线粒体COI基因在少鳞鳜属(Coreoperca)鱼类条形码区段的变异分析

为了研究线粒体COI基因作为DNA条形码对少鳞鳜属(Coreoperca)鱼类进行物种鉴定的可行性.采用PCR扩增与测序技术与GenBank已有序列联合分析的方法,对少鳞鳜属3种84个个体的条形码区段进行比较分析.结果表明,碱基T(U)的平均含量为30.3％,C的平均含量为27.8％,A的含量为23.1％,G的含量为18.8％.在4种碱基中,G的含量最低,其在第三密码子的使用率上也低至9.3％.少鳞鳜属3种鱼类种内平均遗传距离值为0.003 8,种间为0.146 3,种间遗传距离是种内的38倍;通过构建的系统发育树,少鳞鳜属中的分支明确,种间无交叉情况,说明种间具有明显差异,种内没有亚种的分化.研究证明,线粒体COI基因可作为条形码序列对少鳞鳜属鱼类物种鉴别的有效片段,并且还为其物种的鉴定与分类提供辅助方法.     

浙江近海鰓属鱼类形态描述及中国鰓属鱼类分子系统发育分析

为明确浙江近海鲵属鱼类物种组成, 对采自舟山和温州近海共计411尾鲵鱼样品进行形态学测定, 并基于线粒体细胞色素氧化酶Ⅰ亚基(COⅠ)基因片段探讨其序列差异及系统发育关系。结果显示: 浙江近海的鲵属鱼类为少鳞鲵和中国鲵, 两种鲵鱼形态特征鲜明, 鱼鳔形态差异明显。所测得的少鳞鲵和中国鲵COⅠ基因片段长度均为600 bp, 平均GC含量分别为46.6%和49.9%。依据Kimura-2-parameter模型(K2P), 少鳞鲵和中国鲵的种内平均遗传距离分别为0.002和0.000, 两种间平均遗传距离为0.211。采用邻接法构建的系统发育树显示, 中国鲵先和邵氏鲵聚为一支, 然后与少鳞鲵聚为一支, 再与其他鲵属鱼类聚类。研究结果明确了浙江沿海鲵属鱼类的物种组成, 并为探讨少鳞鲵和中国鲵的系统发育关系及基于COⅠ基因的鲵属鱼类物种鉴定提供了参考。     

中国泥鳅属和副泥鳅属鱼类的分类整理

根据形态学特征及线粒体Cyt b和COⅠ基因对我国泥鳅属(Misgurnus)和副泥鳅属(Paramisgurnus)鱼类进行了分类整理。结果表明: 泥鳅属和副泥鳅属鱼类在鳞焦大小, 须长及基枕骨末端愈合程度等特征上存在差异。基于联合基因分析, 泥鳅属和副泥鳅属属间遗传距离(15.2%—17.5%)接近于泥鳅属种间遗传距离(10.7%—18.4%); 分子系统树显示我国泥鳅属鱼类未构成单系, 副泥鳅属嵌套分布于泥鳅属中; 北方泥鳅(Misgurnus bipartitus)和泥鳅(Misgurnus anguillicaudatus)亲缘关系近, 其次是大鳞副泥鳅(Paramisgurnus dabryanus), 黑龙江泥鳅(Misgurnus mohoity)位于系统树的基部。结合形态特征与分子数据, 副泥鳅属应作为泥鳅属同属异名, 大鳞副泥鳅应归入泥鳅属; 北方泥鳅曾为黑龙江泥鳅的同物异名, 与黑龙江泥鳅存在明显的形态差异, 且两者亲缘关系较泥鳅远, 北方泥鳅为有效种。     

斑纹薄鳅(Leptobotia zebra)应该为斑纹沙鳅(Sinibotia zebra)

斑纹薄鳅(Leptobotia zebra)最初是由Wu(1939)描述的一个新种,当时定名为斑纹沙鳅(Botia zebra),后来Chen(1980)根据眼下刺不分叉将其改归为薄鳅属的物种。本研究通过对线粒体DNA细胞色素b基因序列的测定和分析,发现斑纹薄鳅和薄鳅属(除斑纹薄鳅)物种间的平均遗传距离为0.177,和中华沙鳅属物种美丽沙鳅(Sinibotia pulcher)的平均遗传距离仅为0.057。系统发育分析发现斑纹薄鳅并未和薄鳅属的物种聚在一起,而是和中华沙鳅属物种美丽沙鳅聚在一起形成姐妹群。进一步对斑纹薄鳅进行形态学特征检视,发现该物种具有颊部裸露无鳞、颏部具一对纽状突起等中华沙鳅属鱼类的特征,但又具有眼下刺简单不分叉的薄鳅属鱼类的特征。结合分子数据分析的结果,将斑纹薄鳅订正为中华沙鳅属的物种,其命名为斑纹沙鳅(Sinibotia zebra)。另外,对沙鳅科鱼类属的划分标准及形态特征的演化也进行了讨论。     

斑纹薄鳅(Leptobotia zebra)应该为斑纹沙鳅(Sinibotia zebra)

斑纹薄鳅(Leptobotia zebra)最初是由Wu（1939）描述的一个新种,当时定名为斑纹沙鳅(Botia zebra),后来Chen（1980）根据眼下刺不分叉将其改归为薄鳅属的物种。本研究通过对线粒体DNA细胞色素b基因序列的测定和分析,发现斑纹薄鳅和薄鳅属（除斑纹薄鳅）物种间的平均遗传距离为0.177,和中华沙鳅属物种美丽沙鳅(Sinibotia pulcher)的平均遗传距离仅为0.057。系统发育分析发现斑纹薄鳅并未和薄鳅属的物种聚在一起,而是和中华沙鳅属物种美丽沙鳅聚在一起形成姐妹群。进一步对斑纹薄鳅进行形态学特征检视,发现该物种具有颊部裸露无鳞、颏部具一对纽状突起等中华沙鳅属鱼类的特征,但又具有眼下刺简单不分叉的薄鳅属鱼类的特征。结合分子数据分析的结果,将斑纹薄鳅订正为中华沙鳅属的物种,其命名为斑纹沙鳅(Sinibotia zebra)。另外,对沙鳅科鱼类属的划分标准及形态特征的演化也进行了讨论。     

短吻红舌鳎鱼卵、仔鱼的DNA条形码和形态学鉴定

为了准确鉴定2015年7–10月青岛崂山青山湾鱼类浮游生物调查中采集的依形态学初步鉴定为某种舌鳎属的鱼卵、仔鱼样本,本实验同时采集青岛胶州湾短吻红舌鳎(Cynoglossus joyneri)和长吻红舌鳎(C.lighti)的成鱼样本为参照,通过线粒体COI基因测序分析,以及同山东半岛海域分布的6种舌鳎属鱼类的COI基因序列比对,开展了该舌鳎属鱼卵、仔鱼种类的鉴别分析,以期为今后舌鳎属鱼类的分类及其鱼卵、仔鱼的鉴别提供参考资料。形态学研究结果显示:鱼卵为圆球形浮性卵,直径0.68–0.87 mm(0.73±0.03 mm,n=50),卵膜单层,较薄、光滑透明,卵周隙较大,卵膜及卵黄囊均无特殊构造,油球6–15个,直径0.04–0.10 mm(0.07±0.01 mm,n=50),圆形,大小不一,多位于卵黄囊中与胚体相对的一侧,既有聚集分布也有分散分布;仔鱼的2条冠状幼鳍及右眼移位过程中体长、色素分布等的特征和变化是此鱼种仔鱼鉴别的最明显特征。遗传学分析结果显示:该种舌鳎属样品(Cynoglossus sp.)与短吻红舌鳎和长吻红舌鳎的遗传距离最为接近,三者K2P遗传距离为0.006–0.009;短吻三线舌鳎(C.abbreviatus)与紫斑舌鳎(C.purpureomaculatus)亲缘关系最近,两者K2P遗传距离仅为0.002。以带纹条鳎(Zebrias zebra)为外类群构建的NJ系统发育树显示,该种舌鳎属样品与短吻红舌鳎和长吻红舌鳎以及短吻三线舌鳎与紫斑舌鳎分别聚为一支,其他种类各聚为一支。综合形态特征和COI基因比对结果,确定该舌鳎属鱼卵、仔鱼样品为短吻红舌鳎。     

基于线粒体CO 1基因序列的DNA条形码在鲤科鲌属鱼类物种鉴定中的应用

本研究探讨了线粒体CO1基因作为DNA条形码对鲌属鱼类进行物种鉴定的可行性。研究中获得了鲌属4种鱼类共32个个体长度为816bp的CO1基因序列。利用MEGA软件计算鲌属鱼类种间及种内遗传距离,利用邻接法、最大简约法、最大似然法和Bayesian方法分别构建分子系统树。结果显示,鲌属鱼类的种间遗传距离显著大于种内遗传距离。在系统树中,鲌属鱼类每一物种的个体分别形成各自独立的分支。基于CO1基因的DNA条形码在识别鲌属鱼类物种方面和传统形态学基本一致,而且该基因可以探讨鲌属鱼类种间的系统发育关系。本研究表明以CO1基因作为鲌属鱼类DNA条形码进行物种鉴定具有一定的可行性。     

北部湾涠洲岛海域栖息布氏鲸种群的物种鉴定

布氏鲸(Bryde’s whale)是广泛分布于温带和热带海域的一类中等体型须鲸,通常认为存在小布氏鲸(Balaenoptera edeni edeni)和布氏鲸(B. e. brydei)两个亚种。然而,有研究表明它们应该被划分为两个独立物种,即近岸小型布氏鲸(B. edeni)和远洋大型布氏鲸(B. brydei)。由于两者外部形态极其相似,并且存在同域分布现象,很难基于外观进行准确的物种鉴定。近年来,广西北部湾涠洲岛海域出现一个稳定的布氏鲸栖息种群,但目前尚不清楚属于哪种布氏鲸。研究采集了涠洲岛布氏鲸种群中两个体的粪便样品,从其中一份样品成功提取基因组DNA,并基于线粒体Cyt b和COΙ基因序列开展物种鉴定和遗传分析,鉴定结果为小布氏鲸。此外,还鉴定出涠洲岛海域同年死亡的一头须鲸也为小布氏鲸。据此推测涠洲岛水域栖息的布氏鲸种群可能是小布氏鲸。研究首次基于粪便样品,采用分子生物学技术,成功开展了活体布氏鲸的物种鉴定。这种基于非损伤采样的物种鉴定方法值得进一步优化并推广应用。     

云南石林洞穴金线鲃一新种(鲤形目,鲤科)

2006年4月12日和18日作者于云南省石林县石林镇落水洞(蝙蝠洞)地下伏流(属珠江水系)采集到金线鲃属鱼类标本9尾,经鉴定为1新种.新种被命名为宽角金线鲃Sinocyclocheilus broadihornes sp. nov.;以其头上长有一个骨质角状突和体表裸露,仅存侧线鳞等鉴别特征,与犀角金线鲃S.rhinocerous Li et Tao相近,而明显区别于属内的其余种.但新种头上骨质突起为1个等边三角形状的角与后者的犀角型角不同;新种吻端与两鼻孔间有3个突起,呈品字形分布,后者平滑.     

鳜类系统发育的线粒体Cytb基因全序列分析

测定了鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜、中国少鳞鳜等7种鳜类12个个体的线粒体细胞色素b基因全序列。结合GenBank中的同源序列,共分析了9种鳜类的系统发育关系。序列分析表明,鳜属鱼类属内种间的遗传距离(0.015～0.093)明显小于少鳞鳜属鱼类属内种间的遗传距离(0.152～0.178)。在分子系统发育树上,长体鳜与鳜属的鳜、大眼鳜、斑鳜、波纹鳜、暗鳜聚合成一分支,少鳞鳜属的种类聚成另一分支;支持将长体鳜归入鳜属,鳜类分为鳜属和少鳞鳜属等二个属的分类处理。在鳜属鱼类中,鳜和大眼鳜亲缘关系十分密切;斑鳜与波纹鳜亲缘较近;长体鳜与鳜属其它5个种的亲缘关系较远。在少鳞鳜属鱼类中,中国少鳞鳜和日本少鳞鳜的亲缘关系较远,韩国少鳞鳜的系统位置较不明确。鳜类的单系性及其鳜类的系统位置仍有待进一步研究。     

TAXONOMIC STATUS OF THE GENUS SOTALIA: SPECIES LEVEL RANKING FOR "TUCUXI" (SOTALIA FLUVIATILIS) AND "COSTERO" (SOTALIA GUIANENSIS) DOLPHINS

Dolphins of the genus Sotalia are found along the Caribbean and Atlantic coasts of Central and South America and in the Amazon River and most of its tributaries. At present, the taxonomy of these dolphins remains unresolved. Although five species were described in the late 1800s, only one species is recognized currently ( Sotalia fluviatilis ) with two ecotypes or subspecies, the coastal subspecies ( Sotalia fluviatilis guianensis ) and the riverine subspecies ( Sotalia fluviatilis fluviatilis ). Recent morphometric analyses, as well as mitochondrial DNA analysis, suggested recognition of each subspecies as separate species. Here we review the history of the classification of this genus and present new genetic evidence from ten nuclear and three mitochondrial genes supporting the elevation of each subspecies to the species level under the Genealogical/Lineage Concordance Species Concept and the criterion of irreversible divergence. We also review additional evidence for this taxonomic revision from previously published and unpublished genetic, morphological, and ecological studies. We propose the common name "costero" for the coastal species, Sotalia guianensis ( Van Bénéden 1864 ), and accept the previously proposed "tucuxi" dolphin, Sotalia fluviatilis (Gervais, 1853), for the riverine species.     

The Taxonomy and Phylogeny of Echinometra (Camarodonta: Echinometridae) from the Red Sea and Western Indian Ocean

The number of valid species in the genus Echinometra (Echinodermata, Echinoidea) and their associated identification keys have been debated in the scientific literature for more than 180 years. As the phylogeny and dispersal patterns of these species have been widely used as a prominent model for marine speciation, new insights into their taxonomy have the potential to deepen our understanding of marine speciation processes. In this study we examine Echinometra taxonomy, combining morphology and molecular tools. We present the taxonomy and phylogeny of Red Sea and Western Indian Ocean Echinometra. The currently available morphological keys were found to be limited in their ability to delineate all species within this genus. Nonetheless, morphological similarities between the Red Sea and Western Indian Ocean populations were high, and delimited them from the other species. These latter populations together formed a monophyletic clade, genetically distant from any of the other Echinometra species by more than 3%. Combining both traditional taxonomy and molecular evidence, we found that these populations were neither Echinometra mathaei nor E. oblonga, as previously considered. The morphological discrepancies of these populations, and their genetic divergence from the other Echinometra species, suggest that they should be considered as a new Echinometra species.     

Out of Alaska: morphological diversity within the genus <Emphasis Type="Italic">Eurytemora</Emphasis> from its ancestral Alaskan range (Crustacea,Copepoda)

The copepod genus Eurytemora occupies a wide range of habitat types throughout the Northern Hemisphere, with among the broadest salinity ranges of any known copepod. The epicenter of diversity for this genus lies along coastal Alaska, where several species are endemic. Systematic analysis has been difficult, however, because of a tendency toward morphological stasis in this genus, despite large genetic divergences among populations and species. The goals of this study were to (1) analyze patterns of morphological variation and divergence within this genus, focusing on Eurytemora species that occur in North America, and (2) determine patterns of geographic and salinity distribution of Eurytemora species within the ancestral range in Alaska. We applied a comparative multivariate morphological analysis using 16–26 characters from 125 specimens from 20 newly collected sites in Alaska and 15 existing samples predominantly from North America. Results from principal component and hierarchical cluster analyses identified seven distinct morphological species of Eurytemora in North America (E. affinis, E. americana, E. canadensis, E. composita, E. herdmani, E. pacifica, and E. raboti), and identified diagnostic characters that distinguish the species (forming the basis for a new identification key). Several previously named species were regarded as synonyms. The sites we sampled in Alaska were remarkable in the high levels of sympatry of Eurytemora species, to a degree not seen outside of Alaska. Future studies of Eurytemora should shed light on patterns of habitat invasions and physiological evolution within the genus, and yield insights into mechanisms leading to its remarkably broad geographic and habitat range.     

Molecular phylogenetics of the genus <Emphasis Type="Italic">Physalia</Emphasis> (Cnidaria: Siphonophora) in New Zealand coastal waters reveals cryptic diversity

Physalia is a genus of pelagic colonial hydrozoans often known by common names such as ‘Portuguese-man-of-war’ or ‘bluebottle’. Siphonophore systematists generally recognise only a single species in this genus, Physalia physalis, however the name Physalia utriculus is also still in common use, which has led to considerable taxonomic confusion. With some morphological variation between global regions there is the possibility that this genus holds a substantial amount of cryptic variation. We seek to examine the genetic structure of Physalia present in New Zealand coastal waters. Fifty-four specimens collected from 13 locations around New Zealand and Australia were sequenced for both mitochondrial cytochrome c oxidase I (COI) and the first internal transcribed spacer (ITS1) of the nuclear ribosomal cistron. Sequences were analysed using maximum likelihood and split decomposition neighbour networks to determine conflict between clans (the unrooted analog of clades). Three clans were identified from both the COI and ITS sequences. The results are complex and clans are not consistent between the two genes. Nevertheless, it seems that there is substantial cryptic diversity amongst Physalia present in New Zealand coastal waters.     

Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo‐West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach‐cast, remote‐biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population‐level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as‐yet‐unnamed species off northern Australia).     

An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea)

DNA sequences are currently used to propose primary hypotheses of species delimitation, especially when morphological variability is difficult to assess. In an integrative taxonomy framework, these hypotheses are then compared with other characters, such as morphology or geography, to produce robust species delimitations. For this purpose, the cytochrome oxidase subunit I (COI) gene has been sequenced for almost 50 specimens of the genus Benthomangelia , a deep-sea marine gastropod genus, collected in the South-West Pacific. Five genetic groups, displaying low and high genetic distances respectively within and between groups, were defined. COI hypotheses were compared with both the results obtained with the independent nuclear 28S gene and with an elliptic Fourier analysis of the shape of the last whorl of the shell. 28S gene analysis confirmed the same well-supported groups as COI, and elliptic Fourier analysis identified several morphological characters that vary similarly to genetic variability.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 696–708.     

Distributional range extension of the seagrass Halophila nipponica into coastal waters off the Korean peninsula

Eight temperate seagrass species (five in the genus Zostera, two in the genus Phyllospadix, and Ruppia maritima) have been previously reported in coastal waters off the Korean peninsula, which lies between 33°N and 43°N. Recently, a species of Halophila, a genus which occurs predominantly in tropical and subtropical areas, has been observed on the southern coast of Korea for the first time. The species was identified as Halophila nipponica. H. nipponica is distributed in warm temperate regions of Japan influenced by the warm Tsushima Current and was previously unknown outside the Japanese archipelago. Thus, we are able to report a range extension into Korea. The Korean Halophila meadow that we observed covered an area of about 2.1 ha, with average shoot density of about 1300 m⁻². We measured morphological features of vegetative and reproductive organs between June and September 2007. Morphological and reproductive features of the Halophila species in Korea were similar to those of the species in Japan. Increased water temperature in the coastal waters of Korea may at least partially account for the persistence of this new population.     

Kofoidinium, Spatulodinium and other kofoidiniaceans (Noctilucales, Dinophyceae) in the Pacific Ocean

Examples of rarely reported dinoflagellates of the family Kofoidiniaceae F.J.R. Taylor (Noctilucales) from the northwest, equatorial and southeast Pacific Ocean are described and illustrated. Kofoidinium was the most ubiquitous genus with a maximum abundance of 10 cells L(-1). Specimens of this genus were identified to four species: Kofoidinium sp. that showed a pointed extension that emerges from the antero-ventral region and K. velelloides, both of which had diameters that ranged from 40 to 200 microm; Kofoidinium pavillardii which showed a rounded epitheca and a larger size (approximately 300-700 microm in diameter); and another species, tentatively identified as K. splendens, that contained red circular inclusions. Further research is needed to clarify the characteristics that separate K. splendens from the other species. This study is the first to record the genus Spatulodinium in tropical waters and in the southern hemisphere. S. cf. pseudonoctiluca was found in the southeast Pacific Ocean, as well as other smaller specimens with a different shape or disposition of the tentacle that may belong to two other species. In the northwest and equatorial Pacific, specimens of Spatulodinium showed a green pigmentation that suggested the existence of the first species known in the order Noctilucales to contain its own chloroplasts. Immature stages of kofoidiniaceans, some containing symbiotic microalgae, are illustrated, as well as mature stages related to Pomatodinium and to unknown genera of kofoidiniaceans. Kofoidiniaceans are shown to be common and widely distributed in the Pacific, and are probably also frequent in other oceans, but are rarely recognised.