裂腹鱼亚科鱼类Hif-α基因的分子进化及低氧诱导表达

目的 探究低氧诱导因子Hif-α在裂腹鱼亚科鱼类适应低氧环境中的作用及表达调控。方法 利用RT-PCR技术获得了裂腹鱼亚科鱼类13个代表物种的Hif-1αΑ、Hif-1αB、Hif-2αΑ和Hif-2αB基因编码区序列,基于裂腹鱼亚科鱼类系统进化关系开展了基因选择压力分析,并选取花斑裸鲤进行低氧诱导表达研究。结果 Hif-1αΑ、Hif-1αB、Hif-2αΑ和Hif-2αB基因编码区长度分别为2196、2325、2544和2511 bp。通过序列比对发现裂腹鱼亚科鱼类HIF1αΑNODD结构域中保守脯氨酸羟基化基序LxxLAP发生缺失,特化及高度特化的裂腹鱼的HIF1αBCODD结构域中脯氨酸羟基化基序突变为PxxLAP。与常氧组相比,在重度缺氧条件下花斑裸鲤的脑和心脏组织中部分Hif-α基因表达量显著下降,在中度低氧中心脏组织中的Hif-1αA和Hif-2αA基因表达量上调。结论 Hif-α基因在13个物种中受到正向选择作用,但具体物种分支有待进一步研究,同时裂腹鱼亚科鱼类在适应慢性低氧和急性低氧环境可能存在两种不同的表达调控机制。     

中国鲤科鱼类染色体组型的研究Ⅺ．裂腹鱼亚科二种鱼和鳅鮀亚科三种鱼的染色体组型

裂腹鱼亚科(Schizothoracinae)鱼类主要分布于亚洲高原地区的江河上游,在我国分布有10属,54种和亚种。鳅鮀亚科(Gobiobotitaae)仅有1属3亚属,已知有16种和亚种,在我国分布构就有13种。我们考察的3种鳅鮀亚科鱼类即分属3个不同的亚属。     

银色裂腹鱼线粒体基因组序列特征与系统进化分析

银色裂腹鱼(Schizothorax argentatus)在我国仅分布于新疆地区的伊犁河流域,是我国裂腹鱼类中珍稀濒危品种之一,具有较高的科研和经济价值。本研究采用高通量测序技术获得了银色裂腹鱼长度为16580 bp的线粒体基因组全序列,其基因组成和排列顺序均与典型的脊椎动物相似,共有13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和1个非编码区(D-loop)。碱基组成分别为A(30.25%)、G(17.28%)、C(27.20%)和T(25.27%),呈现明显的AT偏好性和反G偏倚。tRNA基因中仅tRNA-Ser(GCU)因缺少二氢尿嘧啶茎而无法形成典型的三叶草结构。ND6基因的AT-skew和GC-skew值波动最大,揭示该基因经历的选择和突变压力可能与其他基因不同。银色裂腹鱼线粒体控制区包含了3个不同的结构域:终止序列区(ETAS)、中央保守区(CSB-F、CSB-E、CSB-D和CSB-B)和保守序列区(CSB1、CSB2和CSB3),且在CSB3下游约50 bp处识别到鲤形目(Cypriniformes)鱼类中普遍存在的保守序列片段TT(AT)nGTG。基于28种裂腹鱼属鱼类线粒体基因组全序列构建的系统发育关系表明银色裂腹鱼分化时间较早,与其他类群亲缘关系较远,这可能与其所生活的水域地理位置和水文环境有密切关系。     

新疆裂腹鱼类的系统发生关系及物种分化时间

文章采用线粒体COI、ND4、16S rRNA基因联合数据分析了新疆分布的裂腹鱼类4属10个种或亚种的分子系统发育,并通过鲤亚科的分化时间、黄河上游和青海湖隔离的地质时间来校正分子钟,进而探讨了裂腹鱼类分化时间与塔里木盆地周边地区主要地质事件和气候变化的关系。结果发现,扁吻鱼属未能形成独立的分支,与塔里木裂腹鱼、厚唇裂腹鱼聚在一起。进一步基于COI基因序列,利用Kimura双参数模型计算遗传距离,发现扁吻鱼属和裂腹鱼属间的遗传距离未达到属间区别,扁吻鱼可能是裂腹鱼属内特化的物种;聚类分析结果不同于裂腹鱼属的形态学分类方法,不支持裂腹鱼属鱼类的亚属划分;原始等级裂腹鱼类(包括裂腹鱼属和扁吻鱼属)两个族群的分化时间(8.18 Ma)与新疆裸重唇鱼和斑重唇鱼的分化时间(7.67 Ma)均发生于晚中新世,这可能与8Ma左右青藏高原北缘和北天山抬升、塔里木盆地气候干旱化等重大地质事件和气候转型导致青藏高原北缘(昆仑山)和北天山水系间出现分离相关。而塔里木盆地裂腹鱼属鱼类现今的分布格局可能与第四纪喜马拉雅运动使盆地形成西高东低的地势、罗布泊成为塔里木盆地周边高山发源河流的汇水中心相关。     

五种裂腹鱼亚科鱼类外胚层发育不良因子A受体基因Edar的克隆和序列分析

裂腹鱼亚科鱼类具有丰富的体表附属器官变异,而Edar是控制这类结构发育的关键基因。以5种裂腹鱼的代表物种为材料克隆其Edar基因的编码区片段,序列分析表明:该基因编码的蛋白在裂腹鱼中存在长度不同的组氨酸重复序列,串联组氨酸插入可能与蛋白定位有关;基因树支持裂腹鱼与金线鲃具有最近的亲缘关系;分子进化分析未检测到正选择信号,裂腹鱼Edar基因的低复杂区可能是受选择区域。以上结果说明裂腹鱼Edar基因的结构变异可能与裂腹鱼表型变异和演化有关。     

青藏高原裸裂尻属鱼类两个疑难种的分子系统学

裸裂尻鱼属[Schizopygopsis（Steindachner）]鱼类广泛分布于青藏高原各河流上游干支流及其湖泊之中,由于其广泛的分布域和特殊的生态环境而被生物学家视为青藏高原隆升过程中淡水鱼类物种起源、进化的模式物种。然而,该属鱼类种间具有非常相似的形态特征,致使大渡软刺裸裂尻鱼（Sp．malacanthus chengi）和前腹裸裂尻鱼（Sp．anteroventris）的分类学地位一直存在争议。本文采用聚合酶链式反应（PCR）和直接测序的方法,获得了裸裂尻鱼属两个分类疑难种和5个指名种（n=17）以及5个近缘种（n=5）共23个个体的细胞色素b（Cytb）基因的全序列（1140bp）,并以同亚科的齐口裂腹鱼（Schizothorax cprenanti）作为外群构建了ML、MP和Bayesian进化树。序列差异和分子系统学分析表明,Sp．malacanthus schengi和软刺裸裂尻鱼（Sp．malacanthus）间存在较大的差异（2．06％）,两者并不聚在同一枝上;Sp．anteroventris独立成一枝,与其它指名裸裂尻鱼间显示出较大差异（4．38％-5．53％）,综合其它形态差异共同提示,Sp．mnlacanthus chengi应提升为独立种,沿用Sp．chengi的种名,而Sp．anteroventris应该是裸裂尻鱼属的一个独立种。     

2种珍稀裂腹鱼类线粒体DNA部分序列片段的比较分析

对扁吻鱼(Aspiorhynchus laticeps)及塔里木裂腹鱼(Schizothorax biddulphi)线粒体CO I(624 bp)、Cyt b(712 bp)和D-loop(457 bp)基因片段进行了PCR扩增和序列测定.通过分析比较发现,3个片段A+T含量与其他鱼类相比均较高,G含量偏低这一现象在...     

青海省6种裂腹鱼COI基因作为DNA条形码的适用性初探

青海省裂腹鱼鱼类至少有20种,占土著鱼类的40%以上,具有重要的生态价值。由于生态环境的恶化和人为因素的干扰,很多物种群已濒临灭绝。快速和准确的物种鉴定对于这些物种的保护至关重要,而基于形态学的传统分类法很难满足这一需求。因此,本研究通过DNA条形码技术初步探讨了在青海省裂腹鱼物种鉴定中的适用性。本研究中,测序获得了青海26尾裂腹鱼(6个物种)的细胞色素c氧化酶亚基I (COI)基因,并经GenBank数据库进行比对;基于K2P模型分析COI序列变异;运用贝叶斯法(BI)和最大似然法(ML)构建系统发育树。结果显示,6种裂腹鱼COI序列检测得到15个单倍型,且各物种间无共享的单倍型。基于K2P模型,最大种内遗传距离和最小种间遗传距离分别为(0.621±0.297)%和(2.792±0.644)%。种间平均遗传距离为(12.205±1.307)%,约为种内平均遗传距离((0.327±0.162)%)的37倍,表明各物种的COI序列间已经形成明显"条形码间隙"。AMOVA分析显示,遗传变异主要来自种间,约占97.05%;FST=0.970 54,p<0.01,说明各物种间分化程度极高。此外,基于BI和ML方法构建的系统树具有一致的拓扑结构,分辨率较高;各物种均单独聚为一个发育枝,拓扑结构合理。以上结果表明,COI基因作为DNA条形码在青海裂腹鱼物种鉴定中具有较高的适用性。     

湖南鱼类新纪录——灰裂腹鱼

<正>2007年9月—2014年8月,作者采用固定样点法对湖南省壶瓶山国家级自然保护区内的鱼类资源进行监测,在长江一级支流——澧水上游的渫水纸棚河段(110°33'25.1″E,30°00'50.0″N,海拔516 m)采集到裂腹鱼标本5尾,根据《中国鱼类系统检索》和《中国动物志(硬骨鱼纲鲤形目下卷)》鉴定为灰裂腹鱼Schizothorax griseus。经查阅相关文献,为湖南省新纪录。测量标本5尾,全长204~231 mm,体长162~186 mm;体长为体高的4.2~4.7倍,为头长的4.3~4.4倍,为尾柄长的     

利用Cyt b基因序列探讨柴达木裸裂尻鱼的分类学地位

长期以来,柴达木裸裂尻鱼(Schizopygopsis kessleri)的分类学地位存在争议。为此,测定了柴达木裸裂尻鱼格尔木河及托素湖种群24个个体及黄河裸裂尻鱼(S.pylzovi)黄河及大通北川河种群12个个体的Cytb基因全序列。通过遗传距离和系统发育分析,探讨了柴达木裸裂尻鱼的分类学地位。结果显示,柴达木裸裂尻鱼与黄河裸裂尻鱼在系统进化树上并未形成相应的单系群;柴达木裸裂尻鱼与黄河裸裂尻鱼种间平均遗传距离为0.54%,明显低于裂腹鱼亚科其他属鱼类的种间遗传距离及本属其他种间遗传距离,表明来自柴达木盆地格尔木河和托素湖的裸裂尻鱼与黄河裸裂尻鱼之间没有达到种级水平的显著分化。综合地质学资料和柴达木水系与黄河水系现今的隔离格局,建议将柴达木裸裂尻鱼作为黄河裸裂尻鱼的一个亚种,即S.pylzovi kessleri。     

Molecular and morphological boundaries of the predatory mite Neoseiulus californicus (McGregor) (Acari: Phytoseiidae)

Neoseiulus californicus (McGregor) is a natural enemy of pest mites used worldwide in many crops. Its correct identification is thus essential to ensure biological control success. The present study aimed to characterize molecular and morphological intraspecific variations for assisting in the diagnosis of the species and to build baseline information about expected variations within a commercially important phytoseiid species. Morphological and molecular [12S rRNA, cytochrome b mitochondrial (mt)DNA, and internal transcribed spacer] analyses were carried out on fourteen populations collected worldwide and on one mass‐reared strain. The genetic distances between the specimens of N. californicus and another related species were high and no overlap was observed, sustaining the reliability of such molecular methods for assisting a specific diagnosis. Furthermore, the genetic distances between populations of N. californicus were very low and overlap between intra‐ and interpopulations distances was observed, except for two populations collected in France (Marsillargues and Midi‐Pyrénées). The high mitochondrial differentiation between these two latter populations and the others questions their specific status: do they belong to the species N. californicus or to another cryptic species? However, using nuclear DNA marker analyses, no distinct differences were observed. Furthermore, even if significant morphological differences were observed between the populations, these differences were very small and the standard errors within each population were very low. We thus concluded that all the populations studied belong to the species N. californicus, despite unexpected high mitochondrial variations. The present study thus displays the importance of an integrative taxonomic approach for avoiding misidentifications. A discussion on morphological and mtDNA variations in relation to diagnostic reliability is developped. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 393–406.     

Molecular systematics and patterns of morphological evolution in the Centropagidae (Copepoda: Calanoida) of Argentina

Recent studies have shown the value of complementing standard taxonomy with genetic analyses to reveal cryptic diversity and to aid in the understanding of patterns of evolution. We surveyed variation in the COI mitochondrial gene in members of the three genera of centropagid copepods from the inland waters in Argentina. In general, we found a close association between molecular and morphological systematics in this group. Similar to findings for marine calanoids, genetic distances within Boeckella species were modest (< 4%), while distances among morphospecies were much larger (> 11%). Parabroteas is currently monotypic, although we detected cryptic genetic diversity, with two lineages showing 5.5% divergence. In contrast, Karukinka was not a valid genus, apparently representing an interesting and atavistic offshoot of B. poppei , a result reinforcing the value of considering both morphological and molecular evidence. Moreover, we used combined genetic and morphological information, analysed with maximum likelihood methods, to evaluate the common assumption that evolution tends to proceed via the loss of structures in crustaceans. Although analysis of other taxa and character types is required to evaluate fully the reduction hypothesis, our results suggest that structures may be gained readily as well as lost.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 279–292.     

Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei: Cyprinidae) in the Qinghai-Tibetan Plateau

The complete mitochondrial DNA (mtDNA) cytochrome b gene (1140 bp) was sequenced in Herzenstein macrocephalus and Gymnocypris namensis and in 13 other species and sub-species ( n = 22), representing four closely related genera in the subfamily Schizothoracinae. Conflicting taxonomies of H. macrocephalus and G. namensis have been proposed because of the character instability among individuals. Parsimony, maximum likelihood and Bayesian methods produced phylogenetic trees with the same topology and resolved several distinctive clades. Previous taxonomic treatments, which variously placed these two species of separate genera or as sub-species, are inconsistent with the mtDNA phylogeny. Both H. macrocephalus and G. namensis appear in a well-supported clade, which also includes nine species of Schizopygopsis , and hence should be transferred to the genus Schizopygopsis . Morphological changes are further illustrated, and their adaptive evolution in response to the local habitat shifts during the speciation process appears to be responsible for conflicting views on the systematics of these two species and hence the contrasting taxonomic treatments. These species are endemic to the Qinghai-Tibetan Plateau, a region with a history of geological activity and a rich diversity of habitats that may have result in the parallel and reversal evolution of some morphological characters used in their taxonomies. Our results further suggest that speciation and morphological evolution of fishes in this region may be more complex than those previously expected.     

Molecular evolution and phylogeny of the human AIDS viruses LAV,HTLV-III,and ARV

Summary A phylogenetic tree for the human lymphadenopathy-associated virus (LAV), the human T-cell lymphotrophic virus type III (HTLV-III), and the acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV) has been constructed from comparisons of the amino acid sequences of their gag proteins. A method is proposed for estimating the divergence times among these AIDS viruses and the rates of nucleotide substitution for their RNA genomes. The analysis indicates that the LAV and HTLV-III strains diverged from one another after 1977 and that their common ancestor diverged from the ARV virus no more than 10 years earlier. Hence, the evolutionary diversity among strains of the AIDS viruses apparently has been generated within the last 20 years. It is estimated that the genome of the AIDS virus has a nucleotide substitution rate on the order of 10^–3 per site per year, with the rate in the second half of the genome being double that in the first half.     

Molecular systematics,evolution and zoogeography of the stonefly genus Siphonoperla (Insecta: Plecoptera,Chloroperlidae)

The stonefly genus Siphonoperla Zwick, 1967 (Chloroperlidae) ranges from the Atlas Mountains of North Africa, throughout Europe and east to the Lesser Caucasus Mountains in Armenia. Systematic relationships within the genus are unknown. We provide the first molecular phylogenetic reconstruction of the genus, based on sequence variation of 1348 bp of the mitochondrial cytochrome c oxidase subunit I gene and relate this phylogeny to a few key morphological features as well as zoogeographical perspectives. A total of 15 taxa (32 individuals), including four outgroup species (Chloroperla Newman, 1836 and Xanthoperla Zwick, 1967 ) were screened. Monophyly of Siphonoperla, as well as each purported taxon was supported, with net pairwise distances ranging from 0.7% to 13.7%. Within‐taxon variability ranged from 0% to 6.2%, whereby the upper value relates to Siphonoperla torrentium Pictet, 1841 represented in our sample by three allopatric subspecific taxa. These taxa, displayed as a polytomy with an estimated time to the most recent common ancestor of about 5.4 Myr, are also shown to have distinct genitalia. These data could be used to support a species‐level distinction for the three subspecific taxa. Siphonoperla ranged from 13% (Xanthoperla) to 16.2% (Chloroperla) divergent from the outgroup genera. The recently described Siphonoperla ottomoogi, Graf, 2008 from Austria is not closely related to the sympatric Siphonoperla montana Pictet, 1841 and is a minimum of 7.8% divergent from congenerics, supporting its status as a micro‐endemic relict surviving on the edge of Alpine glaciation throughout the Pleistocene. Overall, the genus shows the highest levels of diversification in the Mediterranean and Southeast regions whereby at least some of the species found in Central Europe today may have persisted there in peri‐glacial refugia throughout the Pleistocene.     

Molecular systematics of flyingfishes (Teleostei: Exocoetidae): evolution in the epipelagic zone

The flyingfish family Exocoetidae is a diverse group of marine fishes that are widespread and abundant in tropical and subtropical seas. Flyingfishes are epipelagic specialists that are easily distinguished by their enlarged fins, which are used for gliding leaps over the surface of the water. Although phylogenetic hypotheses have been proposed for flyingfish genera based on morphology, no comprehensive molecular studies have been performed. In the present study, we describe a species‐level molecular phylogeny for the family Exocoetidae, based on data from the mitochondrial cytochrome b gene (1137 bp) and the nuclear RAG2 gene (882 bp). We find strong support for previous morphology‐based phylogenetic hypotheses, as well as the monophyly of most currently accepted flyingfish genera. However, the most diverse genus Cheilopogon is not monophyletic. Using our novel flyingfish topology, we examine previously proposed hypotheses for the origin and evolution of gliding. The results support the progressive transition from two‐wing to four‐wing gliding. We also use phylogenetic approaches to test the macroecological effects of two life history characters (e.g. egg buoyancy and habitat) on species range size in flyingfishes. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 161–174.     

Molecular systematics of Eumolpinae and the relationships with Spilopyrinae (Coleoptera, Chrysomelidae)

The 3400 species of Eumolpinae constitute one of the largest subfamilies of leaf beetles (Chrysomelidae). Their systematics is still largely based on late 19th century monographs and remains highly unsatisfactory. Only recently, some plesiomorphic lineages have been split out as separate subfamilies, including the southern hemisphere Spilopyrinae and the ambiguously placed Synetinae. Here we provide insight into the internal systematics of the Eumolpinae based on molecular phylogenetic analyses of three ribosomal genes, including partial mitochondrial 16S and nuclear 28S and complete nuclear 18S rRNA gene sequences. Sixteen morphological characters considered important in the higher-level systematics of Eumolpinae were also included in a combined analysis with the molecular characters. All phylogenetic analyses were performed using parsimony by optimizing length variation directly on the tree, as implemented in the POY software. The data support the monophyly of the Spilopyrinae outside the clade including all sampled Eumolpinae, corroborating their treatment as a separate subfamily within the Chrysomelidae. The systematic placement of the Synetinae remains ambiguous but consistent with considering it a different subfamily as well, since the phylogenetic analyses using all the available evidence show the representative sequence of the subfamily also unrelated to the Eumolpinae. The Megascelini, traditionally considered a separate subfamily, falls within the Eumolpinae. Several recognized taxonomic groupings within Eumolpinae, including the tribes Adoxini or Typophorini, are not confirmed by molecular data; others like Eumolpini seem well supported. Among the morphological characters analyzed, the presence of a characteristic groove on the pygidium (a synapomorphy of the Eumolpini) and the shape of tarsal claws (simple, appendiculate or bifid) stand out as potentially useful characters for taxonomic classification in the Eumolpinae.     

Regeneration of the acorn worm pygochord with the implication for its convergent evolution with the notochord

The origin of the notochord is a central issue in chordate evolution. This study examined the development of the acorn worm pygochord, a putative homologue of the notochord. Because the pygochord differentiates only after metamorphosis, the developmental was followed process by inducing regeneration after artificial amputation in Ptychodera flava. It was found that although the regeneration of the posterior part of the body did not proceed via formation of an obvious regeneration bud, pygochord regeneration was observed within a few weeks, possibly via trans-differentiation of endoderm cells. The expression of the fibrillary collagen gene (Fcol) and elav in the pygochord during regeneration was detected. This indicates that pygochord cells are not part of gut epithelial cells, but that they differentiated as a distinct cell type. Our gene expression analyses do not provide supporting evidence for the homology between the pygochord and notochord, but rather favored the convergent evolution between them.