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.     

中国狼不同地理种群遗传多样性及系统进化分析

为了解中国狼不同地理种群遗传多样性及系统发育情况,从中国境内狼的主要分布区青海、新疆、内蒙古和吉林4个地区采集样品,用分子生物学技术手段成功地获得44个个体线粒体DNA控制区第一高变区(HVRⅠ)序列和40个线粒体Cyt b部分序列。线粒体控制区HVRⅠ共检测到51个变异位点,位点变异率为8.76%;线粒体Cyt b部分序列发现31个变异位点,位点变异率为5.33%,未见插入及缺失现象,变异类型全部为碱基置换。共定义了16个线粒体HVRⅠ单倍型,其中吉林与内蒙种群存在共享单倍型,估计这两地间种群亲缘关系较近。4个地理种群中新疆种群拥有较高的遗传多样性(0.94)。中国狼种群总体平均核苷酸多态性为2.27%,与世界其他国家地区相比,中国狼种群拥有相对较高的遗传多样性。通过线粒体HVRⅠ单倍型构建的系统进化树可以看出,中国狼在进化上分为2大支,其中位于青藏高原的青海种群独立为一支,推测其可能长期作为独立种群进化。基于青海种群与新疆,内蒙种群的线粒体Cyt b遗传距离,推测中国狼2个世系可能在更新世冰川时期青藏高原受地质作用急速隆起后出现分歧,分歧时间大约在1.1 MY前。     

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。     

江西井冈山地区灰胸竹鸡的遗传多样性研究

灰胸竹鸡Bambusicola thoracica是我国特有鸟类.本文采用聚合链式反应和直接测序的方法测定井冈山地区灰胸竹鸡3个种群线粒体DNA(mtDNA)控制区1142 bp的序列,分析其序列变异和种群遗传多样性.30个样本共发现16个变异位点和10种单倍型,其中hapl广泛分布,占所分析样本的23.33%,是其祖先单倍型.3个种群的平均单倍型多样性和核苷酸多样性分别为0.815和0.00243.青原区种群与其它两个种群遗传分化显著,基因交流受限制.受隔离影响,青原区种群遗传多样性最低.在系统发生树上,10种单倍型形成两支,井冈山种群和永新县种群聚在一起,与其地理位置相一致.     

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     

中国圈养梅花鹿的遗传多样性和遗传结构

东北梅花鹿(Cervus nippon hortulorum)的野生种群已濒临灭绝,但其圈养种群遍布全国各地,是我国圈养梅花鹿的主要品种(亚种)。为了探讨圈养梅花鹿种群作为东北梅花鹿野外放归项目资源种群的可行性,测定了来自9个圈养种群45只梅花鹿个体的线粒体DNA控制区的部分序列,以此分析我国圈养梅花鹿种群的遗传多样性和遗传结构。结果表明,我国圈养梅花鹿种群的遗传多样性并不贫乏,种群之间并没有发生显著的遗传分化。因此,东北地区的圈养梅花鹿种群可以作为野外放归项目的资源种群,而野外放归项目的建群者应来源于东北地区的多个圈养种群。     

白腹管鼻蝠华北与东北冬眠群内RAPD分析和亲缘关系的比较研究

用随机扩增ＤＮＡ多态（ＲＡＰＤ）方法分析白腹管鼻蝠在华北和东北两地冬眠群群内与群间个体之间的亲缘关系,探讨冬眠群的结构组成及其相互关系。结果显示：华北两个白腹管鼻蝠冬眠群内个体间遗传相似性平均分别为０８５８和０９３３,两群之间的遗传相似性平均为０８４２,群内与群间个体之间在遗传相似性方面没有明显差别;东北冬眠群内的遗传相似性平均为０６０４;华北和东北两地冬眠群间的相似性只有０５１３和０５２１。据此可认为,在同一及邻近洞中形成的白腹管鼻蝠冬眠群的组成可能是选择来自同一种群中亲缘关系较近的个体,在华北冬眠的种群和在居留地东北冬眠的种群之间的亲缘关系较远。     

黑麂皖-浙分布中心种群的遗传多样性

本文基于黑麂线粒体控制区序列对皖浙分布中心的4个黑麂种群的遗传多样性和基因流进行了研究。结果显示:4个种群的33个个体中有14个变异位点,占分析序列长度的2·91 %,并由此定义了12个单倍型;遗传多样性检测结果显示4个种群中开化种群具有最高的遗传多样性,应予以优先保护;4个种群间尚存在着一定的基因流,但存在可能由于遗传漂变而产生分化的危险。从Tajima’s D和Fu and Li’s D值的估算结果来看,这4个黑麂种群相对于中性进化的歧异度并没有明显的偏离,具有较为稳定的种群结构(P>0·1),没有明显的证据显示这4个黑麂种群间存在很强的平衡选择。     

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     

黑龙江黑斑狗鱼线粒体控制区的遗传变异

测定了黑龙江抚远江段和虎林江段黑斑狗鱼(Esoxreicherti)线粒体控制区5'端的560bp序列,在12尾黑斑狗鱼序列中未检测到任何变异位点,即所有个体的序列均完全一致,共享同一种单倍型,群体内和群体间的核苷酸多样性均为0.黑龙江黑斑狗鱼线粒体DNA如此贫乏的遗传多样性,一方面可能是黑龙江水系黑斑狗鱼在更新世冰期可能曾遭受过严重的瓶颈效应;另一方面则可能因目前是国内黑斑狗鱼种群数量锐减,种质资源急剧衰退,导致种群遗传多样性的丧失.建议广泛取样调查不同地理种群,并采用AFLP和微卫星等分子标记检测遗传多样性,以确定遗传变异丰富的黑斑狗鱼种群加以保护,促进黑龙江流域黑斑狗鱼资源的有效保护和可持续利用.     

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.     

Genetic relationship and distribution of the Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (Sus scrofa riukiuanus) analysed by mitochondrial DNA

Mitochondrial genetic variations were used to investigate the relationships between two Japanese wild boars, Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (S.s. riukiuanus). Nucleotide sequences of the control (27 haplotypes) and cytochrome b (cyt-b) regions (19 haplotypes) were determined from 59 Japanese wild boars, 13 Ryukyu wild boars and 22 other boars and pigs. From phylogenetic analyses, the mtDNA of Ryukyu wild boar has a distinct lineage from that of Japanese wild boar, which was classified into the Asian pig lineage. This result suggests that the Ryukyu wild boar has a separate origin from the Japanese wild boar.     

Geographic population structure and sequence divergence in the mitochondrial DNA control region of the Japanese wild boar (Sus scrofa leucomystax), with reference to those of domestic pigs

Mitochondrial DNA (mtDNA) control regions from 40 Japanese wild boars were examined by direct sequencing after amplification by PCR. From the DNA sequences obtained, we found eight haplotypes, whose differences arose via transitions. The geographical distribution of these different haplotypes indicated that wild boar populations inhabited limited areas and that there was some restricted gene flow between local populations. Eight mtDNA haplotypes from Eastern and Western domestic pigs and the Ryukyu wild boar were also analyzed as references to those from Japanese wild boars. The cluster analyses of the control-region sequences showed that those from Japanese wild boards belong to the Asian type as do those from Eastern domestic pigs and the Ryukyu wild boar, which differed from the European type (Western domestic pigs).     

Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38

Wild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10-fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.     

A genetic method to distinguish crossbred Inobuta from Japanese wild boars

To distinguish pig-wild boar crossbred Inobuta from Japanese wild boar populations, a genetic method by using mitochondrial DNA (mtDNA) haplotypes and the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) was developed. Sixteen mtDNA haplotypes from 152 wild boars from Kyushu, Shikoku and Honshu islands of Japan were distinct from those from Asian and European domestic pigs. Five alleles of GPIP were classified into two groups: 1). alleles GPIP*1, GPIP*3 and GPIP*3a from Japanese wild boars, Asian wild boars and domestic pigs; 2). alleles GPIP*4 and GPIP*4a from European wild boars and domestic pigs. An extensive genetic survey was done to distinguish the crossbred Inobuta from 60 wild boars hunted on Tsushima Island, Goto Islands, and Nagasaki and Ooita Prefectures. The mtDNA haplotypes from the 60 samples showed Japanese wild boars, but four wild boar samples from Nagasaki Prefecture had the European GPIP allele, GPIP*4. These results showed that nuclear DNA polymorphism analysis is useful, in addition to mtDNA haplotype assay, to detect "Inobuta" having the European genotype from Japanese wild boar populations.     

BsaH Ⅰ对猪激素敏感脂肪酶基因外显子Ⅰ的PCR-RFLP分析

以华北野猪、东北野猪和山西黑猪、长白猪、大白猪、马身猪共计287头猪作为研究对象,对其HSL基因外显子Ⅰ区域进行了PCR-RFLP多态性研究,发现不同品种猪间存在多态性。瘦肉型大白猪、长白猪全部表现为GG基因型;山西黑猪表现为AA、AG和GG三种基因型;脂肪型地方猪种马身猪为单一的AA基因型;华北杂种野猪、东北纯种野猪及杂种野猪表现为AG和GG两种基因型。等位基因A、G及三种基因型的频率在不同猪种中不同。该研究首次对华北及东北野猪HSL基因进行了多态性研究,丰富了国内外对野猪的分子生物学研究,为野猪遗传资源的合理开发利用提供了依据。     

The robust phylogeny of Korean wild boar (<Emphasis Type="Italic">Sus scrofa coreanus</Emphasis>) using partial D-loop sequence of mtDNA

In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.     

Variation in mitochondrial DNA of Vietnamese pigs: relationships with Asian domestic pigs and Ryukyu wild boars

Mitochondrial DNA (mtDNA) sequences (574 bp) of 30 Vietnamese pigs (large and small) were examined and compared with those of 61 haplotypes from wild boars and domestic pigs from various locations in Asia. The large Vietnamese pigs had genetic links to Ryukyu wild boars in southern Japan. The small Vietnamese pigs were closely related to other East Asian domestic pigs. These results indicate that Vietnamese pigs are genetically diverse and may be descendents of wild and domestic pigs from other regions of Asia.     

Mitochondrial DNA diversity in wild boar from the Primorsky Krai Region (East Russia)

We have studied the cytochrome B gene and control region DNA variability in 14 wild boars from the Primorsky Region, in the far east corner of Russia. Variability was low (π = 0.00248 overall) compared with the usual estimates in these loci, indicating that this is a rather closed population. Seven haplotypes were found, and one was identical to a Chinese wild boar. Phylogeographically, the sequences clustered among several Asian clades, primarily Chinese domestic pigs and Japanese and Chinese wild boars, and are positioned within the D2 clade reported by Larson et al. [ Science 307 , 2005; 1618 ]. Although North Korean pigs should be studied, our data suggest that the Primorsky mtDNA signature is absent from domestic pigs. Sequences are available through GenBank identifiers HM010461 – HM010488 .