional morphological and geographical classifications and migration history.     

Population genetic structure and phylogeographical pattern of rice grasshopper, <Emphasis Type="Italic">Oxya hyla intricata</Emphasis>, across Southeast Asia

The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu’s F _s values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.     

Phylogeography of Wild Musk Shrew (Suncus Murinus) Populations in Asia Based on Blood Protein/Enzyme Variation

The musk shrew (Suncus murinus) is an insectivore species that inhabits tropical and subtropical Asia widely. To clarify the genetic relationship among wild musk shrew populations, we examined the electrophoretic variants of biparentally inherited genetic markers at 10 loci coding for eight blood proteins/enzymes in a total of 639 animals and compared the results obtained from the mitochondrial DNA data. The principal-component analysis performed using the allele frequency data revealed that the 17 populations could be divided into two major groups, a South Asian group and a Southeast Asian group that includes several island populations bound by Myanmar. The degrees of genetic divergence among populations were higher within the Southeast Asian group than within the South Asian group. This finding was incongruent with the mtDNA diversity. Analysis conducted at the individual level showed that a shrew from the central region in Myanmar that carries a South Asian type of mtDNA showed the electrophoretic variants specific to the Southeast Asian group, suggesting that this region is a contact zone between the two major groups.     

青藏高原濒危植物唐古特大黄的遗传多样性

唐古特大黄(Rheum tanguticum)是中国传统的中藏药材,近几年由于生境的严重破坏,已濒临灭绝,并被列入濒危植物名单。为了探索唐古特大黄物种濒危的原因并保护其野生资源,本研究采集了9个居群87个个体的唐古特大黄样本,基于该物种的叶绿体基因trn S-G序列对其进行了遗传多样性研究。结果表明,唐古特大黄物种具有较高的遗传多样性水平(Ht=0.694),其中95.97%的遗传分化来自于居群间(G_(ST)=0.960),4.03%的遗传分化来自于居群内(Hs=0.028)。AMOVA分析也显示唐古特大黄居群间基因流较小(N_m=0.01),存在较高的遗传分化(F_(ST)=0.9631)。唐古特大黄较高的遗传多样性水平可能与该物种较长的进化史和生活史有关,居群间较高的遗传分化可能与高山地区特殊的地理环境和人类活动有关。根据研究结果,建议对唐古特大黄所有野生居群进行就地保护,同时收集种质资源开展异地繁殖工作,以保护物种的遗传多样性,维持其进化潜力。     

Population genetic evidence for the east–west division of the narrow-barred Spanish mackerel (<Emphasis Type="Italic">Scomberomorus commerson,</Emphasis> Perciformes: Teleostei) along Wallace’s Line

Mitochondrial DNA D-loop (control) region (426-bp) was used to infer the genetic structure of Spanish mackerel (Scomberomorus commerson) from populations in Southeast Asia (Brunei, East and West Malaysia, Philippines, Thailand, Singapore, and China) and northern Australia (including western Timor). An east–west division along Wallace’s Line was strongly supported by a significant AMOVA, with 43% of the total sequence variation partitioned among groups of populations. Phylogenetic and network analyses supported two clades: clade A and clade B. Members of clade A were found in Southeast Asia and northern Australia, but not in locations to the west (Gulf of Thailand) or north (China). Clade B was found exclusively in Southeast Asia. Genetic division along Wallace’s Line suggests that co-management of S. commerson populations for future sustainability may not be necessary between Southeast Asian nations and Australia, however all countries should share the task of management of the species in Southeast Asia equally. More detailed genetic studies of S. commerson populations in the region are warranted.     

Phylogeography of <Emphasis Type="Italic">Ceriops tagal</Emphasis> (Rhizophoraceae) in Southeast Asia: the land barrier of the Malay Peninsula has caused population differentiation between the Indian Ocean and South China Sea

The genetic structure of mangrove species is greatly affected by their geographic history. Nine natural populations of Ceriops tagal were collected from Borneo, the Malay Peninsula, and India for this phylogeographic study. Completely different haplotype compositions on the east versus west coasts of the Malay Peninsula were revealed using the atpB-rbcL and trnL-trnF spacers of chloroplast DNA. The average haplotype diversity (Hd) of the total population was 0.549, nucleotide diversity (θ) was 0.030, and nucleotide difference (π) was 0.0074. The cladogram constructed by the index of population differentiation (G _ST) clearly separated the South China Sea populations from the Indian Ocean populations. In the analysis of the minimum spanning network, the Indian Ocean haplotypes were all derived from South China Sea haplotypes, suggesting a dispersal route of C. tagal from Southeast Asia to South Asia. The Sunda Land river system and surface currents might be accountable for the gene flow directions in the South China Sea and Bay of Bengal, respectively. The historical geography not only affected the present genotype distribution but also the evolution of C. tagal. These processes result in the genetic differentiation and the differentiated populations that should be considered as Management Units (MUs) for conservation measurements instead of random forestation, which might lead to gene mixing and reduction of genetic variability of mangrove species. According to this phylogeographic study, populations in Borneo, and east and west Malay Peninsula that have unique genotypes should be considered as distinct MUs, and any activities resulting in gene mixing with each other ought to be prevented.