小熊猫种群遗传结构和地理分化

本文采用分子系统地理学的研究方法 ,对我国小熊猫 (Ailurusfulgens)地理分布格局的形成原因进行了探讨。我们从四个地理单元的 32号样品中成功地扩增出了 371bp的线粒体DNA控制区片段 ,在所有可比较的 35 7bp的序列中 ,发现 2 9个变异位点 ,其中转换和颠换分别为 2 1和 8,没有插入 /缺失。在四个地理单元中 ,共有 16种线粒体DNA单倍型 ,且在各地理单元中都具有较高的单倍型的多态性。进一步分析表明 ,各单倍型之间的遗传距离平均为 1 6 0 % ,76 5 9%的遗传差异发生在地理单元间 ,仅 2 3 4 1%发生在单元内。分子变异分析和系统重建结果也表明 ,各地理单元之间不存在共享的单倍型 ,YN (云南地理单元 )与XL (相岭地理单元 )和QL (邛崃地理单元 )之间存在着显著的遗传分化 ,FST分别为 0 336和 0 35 1(P <0 0 0 1) ,其余地理种群之间分化不明显 (P >0 0 5 ) ,单倍型缺乏比较明显的地理分布格局 ,各地理单元中的单倍型相互散布在不同的分布群中。经Fs检验 (Fs=- 10 12 1) ,并结合化石资料 ,我们认为由于受第四纪气候和环境变化的影响 ,小熊猫种群在进化过程中曾经历种群暴发而不断扩散 ,从而形成今天的分布格局。     

中国大陆梅花鹿mtDNA控制区序列变异及种群遗传结构分析

测定了37只中国大陆梅花鹿(Cervus nippon)不同种群mtDNA控制区5′端351 bp的序列，共发现23个变异位点，定义了5种单元型。分子变异分析表明，中国大陆梅花鹿出现了显著的种群分化(Φm＝0．45，Fst＝0．60，P＜0．001)，支持把分布于东北、华南和四川的梅花鹿种群归入各自独立的管理单元。中国大陆、日本南部和日本北部之间无共享单元型，且有25个鉴别位点。最小跨度网络图(Minimum spannlng network，MSN)和基于最大似然法和邻接法的系统发生分析均把单元型聚类为对应于中国大陆、日本南部和日本北部的三个单系，其中中国大陆和日本南部梅花鹿有相对较近的亲缘关系，支持日本梅花鹿的祖先通过至少两个大陆桥从亚洲迁移到日本的观点。     

中国大陆黑斑侧褶蛙基于mtDNA控制区序列的种群遗传结构

用分子遗传数据研究了黑斑侧褶蛙 (Pelophylaxnigromaculata)种群的遗传结构和分化。标本采自中国大陆的 12个地点 ,每个种群测定 10只或少于 10只蛙的mtDNA控制区 5′端 6 85bp的序列。 112只蛙的序列经比对后 ,共发现 111个变异位点 ,定义了 6 7种单元型 ,其中 7种单元型为地方种群间共享单元型 ,多数单元型为地方种群内特有。 12个地方种群合并成一个大种群分析时表明 ,中国大陆黑斑侧褶蛙的线粒体单元型多样性相当高 (h=0 98± 0 0 0 5 ) ,总体核苷酸多样性也较高 (π =0 0 30 3± 0 0 0 2 9)。这样高的单元型多样性和核苷酸多样性与黑斑侧褶蛙作为古北界和东洋界的广布种、种群大是相应的。基于最大简约法的单元型系统发生树和基于邻接法的地方种群系统发生分析中 ,吉林通化和辽宁辽阳种群与中国大陆其他地方种群构成姐妹群。分子变异分析表明 ,吉林和辽宁种群代表的吉辽组和其余 10个地方种群代表的综合组间出现了显著的种群分化 (Φ CT=0 80 9,P <0 0 0 1) ,各地方种群间成对的FST及种群间的核苷酸歧异度也均表明两者之间出现了显著的遗传分化。吉辽组与综合组间的遗传分化最可能的原因就是受第四纪冰川的影响     

羚牛的遗传多样性及其种群遗传结构分析

羚牛是亚洲大陆一种特有的大型珍稀动物,目前正面临着栖息地丧失、片段化和人类活动的严重威胁。为了有效地保护这种濒危动物,全面了解羚牛的种群结构、进化历史和整个分布区内遗传多样性的分布是至关重要的。本研究以mtDNA D-loop330bp基因片段为分子标记,比较分析了来自陕西秦岭、甘肃南部、四川岷山、邛崃山和云南贡山的40个样品的序列差异,根据分布特点将所采集到的羚牛分为3个地理单元,即秦岭、四川和云南。结果表明,在3个地理单元中存在4种单倍型,且地理单元间不存在共享单倍型,相互单倍型之间的平均序列差异为1.66％。进一步分析表明,3个地理单元间的基因流较低,存在着显的遗传分化 ,说明羚牛具有明显的系统地理分布格局。同时提出应将分布于秦岭山区、唐家河青川地区、天全以及云南贡山地区作为独立的管理单元分别加以保护。     

塔里木兔种群遗传结构的初步探讨

塔里木兔作为中国特有种, 其种群遗传结构直到现在还未知。我们从采自于新疆维吾尔自治区3 个种群的25 号样品中扩增得到529 bp 线粒体DNA 控制区片段, 共发现存在76 个多态性位点。全部样品中定义了19 个单倍型, 每个种群都显示了很高的单倍型多态性。进一步分析表明, 3 个种群存在明显的遗传分化和较低的基因流。通过错配分布和Fu’s 中性检验分析发现, 阿克苏(AKS) , 若羌(RQ) 和疏勒(SL) 种群相对比较稳定。     

邛崃和相岭山系小熊猫种群的遗传结构

测定了来自小熊猫主要分布的两大山系———相岭和邛崃的 2 3只小熊猫样品的mtDNA控制区 5’端 5 69bp序列 ,共发现 2 3个变异位点 ,定义了 8种单元型 ,其中邛崃山系 5种 ,相岭山系 3种。分析结果表明 ,两山系均表现出较低的核苷酸多态性 ;单元型多态性差异明显 ,其中邛崃山系高于相岭山系。分子变异分析表明 ,两山系的小熊猫种群间具有较高的基因流 (Nm =2 95 ) ,两种群遗传分化不明显 (ΦST=0 1 45 ,P >0 0 5 )。结合细胞色素b序列分析 ,认为两种群可能是从经历了近期瓶颈效应的同一祖先群衍生而来 ,并且可将两山系的小熊猫种群作为一个管理单元进行保护和管理     

四川地区猕猴线粒体DNA 控制区遗传多样性及其种群遗传结构

猕猴是最理想的医学实验灵长类动物,并且是国家二级保护动物。四川地区的猕猴数量多、分布广,全面了解其遗传背景对于该地区猕猴资源的保护与合理利用具有重要的意义。本研究对来自四川8 个地理种群的231个不同猕猴个体的线粒体DNA 控制区部分序列进行了测定和群体分析,发现了110 个变异位点(22. 49% ),定义了56 种单倍型,其单倍型多样性(h)平均值为0. 686、核苷酸多样性(π)平均值为0. 01483,种群总体遗传多样性较高;进一步分析表明,8 个地理种群间存在着明显的遗传分化(F_st = 0. 70412,P < 0. 05),种群间基因交流较低(N_m < 1);系统发育树显示,四川猕猴8 个地理种群的单倍型基本上成簇分布在系统树上,与地理位置呈现一定的对应关系,说明四川猕猴具有明显的系统地理分布格局。地理隔离和人类活动可能是促使四川猕猴种群分化的主要因素。     

长江中下游不同地理种群鳜遗传结构研究

以长江、通江湖泊(洞庭湖、鄱阳湖)、陆封型湖泊(牛山湖、涨度湖、汤逊湖、肖四海湖)不同水体鳜为研究材料,利用微卫星遗传标记对其种群遗传结构进行分析,结果表明:由期望杂合度(He)和多态信息含量指数(PIC)检测的遗传多样性由大到小的顺序为:长江、通江湖泊群体>无放流陆封型湖泊群体>放流的陆封型湖泊群体,并且发现一些稀有等位基因位点在陆封型湖泊鳜群体中消失;由杂合度检验可以看出,所有群体在绝大多数位点都呈现杂合过剩现象,经过哈代-温伯格平衡检验,显示均显著偏离哈代-温伯格平衡(Pst为0.2727,显示群体间已发生较大遗传分化,其变异主要体现在通江湖泊和陆封型湖泊之间,同时由于陆封型湖泊之间放流管理模式的不同,亦会产生中度分化。研究结果表明,江湖阻隔是造成定居性鱼类鳜种群间遗传分化的重要原因之一。       

黄山短尾猴mtDNA控制区序列变异及种群的遗传多样性

短尾猴属灵长目(Primates)猴科(Cercopithecidae)猕猴属(Macaca),是我国特有的国家二级保护动物。为了更有效地保护其野生种群,本文研究了黄山短尾猴种群内的遗传多样性,并对黄山短尾猴与四川短尾猴种群间的遗传差异进行了分析。共测定了黄山短尾猴7个群体中的30个样本的mtDNA控制区5′端493bp的序列,只发现了7个变异位点,定义了3种单倍型,单倍型序列之间缺乏变异,种群中的核苷酸多样性很低(0.006);3种单倍型相应地将黄山种群分为了3个亚群,不同亚群之间呈现出一定的片断化分布,从分子水平上初步揭示了短尾猴黄山种群的遗传多样性。与四川短尾猴的相应序列比较,黄山短尾猴控制区序列存在很大差异,共有59个变异位点,而且存在大片段的碱基插入/缺失,有78%的遗传变异发生在两个种群之间,两个种群间的核苷酸歧异度已达8.21%。进一步分析表明,黄山短尾猴与四川短尾猴之间存在着极显著的遗传分化(FST=0.399,P<0.001),基于最大似然法和邻接法构建的系统发生树均将两者聚为不同的类群,支持将它们归入各自的管理单元。     

黄河裸裂尻鱼五种群mtDNA控制区的遗传结构

黄河裸裂尻鱼（Schizopygopsis pylzovi）主要分布于青藏高原东北部兰州以上黄河干支流水系和高原北部柴达木内流水系,由于其对高原特殊生境表现出独特的适应性而受研究者关注。本文采用聚合酶链式反应（PCR）和直接测序的方法获得了一个分布于柴达木内流水系种群和四个黄河支流种群共99条个体的线粒体DNA（mtDNA）控制区（D-100p）821bp核苷酸的序列,探讨了其种群遗传结构和分化。99条个体的序列经比对后,发现77个（9．37％）多态性位点,共定义了53个单倍型,其中有一个单倍型（DT12）为两个种群（大通种群和互助种群）所共享,其余52个单倍型均为某个种群所特有。遗传多样性分析表明,柴达木种群的单倍型多样度（h=0．79&#177;0．06）和核苷酸多样度（π=0．0027&#177;0．0017）均略低于黄河支流各种群。AMOVA分析结果显示,遗传差异主要发生在种群之内,占75．39％,而小同水系的种群间只有24．61％,各种群间成对的Fst及遗传距离均表明种群间出现了一定程度的种群分化,但系统进化树最示出一种混杂的单倍型分布格局,提示青藏高原东北部地质事件所造成的水系间的隔离形成较晚。单倍型歧点分布呈现为单峰以及中性检验Tajima的D（-1．497,P=0．058）和Fu的Fs（-24．741,P=0．001）结果综合表明,黄河裸裂尻鱼在青藏高原隆升过程中曾经历过近期的种群扩张事件[动物学报54（6）：972—980,2008]。     

基于微卫星标记的中国大陆地区野猪种群结构分析与亚种分化

对中国大陆地区分布的野猪亚种分类尚存在争议.本研究通过对野猪11个微卫星位点的变异分析,探讨了中国大陆地区野猪的遗传结构,以期对野猪亚种分类问题有所启迪.对野猪华北、华南和东北种群的分析表明,各种群基因库中都维持了较高的遗传变异水平.基于遗传距离构建的系统树分析发现,研究中所涉及的所有亚种在系统树中混杂,没有任何亚种在其中构成显著的支系.基于微卫星变异的FCA分析不能区分华南、华北、东北三个种群.基于Fst检验的遗传差异分析发现,长江两侧的华南、华北种群之间的遗传差异较小(Fst=0.014),表明长江两侧的野猪可能存在着较高水平的基因流,长江并非是一个有效的空间隔离;东北地区野猪和华北、华南地区野猪之间的遗传差异相对较大(Fst=0.040、0.042),东北野猪可以作为独立的亚种S.s.ussuricus.     

Genetic variation in isozymes of wild boar (Sus scrofa ferus Linné)

Eleven isozyme systems were investigated in wild boar (Sus scrofa ferus L.) by means of horizontal starch gel-electrophoresis using liver and kidney extracts. Samples of 103 specimen that originated from three adjunct localities from Rhineland-Palatinate (Fed. Rep. Germany) were analysed. AAT, ACO, GDH, GPDH, LDH, ME, MPI, MR, PGDH, and PGI were invariant. Genetic polymorphism is described for PGM. The genetic polymorphism at Pgm2 is explained by a biallelic model. Observed genotypic structure did not differ significantly from Hardy-Wein-berg-proportions at this gene locus. The degree of heterozygosity is 58,3 % and Wright's Fixation Index F =–0.166 at Pgm2. The allelic structure at this gene locus differed to a great extent from that found in domestic swine, i. e. in domestic swine the faster migrating Pgm2 allozyme was only found in relative low frequencies compared to wild boar. The genetic polymorphisms were moderate in the wild boar population compared to electrophoretic data of other animal species.     

Wildlife genetics and disease: allozyme evolution in the wild boar (Sus scrofa) caused by a swine fever epidemy

Enzyme polymorphism at 42 loci was compared before and after a major epidemy of swine fever in wild boars from northern Vosges (France). No change was observed in the 38 monomorphic loci, but allele frequencies at the phosphoglucomutase locus PGM-2* changed significantly. Possible causes for this observation are discussed, and it appears that PGM-2 locus could be a genetic marker of resistance to this viral disease.     

Dispersal of freshwater invertebrates by large terrestrial mammals: a case study with wild boar (Sus scrofa) in Mediterranean wetlands

1. Many invertebrates inhabiting insular aquatic habitats rely on external agents or vectors to disperse. Besides water connections and wind, waterfowl and amphibians are known to mediate passive dispersal of freshwater invertebrates. However, the possibility of dispersal by terrestrial mammals has been largely overlooked. 2. We investigated the potential of both external and internal zoochorous dispersal of aquatic invertebrates by the wild boar (Sus scrofa) in Mediterranean wetlands in the Camargue (France). As wild boar frequently visit wetlands for feeding and wallowing purposes, we hypothesized that they may be important passive dispersal vectors of aquatic invertebrates at a local scale. Dried mud was collected from selected ‘rubbing trees’ used by boars to dispose of parasites. Additionally, faecal pellets were collected from different locations in the wetland area. 3. Seventeen freshwater invertebrate taxa including rotifers, cladocerans, copepods and ostracods hatched from sediment obtained from ‘rubbing trees’, while invertebrates hatching from dried faeces (10 taxa) were mainly rotifers. Dispersing invertebrates were collected up to 318 m from a nearest potential dispersal source. Both abundance and richness of invertebrates significantly decreased with dispersal distance. 4. Our results demonstrate that large mammals such as wild boar can act as dispersal vectors of aquatic invertebrates at a local scale in the wetland area of the Camargue and suggest that external transport may be quantitatively more important than internal transport. As wallowing (mud bathing) is common in many terrestrial mammals, this mode of dispersal may be quite widespread.     

Investigation of wild boar (Sus scrofa) for porcine reproductive and respiratory syndrome in some territories of Russia

Samples of blood sera and internal organs were collected from 90 shot wild boars (Sus scrofa) in five regions of Russian Federation. Blood sera were tested for antibodies against porcine reproductive and respiratory syndrome virus (PRRSV) using enzyme-linked immunosorbent assay (ELISA). In addition, samples of internal organs (lungs, lymph nodes, spleen) were tested by polymerase chain reaction (nested PCR) for PRRSV antigen. The result of our investigation showed that all samples were negative. However, PRRSV is widespread in domestic swine throughout Russia including the examined regions. Since the results show the absence of PRRSV infection in wild boars in the five examined regions of Russia, wild boars seem not to play any role in the epidemiology of PRRSV in Russia.     

The sexual function of wallowing in male wild boar (Sus scrofa)

The wild boar (Sus scrofa) is a medium-sized ungulate that produces a large variety of marks. Traditionally, wallowing is an activity that has fundamentally been related to several processes such as thermoregulation, reduction in the number of ectoparasites or disinfection of wounds in the skin of males resulting from fights to reach females. In this study, I analysed another possible function of wallowing in free-ranging wild boar populations when temperatures are low and parasitic numbers are not significant. The results indicate that during the sampling time, from October to February, the number of wild boars with a mud layer on their skin was 47, out of a total of 558 wild boar analysed. Of these 47 wild boars, 44 were males and within this group, 40 individuals were adult males. The wallowed males were bigger and older than non-wallowed males hunted at the same time. In addition, I found that males wallowed mainly during autumn (90.9% of all cases). In the total number of wild boars analysed, I did not notice individuals with wounds resulting from fights other than from the hunting day. On the other hand, the analysis of the females reproductive systems indicated that the rut period took place during the last days of October and the first days of November. From these results, the coincidence of the rut period with the maximum of wallowing in adult males could be indicative of a sexual function of this activity.     

Influence of methylmalonyl-CoA mutase alleles on resistance to bovine tuberculosis in the European wild boar (Sus scrofa)

An association study was carried out to examine the influence of methylmalonyl-CoA mutase (MUT) polymorphisms on the susceptibility of a well-studied wild boar population from southern Spain to develop bovine tuberculosis (bTB). To this end, we examined polymorphisms at a closely linked dinucleotide microsatellite flanking exon 2 of the MUT gene in 37 wild boars with bTB and 36 non-infected individuals. The microsatellite showed low polymorphism in the studied population, with only three alleles (MUTm-A, MUTm-B and MUTm-C) found, in contrast to the 11 alleles previously reported for domestic pigs. Our case-control study showed that the MUTm-B allele was associated with disease in a dominant pattern (odds ratio = 3.36; 95% CI = 1.05-10.72; P = 0.04), while the MUTm AA genotype appeared to have a protective effect against bTB infection (odds ratio = 4.33; 95% CI = 1.20-14.96; P = 0.02). Interestingly, infected wild boars heterozygous for MUTm AB are at an advantage (11-fold) to contain the systemic spread of the disease when compared to other genotypes, implying that a balanced polymorphism may be present in the population. These results strengthen previous observations regarding the importance of the MUT gene on bTB resistance in wild boars and indicate that polymorphisms at this locus will influence the risk of acquiring and maintaining bTB in the studied population.     

完达山东部林区野猪种群数量和栖息地特征的初步分析

2008 年11 月18 日至2009 年3 月20 日,为了调查黑龙江省完达山东部林区野猪种群数量和栖息地特征,我们采用随机布设样线的方法在东方红林业局境内13 个林场共布设大样方40 个,样线200 条。调查结果表明,东方红林业局境内野猪分布平均密度为0.175 头/ km² , 种群数量为546 ～ 680 头;野猪主要分布在河口、奇源、青山、五林洞、独木河、海音山和东林7 个林场,位于海拔300 ～ 800 m 的范围内。1989 年调查的野猪平均密度为0.372 头/ km² ,种群数量为1302 ; 2002 年调查的野猪平均密度为0. 342 头/ km² , 种群数量为1 198 头。近年来野猪种群密度降低,种群数量呈加速下降趋势。对野猪栖息地特征分析表明,野猪喜欢选择中坡位、阳坡、坡度小于5°、地表植被盖度大于30% 、隐蔽度和郁闭度在25% ～ 50% 之间的生境。阔叶林、灌丛是野猪的主要栖息地。非法捕猎、森林采伐、坚果采摘和东北虎的捕食是造成野猪种群数量减少、栖息地质量下降的主要因素。     

Phylogeography and population structure of the Japanese wild boar Sus scrofa leucomystax: mitochondrial DNA variation

Phylogeographic characteristics and population structure of Japanese wild boar (Sus scrofa leucomystax) were investigated using mitochondrial DNA (mtDNA) sequence data. Sixteen Japanese wild boar haplotypes detected from partial sequences of the mtDNA control region (574-bp) from 180 Japanese wild boar specimens from 10 local populations on Honshu, Shikoku, and Kyushu islands and 41 haplotypes from other S. scrofa were analyzed using the neighbor-joining method. The Japanese wild boars were more closely related to Northeast Asian wild boars from Mongolia than to the other Asian continental S. scrofa. The Japanese and Northeast Asian wild boars were not significantly distinguished by corrected average pairwise difference analysis. The ancestors of Japanese wild boars are suggested to have been part of the continental S. scrofa population that spread from Southeast to Northeast Asia during the Middle to Late Pleistocene. The Japanese wild boar mtDNA haplotype cladogram shows 95% parsimoniously plausible branch connections supporting three sympatric clades. Nested clade analysis indicates that these three clades are the result of distinct historical events or gene flow. The present population of Japanese wild boars may have been formed by a few independent migrations of distinct clades from the continent with subsequent mixing on the Japanese Islands.