猪科的系统发育与系统地理分化

猪科动物是最为昌盛的哺乳动物之一，但它们的分类及系统发育关系却尚待解决。为此， 用PCR直接测序法测定了一个红河猪(Potamochoerus porcus)、一个马来西亚野猪(Sus barbatus)以及数头欧亚野猪(Sus scorfa)线粒体细胞色素b全序列1 140 bp。结合从GenBank中获得的其他猪科物种胞色素b序列，用邻接法和最大简约法构建了猪科物种的系统发育关系，其结果显示苏拉威西鹿猪与其他猪科物种为姐妹群的关系。非洲物种疣猪和河猪聚为一枝，而欧亚猪属物种聚为另一支。各物种在系统发育关系中的位置与它们的地理分布对应。猪属物种可以被划分为3个种组：分布于菲律宾群岛、苏拉威西岛及其邻近岛屿的猪属物种形成一个种组，包括苏拉威西岛疣猪、菲律宾疣猪和印度尼西亚疣猪；欧亚野猪种组，包括欧亚野猪和姬猪；须猪和爪哇疣猪形成一个种组。     

6个中国猪地方品种和3个瑞典猪DNA分子系统发育相关关系

线粒体DNA遗传多样性用于评价6个中国地方猪种和3个瑞典家猪系统发育关系。采用PCR和序列分析方法得到了来自9个品种140头猪的线粒体中控制区440bp和细胞色素b基因798bp核苷酸序列。系统发育分析结果表明：6个中国地方猪种起源于亚洲野猪。中国地方猪种和欧洲野猪的线粒体DNA核苷酸序列变异发生在413000－875000年以前,而亚洲紧猪的变异仅发生在7000－156000上以前,由于2000年以前或18世纪初中国猪种导入欧洲家猪,因此瑞典家猪既属于欧洲类也属于亚洲类。     

CO Ⅰ SEQUENCE VARIATIONS AND PHYLOGENETIC RELATIONSHIPS AMONG 13 SPECIES OF TETRAONIDAE BIRDS

线粒体DNA中的细胞色素C氧化酶亚基Ⅰ基因,即CO Ⅰ是DNA条形编码的主要基因,是一个很好的物种鉴定工具,目前广泛应用于鸟类系统发育研究.通过测定花尾榛鸡和黑琴鸡CO Ⅰ基因的序列,并结合GenBank中松鸡科13种鸟类的同源序列,对松鸡科鸟类进行了序列变异和系统发育分析.结果显示,松鸡科物种的种间变异大于种内变异.序列分歧和系统分析结果支持花尾榛鸡Tetrastes bonasia归于松鸡科Tctraonidae榛鸡属Tetrastes.黑琴鸡Lyrurus tetrix与Tetrao属中其它物种的分歧小于松鸡科其它属间分歧,且黑琴鸡聚在Tetrao内,研究结果倾向支持黑琴鸡归于松鸡属Tetrao.     

松鸡科13种鸟类COⅠ序列变异及系统发育分析

线粒体DNA中的细胞色素C氧化酶亚基Ⅰ基因,即COⅠ是DNA条形编码的主要基因,是一个很好的物种鉴定工具,目前广泛应用于鸟类系统发育研究。通过测定花尾榛鸡和黑琴鸡COⅠ基因的序列,并结合GenBank中松鸡科13种鸟类的同源序列,对松鸡科鸟类进行了序列变异和系统发育分析。结果显示,松鸡科物种的种间变异大于种内变异。序列分歧和系统分析结果支持花尾榛鸡Tetrastes bonasia归于松鸡科Tetraonidae榛鸡属Tetrastes。黑琴鸡Lyrurus tetrix与Tetrao属中其它物种的分歧小于松鸡科其它属间分歧,且黑琴鸡聚在Tetrao内,研究结果倾向支持黑琴鸡归于松鸡属Tetrao。     

广西地区野猪化石古DNA及猪的驯化初探

猪的起源驯化一直是人们关注的问题,古DNA技术可为家猪起源驯化研究提供历史分子证据。为探讨广西地区更新世晚期野猪与当地家猪的关系,我们收集了广西壮族自治区晚更新世三个不同地点的30个猪科动物化石样品,测定了这些样品的线粒体DNA细胞色素b基因的核苷酸序列。结合现代不同品种家猪和野猪DNA同源序列信息,构建Network网络结构图,进一步证实了家猪多地起源学说。研究显示广西古代野猪与现存欧洲猪的基因型最为接近,属于欧洲单倍型H1,从而推测其对该地区现代家猪的遗传贡献可能较低,对考古形态学研究中关于广西地区家猪独立起源的推测提出了质疑。     

多刺蚁属细胞色素C氧化酶亚基Ⅱ序列变异及其进化关系

从Gen Bank下载多刺蚁属26个不同种的细胞色素C氧化酶亚基Ⅱ(COXⅡ)蛋白部分氨基酸序列进行分析,研究多刺蚁细胞色素C氧化酶亚基Ⅱ的氨基酸序列变异和系统进化关系。多刺蚁属种间存在氨基酸变异位点84个,占总氨基酸数目的 36%,而N端跨膜螺旋区氨基酸保守性最高。采用MEGA 4.0构建的邻接法(NJ)系统发育树表明:佛瑞尔刺蚁(Polyrhachis foreli)和甲胄刺蚁(Polyrhachis andromache)聚为一枝,双钩刺蚁(Polyrhachis bihamata)和叉形刺蚁(Polyrhachis ypsilon)聚为一枝,麦凯刺蚁(Polyrhachis mackayi)、澳洲刺蚁(Polyrhachis australis)和软毛刺蚁(Polyrhachis pilosa)三个种聚为一枝,这些种间亲缘关系较近;基于COXⅡ蛋白序列的系统发育关系分析与基于细胞色素b蛋白的系统发育关系既存在一致性,也存在一定的差异。多刺蚁属中序列变异度最大的4个种的COXⅡ对应的3D结构在螺旋和折叠排列方式上完全相同,表明多刺蚁属内COXⅡ序列变异并不影响其结构的形成。     

从D环和细胞色素b基因序列探讨懒猴属的分子系统发育关系(英文)

本研究测定了懒猴属(Nycticebus)D环的部分序列和细胞色素b基因的全序列(1140bp),分析了该属物种之间的系统发育进化关系。在DNA水平上,序列分析结果一致地提供了新的分类学证据：支持Rataiszczak和Groves的观点,即N．intermedus只是N．pygmaeus的成体(Ratajszczak,1998;Groves,1971)。对两种序列的数据做了联合及个别分析,获得相似的系统树,支持懒猴属由两个单系群组成：第一群由N．pygmaeus聚成,第二群由N．coucang聚成。该结果也提供了新的分子遗传证据,支持懒猴属由N．coucang和N．pygmaeus两物种组成。     

从线粒体Cyt b基因探讨红瘰疣螈物种地位的有效性

疣螈属的红瘰疣螈(Tylototriton shanjing)和棕黑疣螈(T.verrucosus)的物种界限一直不清楚。测定了来自中国西南地区14个地点的T.shanjing和T.verrucosus共40只标本的线粒体DNACytb基因(753bp)。结果表明:(1)用邻接法、最大简约法和贝叶斯法等3种系统发育分析法分别重建棕黑疣螈种组系统发育树的拓扑结构不支持T.shanjing是单系群;(2)T.shanjing与T.verrucsus的mtDNA Cytb序列差异平均值仅为1.2%,未达到种级水平。因此,全部T.shanjing样品都属于同一个物种,即T.verrucosus,不支持T.shanjing的物种地位,T.shanjing为T.verrucosus的同物异名,并建议恢复T.verrucosus的中文名红瘰疣螈。根据基于40个样品Cyt b基因序列的系统发育树和遗传变异以及地理分布,这些红瘰疣螈(T.verrucosus)样品聚为3支,即中国西南地区的红瘰疣螈可分为片马、滇中滇西和滇东南3个地理居群。     

小孢盘菌属种间关系初探（英文）

3个编码蛋白的基因RPB1、RPB2和TEF1以及1个非编码序列28S rD NA的联合分析结果表明,小孢盘菌属位于系统树的上端,形成一个单系群,其中长春小孢盘菌和北京小孢盘菌为姐妹群,它们进一步与该属另3个种(包括该属的模式种)聚类在一起。序列分析结果支持将子囊孢子大小作为小孢盘菌属区分物种的依据,还表明火丝菌科可能不是一个单系群。在参试属中,小孢盘菌属与侧盘菌属的关系较为密切,它们具有极其相似的薄壁子囊,这表明在属的等级上子囊形态可能携带系统发育方面的信息。     

基于ITS序列分析仲彬草属植物的亲缘关系

以旱雀麦为外类群,用PAUP 4.0b10软件并采用最大简约法和邻接法对11份仲彬草属物种的ITS区序列进行系统发育分析,两种方法得到的系统发育树基本一致。结果表明:(1)整个ITS序列长度变异范围为596~601 bp;G C含量在所有ITS中的变化范围为61.20%~62.44%;序列间的遗传分化距离为0.003~0.033,平均值为0.015;(2)疏花仲彬草和塔克拉干仲彬草2个物种聚为一支,位于系统发育树的底部,在最大简约法和邻接法分析中分别获得78%和82%的自展支持率,它们之间的亲缘关系较近;(3)形态相似、地理分布一致的物种有聚在一起的倾向,表现出较近的亲缘关系;(4)ITS区序列分析的结果与细胞学、形态学的研究结果基本一致,因此ITS区序列分析能反映仲彬草属种间关系。     

Numerical variation of nucleolar organizer regions after silver staining in domestic and wild Suidae (Mammalia)

Selective silver staining was used to investigate the cellular distribution of numbers of nucleolar organizer regions (NORs) in domestic pigs (Sus scrofa) of eight different breeds, the European wild boar (S. scrofa scrofa), Indonesian wild boar (S. scrofa vittatus), Javan warty pig (S. verrucosus), Sulawesi warty pig (S. celebensis), and pigmy hog (S. salvanius). In the domestic pig as well as in the wild (sub)species of Sus, actively transcribing ribosomal RNA genes were found to be present in the secondary constrictions of chromosome pairs 10 and 8. Chromosomes 10 were consistently Ag-positive. Chromosomes 8 less frequently showed Ag-NORs, resulting in different mean numbers of Ag-NORs per individual animal. Mean Ag-NOR numbers per breed or (sub)species were generally higher in the wild representatives of Sus than in the domestic breeds. The highest mean numbers of Ag-NORs were observed in the Meishan breed and in S. celebensis and S. salvanius. The Meishan breed appears to be conservative in Ag-NOR staining pattern, being more comparable to the Asian wild Suidae than to the European breeds.     

PGD variants in several wild pig populations of East Asia

PGD (6-phosphogluconate dehydrogenase) gene frequencies were reported in wild pigs, Sus scrofa, of three subspecies, i.e. Japanese wild pig, S.s. leucomystax, Ryukyu wild pig, S.s. riukiuanus, and Formosan wild pig, S.s. taivanus. Five phenotypes (A, AB, B, AC' and C') were observed. The C' variant was found only in the S.s. leucomystax, and may be identical to PGD-C reported by Archibald & McTeir (1988). PGD-A was a common variant in all the species in the genus Sus including wild pig, Sus scrofa, Javan pig, Sus verrucosus, and Bearded pig, Sus barbatus, and predominated in the whole populations examined except some of those of the S.s. riukiuanus. This suggested that the PGDA appeared before the other two alleles (B and C') during the evolution of the genus Sus.     

The Balkans and the colonization of Europe: the post‐glacial range expansion of the wild boar,Sus scrofa

Aim We focus on the biogeographical role of the Balkan Peninsula as a glacial refugium and source of northward post‐glacial dispersal for many European taxa. Specifically, we analysed the genetic structure and variation of wild boar (Sus scrofa) samples primarily from Greece, a region that has repeatedly served as a glacial refugium within the Balkan Peninsula. Location Continental Greece, the Aegean island of Samos and Bulgaria. Methods We analysed wild boar samples from 18 localities. Samples from common domestic breeds were also examined to take into account interactions between wild and domesticated animals. Phylogenetic analyses were carried out on a 637‐bp fragment of the mitochondrial DNA control region in 200 wild boar and 27 domestic pigs. The sequences were also compared with 791 Eurasian wild boar and domestic pig D‐loop sequences obtained from GenBank. Results Ninety‐four haplotypes were identified in the European wild boar data set, of which 68 were found in the Balkan samples and assigned to two previously described clades: the E1 European and Near Eastern clades. All of the continental samples clustered in the E1 clade and the samples from Samos fell into the Near Eastern clade, consistent with the island’s proximity to Asia Minor. Intriguingly, 62 novel haplotypes were identified and are found exclusively in the Balkans. Only six haplotypes were shared between wild boar and domestic pigs. Main conclusions Our data reveal numerous novel and geographically restricted haplotypes in wild boar populations, suggesting the presence of separate refugia in the Balkans. Our analyses support the hypothesis of a post‐glacial wild boar expansion consistent with the leading edge model, north and west from modern day Greece, and suggest little maternal introgression of Near Eastern and domestic haplotypes into wild Balkan populations.     

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.     

The pygmy hog is a unique genus: 19th century taxonomists got it right first time round

The pygmy hog, Sus salvanius, the smallest and rarest extant suid was first described as the only member of the genus Porcula. It is currently regarded as member of the genus Sus and a sister taxon of the domestic pig/Eurasian wild boar (Sus scrofa). Phylogenetic analyses of 2316 bp from three mtDNA loci (control-region, cytochrome b, 16S) by Bayesian inference and statistical testing of alternative phylogenetic hypotheses all support the original classification of the pygmy hog as a unique genus. Thus, we propose that the species name Porcula salvania should be resurrected. The reclassification will heighten awareness of the need for the future protection and survival of this unique species.     

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.     

Evolutionary genetics of the suiformes as reconstructed using mtDNA sequencing

We have amplified and sequnced the entire mitochondrial DNA cytochromeb gene from four species of Suidae: babirusa, warthog, bearded pig, and some specimens belonging to different subspecies and populations of wild and domestic pigs (Sus scrofa). These sequences were aligned with additional mammalian sequences retrieved from the literature and were used to obtain phylogenetic trees of the Suiformes (Artiodactyla). Several species of Carnivora, Perissodactyla. Cetacea, and other Artiodactyla were used as outgroups. Molecular phylogenetic relationships among the Suiformes reflect their current taxonomy: Hippopotamidae, Tayassuidae, and Suidae are separated by deep genetic gaps, and the division of the Suidae into the subfamilies Babyrousinae., Phacochoerinae, and Suinae has strong genetic correlates. Cytochromeb sequences show differences among Asian and Western populations ofSus scrofa, agreeing with other genetic information (karyotypes blood groups, and protein variability). The two Italian subspecies of wild boar have unique mtDNA cytochromeb haplotypes. The evolutionary rates of cytochromeb sequences are different at transitions versus transversions as well as at first, second, and third positions of codons. Therefore, these classes of substitutions reached different levels of mutational saturation. Only transversions and the conservative first and second position substitutions are linearly related to genetic distances among the Suiformes. Therefore, divergence times were computed using unsaturated conserved nucleotide substitutions and calibrated using paleontological divergence times between some Artiodactyla. Transversions apparently evolve at remarkably regular rates in ungulate taxa which have accumulated less than 20% estimated sequence divergence, corresponding to about 40–45 million years of independent evolution. Molecular, information suggests that Hippopotamidae and Tayassuidae are not closely related (as stated by Pickford, 1986, 1989, 1993) and that the origin of babirusa and warthog (about 10–19 and 5–15 million years ago, respectively) is more recent than supported by current evolutionary reconstructions. The inferred origin of bearded pig is about 2.1 million years old, and genetic divergence among differentSus scrofa populations is probably a Pleistocene event. The addition of new sequences of Suiformes does not help in resolving the phylogenetic position ofHippopotamus amphibius, which shows weak but recurrent linkages with the cetacean evolutionary lineage.To whom correspondence should be addressed.     

Inferring the origin and genetic diversity of the introduced wild boar (<Emphasis Type="Italic">Sus scrofa</Emphasis>) populations in Argentina: an approach from mitochondrial markers

The Eurasian wild boar (Sus scrofa Linnaeus, 1758) was introduced into Argentina at the beginning of the twentieth century when individuals from Europe were taken to La Pampa province for hunting purposes. Starting from there, a dispersal process began due to the invasive characteristics of the species and to human-mediated translocations. The main objective of this study was to characterize for the first time, the phylogenetic relationships among wild boars from Argentina with those from Uruguay, Europe, Asia, and the Near East, along with diverse domestic pig breeds in order to corroborate the historical information about the origin of the local populations. To this end, we used mitochondrial Control Region and Cytochrome b sequences from sampled Argentinian wild boars and retrieved from GenBank. The results showed that the majority of the Argentinian wild boar populations descend from European lineages, in particular of the E1 clade, according to the historical records. Remarkably, the population of El Palmar National Park had Asian origin that could be attributed to hybridization with local domestic pigs or to unrecorded translocations. Finally, genetic diversity in Argentinian populations was lower than in Europe and Uruguay meaning that wild boar in Argentina is still under the influence of founder effect and has experienced minor genetic introgression from domestic pigs, representing in this sense a reservoir of the original wild boar genetic variability.     

The origin of the domestic pig: independent domestication and subsequent introgression

The domestic pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and domestic pigs from Asia and Europe. Clear evidence was obtained for domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at approximately 500,000 years, well before domestication approximately 9,000 years ago. Historical records indicate that Asian pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major "European" pig breeds. The study is an advance in pig genetics and has important implications for the maintenance and utilization of genetic diversity in this livestock species.     

Wound myiasis in a wild boar by Lucilia caesar (Diptera: Calliphoridae): First case and current status of animal myiasis by this species

The first case of myiasis caused by Lucilia caesar (L.) (Diptera: Calliphoridae) in a wild boar, Sus scrofa L. (Artiodactyla: Suidae) is described. The myiasis occurred in October 2019 in Southern Italy and the identification of the agent was based on adult male morphology. The wild boar had a wound on its right side, near the neck, which was largely infested by larvae. The ecology, distribution and current literature status about cases of animal myiasis by this species is also included.