利用mtDNA序列及形态特征重新鉴定福建长乐搁浅喙鲸

<正>中国大陆沿岸属大陆棚水域,常见的齿鲸物种以近岸型的海豚科(Delphinidae)、小抹香鲸科(Kogiidae)及鼠海豚科(Phocaenidae)动物为主(王丕烈,2012),而喙鲸科(Ziphiidae)发现纪录相对较少,近年来仅由王丕烈等(2011)针对喙鲸科的中喙鲸属(Mesoplodon)标本进行检视校正,认为中国大陆沿岸存在柏氏中喙鲸     

三种海豚线粒体COI基因的序列分析

对瓶鼻海豚(Tursiops truncatus)、中华白海豚(Sousa chinensis)和糙齿海豚(Steno bredanensis)的线粒体DNA COI基因进行了测序分析。PCR产物约700bp。扩增产物直接测序,去除引物序列后分别获得643、618和618bp的核苷酸序列。碱基组成平均为,T:31·07%,C:26·13%,A:27·27%,G:15·50%,GC含量为41·63%,其中碱基G的含量明显较低。与Gen Bank中9种鲸的同源序列比对,去除部分端部序列后得到597个比对位点,包括141个简约信息位点,43个单突变子,无插入/缺失位点。12种鲸的种间序列差异较大,其序列变异度在2·1%～17·1%之间。597个比对位点编码199个氨基酸,其中有9个氨基酸发生改变,其中一个氨基酸突变可将齿鲸亚目和须鲸亚目分开。NJ系统树表明,海豚科形成单系类群,瓶鼻海豚和中华白海豚的亲缘关系较近。上述分析表明,COI基因可用于鲸类的种类鉴定和系统发育分析。     

委内瑞拉东南加勒比海岸七种海洋鲸类的潜在地理分布

本研究阐述了委内瑞拉沿海最常见的海洋鲸类的潜在地理分布情况。通过GIS分析,鲸类分布与地形和深度是相反的,以此可以获得鲸类潜在的分布图。已报告确认了16个物种(有402个目击报告),其中小布氏鲸(Balaenoptera edeni)、座头鲸(Megaptera novaeangliae)、海豚(Delphinus spp.)、圭亚那侏型豚(Sotalia guianensis)、花斑原海豚(Stenella frontalis)、长吻原海豚(Stenella longirostris)和宽吻海海豚(Tursiops truncatus)是最常见的。小布氏鲸和宽吻海海豚有可能分布于整个海岸,包括江河区域。座头鲸则可能季节性地集中分布在大陆架上的海岛沿岸和浅水区域。海豚(Delphinus spp.)有可能分布于高边坡区或沿海上升流区。花斑原海豚可能分布在东北区的西部,中部沿海以及与委内瑞拉海岸平行的岛屿周围。长吻原海豚则分布于浅海和远海区域。在一些高产的生态系统内新的物种可能正在形成,而这些潜在可能的分布图可以作为在高产生态系统内确立关键栖息地的标准,由此我们可以在委内瑞拉水域为鲸类建立新的保护区。     

直翅目昆虫线粒体基因组特征及系统发育研究

目前GenBank数据库共收录167种直翅目昆虫全线粒体基因组序列,涉及蝗亚目9个总科22个科99个物种,螽亚目7个总科12个科68个物种。在此基础上,该文分析了直翅目昆虫线粒体基因组的基本特征,概述了线粒体全基因组在直翅目昆虫系统发育研究上的应用;同时基于线粒体全基因组序列重建了直翅目昆虫的系统发育关系。主要结果如下:(1)直翅目昆虫存在8种线粒体基因组排列类型,其中trnK-trnD重排现象仅发生在蝗总科中,trnN-trnS-trnE重排现象仅发生在蟋蟀总科中,trnM-trnI-(-trnQ)重排现象仅发生在拟叶蟲亚科中;(2)直翅目昆虫全线粒体基因组的碱基组成具有明显的AT偏向性;(3)不同的蛋白质编码基因在直翅目昆虫中的进化速率不同;(4)支持直翅目以及螽亚目和蝗亚目的单系性;(5)不支持沙螽总科单系性;(6)支持蝗亚目各总科阶元的单系性,且各总科间的系统发育关系为:(蚤蝼总科+(蚱总科+(?蜢总科+(蜢总科+(长角蝗总科+(牛蝗总科+叶翅蝗总科)+(锥头蝗总科+蝗总科))))))。     

人工饲养条件下白鱀豚雌雄个体某些血清生殖激素的初步研究

外国鲸类学家,根据血清皋丸酮浓度变化研究了雄性宽吻海豚(Tursiops truncatus Montagu)和长吻原海豚(Stenella lonqirostris Gray)的生殖季节性1,2,并且提出了雄性宽吻海豚血清翠酮浓度与其精子密度之间互为反比关系3.       

鲸类分子系统学研究进展

综述了近年来分子生物学标记技术在鲸类系统学研究中的进展。分子生物学证据支持鲸目与有蹄类之间有较近的亲缘关系,并支持鲸类的单系起源,但鲸类不同类群(须鲸类、抹香鲸类及不包括抹香鲸类的齿鲸类)之间的系统发生关系仍存在争议。抹香鲸类到底与须鲸类还是与其它齿鲸类有更近的亲缘关系,不同的分子生物学家所得到的结果并不一致。此外,分子生物学技术还被用于解决须鲸亚目和齿鲸亚目内科间以及科内种间的系统发生关系,特别是齿鲸亚目的海豚科、鼠豚科和淡水豚类。通过分子标记技术来研究鲸类种下的遗传结构是鲸类分子系统学研究中的一个新热点,使用的标记主要是mtDNA控制区、核DNA微卫星和主要组织相容性复合体(major histo-compatibilitv complex,MHC)等。     

两头人工饲养南瓶鼻海豚的病理解剖及死因分析

<正>南瓶鼻海豚(Tursiops aduncus)是我国二级重点保护的水生哺乳动物,属于鲸目(Cetacea),海豚科(Delphinidae),瓶鼻海豚属(Tursiops)(Mller and Beheregaray,2001;Wells and Scott,2002)。南瓶鼻海豚是人工主要饲养的鲸类品种之一(刘仁俊等,2002;Zhang et al.,2012)。2011年4月30日,厦门市小嶝岛休闲渔村从福建东山引进两头南瓶鼻海豚进行人工饲养。饲养池位于北     

基于叶绿体基因组数据的芸香科属间系统发育初步分析

为探究花椒属种水平系统进化关系以及为新品种培育研究奠定理论基础，该研究以芸香科物种的叶片为材料，采用改良CTAB法提取叶绿体DNA,利用BGISEQ-500平台进行叶绿体基因组测序，并对叶绿体基因组进行组装、注释，联合NCBI数据库数据，共获得芸香科19属49个物种的全叶绿体基因组序列。构建了芸香科属间系统进化关系。结果表明，(1)基于叶绿体基因组序列矩阵(总长196 641 bp),ML和BI 2种方法得到的系统发育树的拓扑结够基本一致，系统发育树各分支具有较强的支持率，叶绿体基因组数据可以解决芸香科属间的系统发育关系。(2)芸香科为单系类群，并进一步形成两大分支，其中柑橘亚科为单系，与芸香亚科内的芸香属聚为分支I,分支Ⅱ由芸香亚科和飞龙掌血亚科组成，两亚科均不是单系，其中飞龙掌血亚科的香肉果属，茵芋属与芸香亚科的白鲜属，臭常山属是最早分化出来的类群，其次是蜜茱萸属和山油柑属；黄檗属和吴茱萸属与花椒属类群形成姊妹群，飞龙掌血属的物种飞龙掌血嵌套于花椒属分支中，支持飞龙掌血物种并入花椒属的处理。     

基于线粒体COI基因的大蚊属Tipula系统发育及长角大蚊亚属Tipula (Sivatipula)分类地位初步研究(双翅目:大蚊总科)

大蚊属Tipula Linnaeus,1758是大蚊科中种类最多的属,目前其单系性尚未得到全面验证.此外,长角大蚊亚属Tipula (Sivatipula) Alexander,1964因其极长的触角以及独有的精子泵结构,明显不同于大蚊属其他亚属,使其亚属的分类地位存在争议.本研究基于COI序列对19个大蚊属物种及5个其他属物种进行了系统发育分析,并计算了物种间的遗传距离.研究结果表明:(1)邻接树(NJ)和最大似然树(ML)均显示长角大蚊亚属与大蚊属其他亚属未形成单系,大蚊属的单系性没有得到支持;(2)基于遗传距离和系统发育分析并结合形态信息,结果显示长角大蚊亚属独立于大蚊属内其他亚属,应将其提升为属级分类单元.     

鲸偶蹄目核糖核酸酶10基因的分子进化研究

核糖核酸酶10由RNase10序列编码,是脊椎动物特有的生殖酶,其研究主要集中在生理功能,系统的分子进化研究相对甚少。本文,我们基于24个鲸偶蹄目代表物种的基因组分析,共获得26条RNase10序列。在偶蹄目的印度水牛和野猪中首次检测到RNase10发生基因复制,而其它22个物种均为单个基因。系统发育分析揭示鲸目的齿鲸亚目和须鲸亚目形成单系;偶蹄目的反刍亚目最先分歧,猪次目和胼足亚目形成单系。具有核糖核酸酶活性的保守功能区“CKXXNTF”发生了改变,等电点显著低于RNASE A的典型成员,揭示鲸偶蹄目RNase10可能丢失了RNASE A具有的核糖核酸活性和抗菌活性。另外,选择压力分析共检测到13个正选择位点,其中2个位点在结构半胱氨酸附近。总之,我们基于基因组分析深入揭示了鲸偶蹄目RNase10的分子进化机制,解开了鲸偶蹄目RNase10的分子进化之谜,为今后开展RNase10功能研究奠定了理论基础。     

Bayesian inference of cetacean phylogeny based on mitochondrial genomes

The phylogeny of Cetacea (whales, dolphins, porpoises) has long attracted the interests of biologists and has been investigated by many researchers based on different datasets. However, some phylogenetic relationships within Cetacea still remain controversial. In this study, Bayesian analyses were performed to infer the phylogeny of 25 representative species within Cetacea based on their mitochondrial genomes for the first time. The analyses recovered the clades resolved by the previous studies and strongly supported most of the current cetacean classifications, such as the monophyly of Odontoceti (toothed whales) and Mysticeti (baleen whales). The analyses provided a reliable and comprehensive phylogeny of Cetacea which can provide a foundation for further exploration of cetacean ecology, conservation and biology. The results also showed that: (i) the mitochondrial genomes were very informative for inferring phylogeny of Cetacea; and (ii) the Bayesian analyses outperformed other phylogenetic methods on inferring mitochondrial genome-based phylogeny of Cetacea.     

Morphology,molecules, and the phylogenetics of cetaceans

Recent phylogenetic analyses of cetacean relationships based on DNA sequence data have challenged the traditional view that baleen whales (Mysticeti) and toothed whales (Odontoceti) are each monophyletic, arguing instead that baleen whales are the sister group of the odontocete family Physeteridae (sperm whales). We reexamined this issue in light of a morphological data set composed of 207 characters and molecular data sets of published 12S, 16S, and cytochrome b mitochondrial DNA sequences. We reach four primary conclusions: (1) Our morphological data set strongly supports the traditional view of odontocete monophyly; (2) the unrooted molecular and morphological trees are very similar, and most of the conflict results from alternative rooting positions; (3) the rooting position of the molecular tree is sensitive to choice of artiodactyls outgroup taxa and the treatment of two small but ambiguously aligned regions of the 12S and 16S sequences, whereas the morphological root is strongly supported; and (4) combined analyses of the morphological and molecular data provide a well-supported phylogenetic estimate consistent with that based on the morphological data alone (and the traditional view of toothed-whale monophyly) but with increased bootstrap support at nearly every node of the tree.     

Polyphyly across oceans: a molecular phylogeny of the Chromodorididae (Mollusca, Nudibranchia)

The Chromodorididae is a large and colourful family of nudibranch sea slugs distributed across the world's oceans. Most diversity is centred in the Indo-Pacific, but several genera are present in multiple ocean basins, or across regions separated by biogeographical barriers. The monophyly of these widespread genera had not been tested previously. We used 18S rDNA, 16S rDNA and COI sequence data to generate a molecular phylogeny for this group. We recovered evidence of paraphyly or polyphyly in all of the widespread genera examined ( Hypselodoris , Mexichromis , Chromodoris and Glossodoris ). East Atlantic Hypselodoris and west Atlantic + east Pacific Mexichromis species were more closely related to each other than they were to their Indo-Pacific congeners. The addition of Southern Ocean species of Digidentis demonstrated an interesting alternative to this relationship, becoming the sister group for the east Atlantic Hypselodoris on the basis of 16S and 18S data, but not COI data. Sister group relationships were recovered for most monotypic or enigmatic genera. Ardeadoris is linked to Glossodoris , as is Diversidoris ; Pectenodoris is sister to the Indo-Pacific Mexichromis clade, and Verconia is the sister to Noumea haliclona . Controversy surrounding the placement of the three most basal genera was only partially resolved. Using Actinocyclus to root the mitochondrial trees, Cadlinella was the unsupported sister to the Chromodorididae (excluding Cadlina ), and Tyrinna occupied a relatively basal position, although this also did not receive significant statistical support. Adding nuclear 18S data gave support for Cadlina as the sister group to the rest of the Chromodorididae s.s. Otherwise, like previous molecular studies, mitochondrial genes supported an alternative position for Cadlina (with other dorid genera).     

Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea

Nucleotide sequences of the nuclear c-mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe's [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages within the superfamily, as well as genera membership in major lineages was also assessed. Analyses suggest that Bombycillidae is not a part of Muscicapoidea, and there is strongly supported evidence to suggest that Turdinae is not part of the Muscicapidae, but is instead sister to a Sturnidae+Cinclidae clade. This clade is in turn sister to Muscicapidae (Muscicapini+Saxicolini). Of the 49 Turdinae and Muscicapidae genera that we included in our analyses, 10 (20%) are shown to be misclassified to subfamily or tribe. Our results place one current Saxicolini genus in Turdinae, two Saxicolini genera in Muscicapini, and five Turdinae and two Muscicapini genera in Saxicolini; these relationships are supported with 100% Bayesian support. Our analyses suggest that c-mos was only marginally useful in resolving these "deep" phylogenetic relationships.     

Reverse evolution and cryptic diversity in putative sister families of the Oribatida (Acari)

The family Zetorchestidae is a morphologically and ecologically diverse group assigned to the higher oribatid mites (Brachypylina). We addressed the phylogeny of the family by including species of the genera Belorchestes, Litholestes, Microzetorchestes and Zetorchestes. We also analysed the affinities of the putative sister taxon (Eremaeidae), investigating Eremaeus and Eueremaeus. Zetorchestidae, Eremaeidae and Niphocepheidae were recently combined in one superfamily (Zetorchestoidea). These taxa were placed into a wider phylogenetic context by adding other presumably closely related taxa. Phylogenetic analyses based upon nuclear and mitochondrial DNA‐sequences revealed the monophyly of the Zetorchestidae as well as of all investigated species and genera of this family. Ancestral state reconstruction of jumping ability in latter family, moreover, suggested reverse character evolution within the studied zetorchestid taxa. Genetic diversity of the genera Eremaeus and Eueremaeus turned out to be higher than known, suggesting the existence of cryptic species. However, none of our analyses supported a sister group relationship among Zetorchestidae and Eremaeidae. Moreover, all calculated trees show a paraphyletic position between Zetorchestidae respectively Eremaeidae and Niphocepheidae.     

A molecular phylogeny of eurytomid wasps inferred from DNA sequence data of 28S, 18S, 16S, and COI genes

Using partial DNA sequence data from nuclear 28S and 18S genes and mitochondrial 16S and COI genes, we reconstructed a phylogeny of the family Eurytomidae. Both maximum parsimony and Bayesian methods were employed. The analysis revealed a significant incongruence between the mitochondrial genes and the nuclear genes, and we chose the results from the nuclear genes as our preferred hypothesis. Our phylogeny suggested that the family Eurytomidae is not a monophyletic group; neither are the genera Eurytoma and Bruchophagus. The monophyly of genera Sycophila and Plutarchia was well supported, as was the close association of the genera Aiolomorphus, Tenuipetiolus, Bephratelloides, and Phylloxeroxenus. Our phylogeny also revealed an anticipated pattern, in which species groups from the genera Eurytoma and Bruchophagus are often more closely related to other small genera than to other species groups of the same genus. Subsequent taxonomic revisions include elevating the subfamily Rileyinae to a family status and the divisions of the genera Eurytoma and Bruchophagus.     

A preliminary phylogeny of the Pentatomomorpha (Hemiptera: Heteroptera) based on nuclear 18S rDNA and mitochondrial DNA sequences

Pentatomomorpha is the second suborder in size only to Cimicomorpha in Heteroptera. However, the phylogenetic relationships among members of the suborder are not well established. Sequences from partial nuclear ribosomal 18S gene and mitochondrial COX1 gene were analyzed separately and in combination to generate a preliminary molecular phylogeny of Pentatomomorpha based on 40 species representing 17 putative families. Analyses of the combined sequence data provided a better-resolved and more robust hypothesis of Pentatomomorpha phylogeny than did separate analyses of the individual genes. The phylogenies were mostly congruent with morphological studies. Results strongly supported the monophyly of the infraorder Pentatomomorpha, and the placement of Aradoidea as sister to Trichophora. The monophyletic Trichophora was grouped into two major lineages, one being the superfamily Pentatomoidea, and the other comprising Lygaeoidea, Coreoidea, and Pyrrhocoroidea. The analysis of the ML and ME trees of combined dataset supported the monophyletic Pentatomoidea. In all analysis the Pyrrhocoroidea was polyphyletic; the monophyletic Lygaeoidea was supported only in the analysis of ME tree, and Coreoidea was polyphyletic except in the MP tree of combined dataset. The molecular and morphylogical data both indicated that the family Coreoidae should be revised subsequently. Our phylogenetic results suggested that the COX1 segment alone might not be an optimal molecular marker for the phylogeny of Pentatomomorpha.     

Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species

Morphological data have indicated that toothed whales form a monophyletic group. However, research published in the last several years has made the issue of the monophyly or paraphyly of toothed whales a subject of debate. Our group previously characterized three independent loci in which SINE insertions were shared among dolphins and sperm whales, thus supporting the traditional, morphologically based hypothesis of toothed whale monophyly. Although in recent years a few additional molecular works proposed this topology, there is still skepticism over this monophyly from the view point of molecular systematics. When the phylogeny of rapidly radiated taxa is examined using the SINE method, it is important to consider the ascertainment bias that arises when choosing a particular taxon for SINE loci screening. To overcome this methodological problem specific to the SINE method, we examined all possible topologies among sperm whales, dolphins and baleen whales by extensively screening SINE loci from species of all three lineages. We characterized nine independent SINE loci from the genomes of sperm whales and dolphins, all of which cluster sperm whales and dolphins but exclude baleen whales. Furthermore, we characterized ten independent loci from baleen whales, all of which were amplified in a common ancestor of these whales. From these observations, we conclude that toothed whales form a monophyletic group and that no ancestral SINE polymorphisms hinder their phylogenetic assignment despite the short divergence times of the major lineages of extant whales during evolution. These results suggest that a small population of common ancestors of all toothed whales ultimately diverged into the lineages of sperm whales and dolphins.     

Mitochondrial phylogenetics and evolution of mysticete whales

The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations.     

Phylogenetic relationships of North American nymphophiline gastropods based on mitochondrial DNA sequences

Phylogenetic relationships of 36 nymphophiline species representing 10 genera were inferred from mtCOI sequence data and compared to recent morphology-based classifications of this group. Parsimony and maximum likelihood analyses of the molecular data set suggested monophyly of the North American nymphophilines and a sister or otherwise close relationship between this fauna and a European species assigned to the subfamily. Results also supported a previously hypothesized close relationship between the predominantly freshwater nymphophilines and the brackish-water genus Hydrobia . Our analyses resolved a North American nymphophiline subclade composed of Floridobia , Nymphophilus , and Pyrgulopsis , and depicted the remaining North American genera ( Cincinnatia , Marstonia , Notogillia , Rhapinema , Spilochlamys , Stiobia ) as either a monophyletic or paraphyletic group. Two of the large North American genera ( Floridobia , Marstonia ) were supported as monophyletic groups while monophyly of Pyrgulopsis , a western North American group containing > 100 species, was equivocal. North American nymphophiline phylogeny implies that vicariance of eastern and western North American groups was followed by a secondary invasion of eastern coastal areas from the west. We attribute this to dispersal of salt-tolerant progenitors along the Gulf of Mexico coast