Phylogeographic analysis of the threatened and endangered superconglutinate-producing mussels of the genus Lampsilis (Bivalvia: Unionidae)

Several species of freshwater unionid mussels in the genus Lampsilis exhibit a remarkable reproductive strategy. Female mussels of these species enclose their larvae in a minnow-like lure, called a 'superconglutinate', to attract piscivorous fishes. When a fish attempts to ingest the superconglutinate the lure ruptures and the larvae are released to parasitize the fish. Of the four species of mussel which exhibit this strategy and are endemic to the Gulf Coast drainages of the southeastern United States, three are protected under the Endangered Species Act, and one is recognized as imperiled. Phylogenetic analysis of nucleotide sequences of the mitochondrial 16S ribosomal RNA and the first subunit of the cytochrome oxidase c genes was conducted on 18 individual specimens representing these four species and six outgroup taxa. Phylogenetic analyses of these data support the monophyly of the superconglutinate-producing mussels, and indicates a strong geographical component to the data. The zoogeographic patterns of the four taxa included in the study are congruent with those seen in freshwater vertebrates, and are consistent with a vicariant pattern resulting from fluctuations in sea level during the Pleistocene. Despite the strong geographical structuring of the data, only one species, Lampsilis subangulata, was recovered as monophyletic. The authors attribute the lack of support for the monophyly of the remaining species to insufficient sequence variation and the recent origin of the ancestor of these taxa. Based on these data, any future captive breeding projects aimed at augmenting or re-establishing populations should do so only from the appropriate source populations so as to maintain the genetic integrity of these nascent species.     

Complete mitochondrial genome sequence and phylogenetic position of the Amu Darya sturgeon,Pseudoscaphirhynchus kaufmanni (Acipenseriformes: Acipenseridae)

In this study, we successfully assembled the complete mitochondrial genome of the Amu Darya sturgeon Pseudoscaphirhynchus kaufmanni. Based on this mitochondrial genome and previously published mitochondrial genomes of members of the Acipenseridae family, we assessed the phylogenetic position of P. kaufmanni using maximum likelihood and Bayesian inference for phylogeny reconstruction. The resultant phylogenetic trees were well-resolved, with congruence between different phylogenetic methods. This robust phylogenetic analysis elucidated the relationship among the four acipenserid genera and strongly supported the division of the family into three main clades. Evaluation of molecular phylogeny using maximum likelihood and Bayesian analysis led to the following conclusions: (a) the most basal position within the Acipenseridae remains in the clade containing Acipenser oxyrinchus and Acipenser sturio; (b) the genus Scaphirhynchus belongs to the Atlantic clade and is a sister group of the remaining species of the clade; and (c) the close relationship between P. kaufmanni and Acipenser stellatus is well supported.     

Complete sequence of the Tibetan Mastiff mitochondrial genome and its phylogenetic relationship with other Canids ( Canis, Canidae)

In this study, the complete sequence of the Tibetan Mastiff mitochondrial genome (mtDNA) was determined, and the phylogenetic relationships between the Tibetan Mastiff and other species of Canidae were analyzed using the coyote (Canis latrans) as an outgroup. The complete nucleotide sequence of the Tibetan Mastiff mtDNA was 16 710 bp, and included 22 tRNA genes, 2S rRNA gene, 13 protein-coding genes and one non-coding region (D-loop region), which is similar to other mammalian mitochondrial genomes. The characteristics of the protein-coding genes, non-coding region, tRNA and rRNA genes among Canidae were analyzed in detail. Neighbor-joining and maximum-parsimony trees of Canids constructed using 12 mitochondrial protein-coding genes showed that as the coyotes and Tibetan wolves clustered together, so too did the gray wolves and domestic dogs, suggesting that the Tibetan Mastiff originated from the gray wolf as did other domestic dogs. Domestic dogs clustered into four clades, implying at least four maternal origins (A to D). The Tibetan Mastiff, which belongs to clade A, appears to be closely related to the Saint Bernard and the Old English Sheepdog.     

The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants

The phylogenetic positions of bryophytes and charophytes, together with their genome features, are important for understanding early land plant evolution. Here we report the complete nucleotide sequence (105,340 bp) of the circular-mapping mitochondrial DNA of the moss Physcomitrella patens. Available evidence suggests that the multipartite structure of the mitochondrial genome in flowering plants does not occur in Physcomitrella. It contains genes for 3 rRNAs (rnl, rns, and rrn5), 24 tRNAs, and 42 conserved mitochondrial proteins (14 ribosomal proteins, 4 ccm proteins, 9 nicotinamide adenine dinucleotide dehydrogenase subunits, 5 ATPase subunits, 2 succinate dehydrogenase subunits, apocytochrome b, 3 cytochrome oxidase subunits, and 4 other proteins). We estimate that 5 tRNA genes are missing that might be encoded by the nuclear genome. The overall mitochondrial genome structure is similar in Physcomitrella, Chara vulgaris, Chaetosphaeridium globosum, and Marchantia polymorpha, with easily identifiable inversions and translocations. Significant synteny with angiosperm and chlorophyte mitochondrial genomes was not detected. Phylogenetic analysis of 18 conserved proteins suggests that the moss-liverwort clade is sister to angiosperms, which is consistent with a previous analysis of chloroplast genes but is not consistent with some analyses using mitochondrial sequences. In Physcomitrella, 27 introns are present within 16 genes. Nine of its intron positions are shared with angiosperms and 4 with Marchantia, which in turn shares only one intron position with angiosperms. The phylogenetic analysis as well as the syntenic structure suggest that the mitochondrial genomes of Physcomitrella and Marchantia retain prototype features among land plant mitochondrial genomes.     

An integrative approach underscores the taxonomic status of Lamellidens exolescens,a freshwater mussel from the Oriental tropics (Bivalvia: Unionidae)

The Oriental Region harbours the second richest fauna of freshwater bivalves in the world, including many endangered endemic taxa. However, the Oriental fauna of the Unionidae have been very poorly studied using an integrative taxonomic approach, which may provide reasonable revisions of complicated (cryptic) taxa based on morphological, molecular, biogeographic and ecological evidence. Here, we present the first example of an integrative taxonomic revision concerning the status of Unio exolescens Gould (1843 Gould, A.A. (1843). Dr. Gould had examined the shells not long since announced as having been received from the Rev. Francis Mason, missionary at Tavoy, in British Burmah. Proceedings of the Boston Society of Natural History, 1, 139–141. [Google Scholar]), a nominal mussel taxon that was accepted as a valid species within the genus Trapezoideus Simpson (1900). Currently, Trapezoideus exolescens is considered the type of the genus as far as the originally designated type species, U. foliaceus Gould (1843 Gould, A.A. (1843). Dr. Gould had examined the shells not long since announced as having been received from the Rev. Francis Mason, missionary at Tavoy, in British Burmah. Proceedings of the Boston Society of Natural History, 1, 139–141. [Google Scholar]), was considered to be a synonym of T. exolescens. Using nucleotide sequences obtained from mitochondrial (COI and 16S rRNA) and nuclear (28S rDNA) genes, we found that the topotypes of Unio exolescens Gould (1843 Gould, A.A. (1843). Dr. Gould had examined the shells not long since announced as having been received from the Rev. Francis Mason, missionary at Tavoy, in British Burmah. Proceedings of the Boston Society of Natural History, 1, 139–141. [Google Scholar]) cluster together with representatives of another mussel genus, Lamellidens Simpson (1900). Based on these results and on morphological data, we transfer Unio exolescens Gould (1843 Gould, A.A. (1843). Dr. Gould had examined the shells not long since announced as having been received from the Rev. Francis Mason, missionary at Tavoy, in British Burmah. Proceedings of the Boston Society of Natural History, 1, 139–141. [Google Scholar]) from Trapezoideus to Lamellidens and propose Lamellidens exolescens (Gould, 1843 Gould, A.A. (1843). Dr. Gould had examined the shells not long since announced as having been received from the Rev. Francis Mason, missionary at Tavoy, in British Burmah. Proceedings of the Boston Society of Natural History, 1, 139–141. [Google Scholar]) comb. nov. In addition, we revisited the status of Unio foliaceus Gould (1843 Gould, A.A. (1843). Dr. Gould had examined the shells not long since announced as having been received from the Rev. Francis Mason, missionary at Tavoy, in British Burmah. Proceedings of the Boston Society of Natural History, 1, 139–141. [Google Scholar]) as a valid species and the type of the genus Trapezoideus based on the morphological study of the type specimen, although a question concerning the true position of this taxon is still open because its molecular sequences are not available. Our findings highlight that an integrative taxonomic approach is an important tool, particularly when dealing with such species-rich Unionidae fauna as those of the Oriental Realm.     

Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae

In previous molecular phylogenetic analyses of the freshwater mussel family Unionidae (Bivalvia: Unionoida), the Afrotropical genus Coelatura had been recovered in various positions, generally indicating a paraphyletic Unionidae. However that result was typically poorly supported and in conflict with morphology-based analyses. We set out to test the phylogenetic position of Coelatura by sampling tropical lineages omitted from previous studies. Forty-one partial 28S nuclear rDNA and partial COI mtDNA sequences (1130 total aligned nucleotides) were analyzed separately and in combination under both maximum parsimony and likelihood, as well as Bayesian inference. There was significant phylogenetic incongruence between the character sets (partition homogeneity test, p < 0.01), but a novel heuristic for comparing bootstrap values among character sets analyzed separately and in combination illustrated that the observed conflict was due to homoplasy rather than separate gene histories. Phylogenetic analyses robustly supported a monophyletic Unionidae, with Coelatura recovered as part of a well-supported Africa–India clade (= Parreysiinae). The implications of this result are discussed in the context of Afrotropical freshwater mussel evolution and the classification of the family Unionidae.     

Integrative taxonomy reveals phenotypic plasticity in the freshwater mussel Contradens contradens (Bivalvia: Unionidae) in Thailand,with a description of a new species

The freshwater mussel Contradens contradens (Lea, 1838) occurs in most types of freshwater habitats throughout Thailand. The species shows extensive variation in shell morphology, which has led to the recognition of six different subspecies. In this study, the validity of these six subspecies plus one unknown species was assessed using an integrative taxonomic approach. Geometric morphometric analyses revealed significant differences in shell shapes among these six nominal morphological subspecies, although a considerable degree of overlap was detected in some groups. In contrast, the phylogenetic tree obtained from the concatenated data of mitochondrial COI and nuclear H3 gene sequences and molecular species delimitation analyses revealed only three supported clades. These clades are proposed herein as three distinct species, and strongly corresponded to the biogeographically disjunct drainage systems in Thailand. They consisted of the (i) C. contradens clade found in the Chao Phraya Basin and other rivers that drain into the Gulf of Thailand, (ii) C. crossei clade that is restricted to the Middle Mekong Basin, and (iii) a clade containing only the newly discovered species from Huai Luang River in the north-east of Thailand, which is described herein as Contradens rolfbrandti Jeratthitikul & Panha, sp. nov. Speciation among these congeners was probably caused by the restriction of gene flow due to the past geomorphology of the river systems. The intraspecific variation in the shell shape detected here does not reflect the evolution of the mussel, but rather is evidence of phenotypic plasticity.http://zoobank.org/urn:lsid:zoobank.org:pub:649B6093-E1DD-4FD8-8185-A4696C43AD36; http://zoobank.org/urn:lsid:zoobank.org:act:777DDE86-8397-4FF3-AA78-0BE0F34611F4     

啮总目昆虫的线粒体基因组多样性及系统发育研究进展

啮总目包括啮虫目（皮虱和书虱）和虱目（羽虱和吸虱）,是农业和医学等领域具有重要经济意义和研究价值的类群,目前已鉴定和描述的物种超过10 000个。啮总目昆虫线粒体基因组的变异性在昆虫各类群中最为剧烈,这些变异包括基因组的结构、基因排序、基因含量和链上分布等诸多方面。本文全面分析和总结了啮总目昆虫裂化线粒体基因组的进化属性,并结合两侧对称动物线粒体基因组的裂化特征重构了线粒体基因组环裂化的过程。引入“线粒体基因组核型”的概念来描述动物线粒体基因组丰富的变异程度。动物线粒体的染色体有减小的趋势,而线粒体基因组的裂化正是体现这种趋势的一种重要策略。同时,总结和探讨了目前具有争议的啮总目主要类群间的系统发育关系。本综述为啮总目昆虫线粒体基因组学、啮总目系统发生关系以及两侧对称动物线粒体基因组进化模式的研究提供一个新的视角。     

Global diversity of freshwater mussels (Mollusca, Bivalvia) in freshwater

The term freshwater bivalve is very inclusive and not very informative. There are representatives of at least 19 families that have at least one representative living in freshwater. This suggests at least 14 different invasions of freshwater. At least nine families have small to large radiations in the freshwater environment: Corbiculidae, Sphaeriidae, Dreissenidae, and the unioniforme families: Hyriidae, Margaritiferidae, Unionidae, Etheriidae, Iridinidae, and Mycetopodidae. The unioniforme families contain at least 180 genera and about 800 species. This order is characterized by the unique parasitic larval stage on the gills, fins or the body of a particular host fish. This order of freshwater bivalves is suffering a very high rate of extinction, with about 37 species considered presumed extinct in North America alone. The level of endangerment and extinction facing these animals is primarily the result of habitat destruction or modification. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

Complete mitochondrial genome sequence of the Himalayan Griffon,Gyps himalayensis (Accipitriformes: Accipitridae): Sequence,structure, and phylogenetic analyses

This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein‐coding genes, 22 tRNA coding genes, two rRNA‐coding genes, a control region (CR), and an extra pseudo‐control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5′ end of the domain I region, a long continuous poly‐C sequence was found. Two tandem repeats were found in the pseudo‐control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein‐coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.     

Characterization of four mitochondrial genomes of Crambidae (Lepidoptera,Pyraloidea) and phylogenetic implications

Loxostege turbidalis, Loxostege aeruginalis, Pyrausta despicata, and Crambus perlellus belong to Crambidae, Pyraloidea. Their mitochondrial genomes (mitogenomes) were successfully sequenced. The mitogenomes of L. turbidalis, L. aeruginalis, P. despicata, and C. perlellus are 15 240 bp, 15 339 bp, 15 389 bp, and 15 440 bp. The four mitogenomes all have a typical insect mitochondrial gene order, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one A + T rich region (control region). The PCGs are initiated by the typical ATN codons, except CGA for the cox1 gene. Most PCGs terminate with common codon TAA or TAG, the incomplete codon T is found as the stop codon for cox2, nad4, and nad5. Most tRNA genes exhibit typical cloverleaf structure, except trnS1 (AGN) lacking the dihydrouridine (DHU) arm. The secondary structure of rRNA of four mitogenomes were predicted. Poly-T structure and micro-satellite regions are conserved in control regions. The phylogenetic analyses based on 13 PCGs showed the relationships of subfamilies in Pyraloidea. Pyralidae, and Crambidae are monophyletic, respectively. Pyralidae comprises four subfamilies, which form the following topology with high support values: (Galleriinae + ((Pyralinae + Epipaschiinae)+ Phycitinae)). Crambidae includes seven subfamilies and is divided into two lineages. Pyraustinae and Spilomelinae are sister groups of each other, and form the “PS clade.” Other five subfamilies (Crambinae, Acentropinae, Scopariinae, Schoenobiinae, and Glaphyriinae) form the “non-PS clade” in the Bayesian inference tree. However, Schoenobiinae is not grouped with the other four subfamilies and located at the base of Crambidae in two maximum likelihood trees.     

Revisiting the North American freshwater mussel genus Quadrula sensu lato (Bivalvia Unionidae): Phylogeny,taxonomy and species delineation

Freshwater mussels (Bivalvia, Unionidae) have suffered strong declines over the last century. High morphological plasticity of Unionidae causes disturbances in their systematics and taxonomy, hampering conservation efforts. Species that have historically been placed under the North American genus Quadrula have suffered from numerous taxonomic and species delineation problems since its inception. Four genera are presently recognized within Quadrula sensu lato, that is, Cyclonaias, Quadrula, Theliderma and Tritogonia, but their phylogenetic basis remains incompletely tested. In the present study, we reconstructed several two‐marker (mtDNA cytochrome c oxidase subunit I—COI and NADH dehydrogenase subunit 1—ND1) phylogenies with newly collected specimens and all previously available sequences covering most species within this group. We then delineated the species within the group using an integrative approach with the application of molecular statistical methods, morphometric (Fourier Shape) analyses and geographic distribution data. Four clades corresponding to these genera were consistently recovered in all phylogenies. To validate the generic status of these clades, molecular analyses were complemented with morphological, anatomical and ecological data compiled from the literature. Several revisions are here proposed to the current systematics and taxonomy of these genera, including the synonymization of Cyclonaias asperata under Cyclonaias kieneriana; the inclusion of Quadrula apiculata and Quadrula rumphiana under Quadrula quadrula; the placement of Quadrula nobilis under Tritogonia; and finally the separation of the Mobile River basin populations of Theliderma metanevra as a new species, that is, Theliderma johnsoni n. sp. The conservation implications of the proposed changes are then discussed.     

Evaluation of conservation status, distribution, and reproductive characteristics of an endemic Gulf Coast freshwater mussel, Lampsilis australis (Bivalvia: Unionidae)

The southern sandshell, Lampsilis australisSimpson, 1900, is a rare freshwater mussel endemic to the Escambia, Yellow, andChoctawhatchee river drainages in Alabama and Florida. Laboratory observationsconfirmed L. australis as a superconglutinate producer.Superconglutinate and glochidial morphology are similar to those of othersuperconglutinate producers. The current distribution of L.australis, as determined from recent surveys (1995–2000) andfield notes (1990–2000), is compared with its historical distribution asdefined by museum collections and field notes made between 1900 and 1989. Thecurrent distribution of L. australis is reduced by76% compared to its historical distribution, although L. australis waslocated at new sites in the recent surveys. Relative abundance of L.australis was low at all but two sites. Based on reproductivestrategy, range reductions, low relative abundance, and potential threats withinthe Escambia, Yellow, and Choctawhatchee river drainages, we believeL. australis should be considered for protection under theEndangered Species Act.     

变灰青霉线粒体基因组特征及系统发育分析

本研究对一株分离自细虫草上的变灰青霉SFY00C3菌株线粒体基因组进行测定,分析其组成特征,并探究其与青霉属真菌的系统发育关系。结果表明,SFY00C3的线粒体基因组是一条长度为28 301 bp的环状DNA分子,共编码42个基因(15个蛋白编码基因、2个rRNA基因和25个tRNA基因),其碱基组成有显著的A-T偏好性,25个tRNA基因均可形成典型三叶草结构,并存在32处G-U错配。通过青霉属物种间共线性分析发现其线粒体基因组发生了基因重排;共有的14个蛋白编码基因的Ka/Ks值均小于1,表明受到了纯化选择压力的影响;系统发育分析表明：SFY00C3在青霉属中是一个独立的分支,应该是6种青霉祖先的姊妹。本研究丰富了变灰青霉的线粒体基因组序列信息,为青霉属的系统发育、资源保护及遗传多样性研究提供基础数据。     

Complete mitochondrial genome sequence of Bonasa sewerzowi(Galliformes: Phasianidae) and phylogenetic analysis

Bonasa sewerzowi, the smallest and most southerly distributed grouse species in the world, is a bird endemic to China. The population of B. sewerzowi had shown a declining trend, which made it to be the endangered species in the China Red Data Book and Category I of nationally protected animals. So far, however, most studies about this species were mainly focused on the morphological and ecological aspects. In order to further study the feature of B. sewerzowi, the complete mitochondrial genome(mitogenome) of B. sewerzowi was sequenced by Illumina Hiseq 2000 high-throughput sequencing. Then, we focused on comparative genomics of two Bonasa species to find their characteristics. Finally, phylogenetic position of Bonasa was made based on the mitogenome dataset. Our results revealed that:(1) the mitogenome of B. sewerzowi, consisting of 16 658 bp, displayed typical genome organization and gene order found in other previously determined Galliformes mitogenomes;(2) the structure and composition of mitogenomes were similar between B. sewerzowi and B. bonasia;(3) the monophyly of Bonasa was well supported, which had a closer phylogenetic relationship with Meleagris gallopavo.     

蚕豆象的线粒体基因组研究及系统发育分析

【目的】蚕豆象是农业上一种重要害虫,本文测序、分析了蚕豆象的线粒体全基因组,以期为更好地理解茎甲亚科分支类群、豆象亚科和蚕豆象的系统发育提供线粒体基因组数据。【方法】在系统发育分析中,内群取样包含茎甲亚科分支类群的22种昆虫,外群选择2个肖叶甲亚科（Basilepta fulvipes和Basilepta melanopus）昆虫,分别利用最大似然法和贝叶斯法重建茎甲亚科分支类群的系统发育关系。【结果】蚕豆象的线粒体基因组全长为16586 bp （GenBank序列号：OP650255）,包含37个基因（13个蛋白质编码基因、2个核糖体RNA基因和22个转运RNA基因）和一段非编码控制区。所有转运RNA基因中,除trnS1因缺少二氢尿嘧啶（DHU）臂而形成一个简单的环,无法构成稳定的三叶草结构外,其余转运RNA基因均能形成典型的三叶草结构。此外,trnS1的反密码子不是常见的GCU,而是UCU。【结论】本研究首次获得了蚕豆象的线粒体基因组全序列。2种不同的系统发育分析方法构建的系统发育关系显示：豆象亚科、茎甲亚科、水叶甲亚科和负泥虫亚科为单系群;豆象亚科与水叶甲亚科+负泥虫亚科为姐妹群;蚕豆象与四纹豆象为姐妹群。     

传粉和非传粉榕小蜂线粒体基因组进化差异

[目的]目前关于榕小蜂类群的线粒体基因组报道很少,本研究旨在探讨传粉和非传粉榕小蜂两个群体的线粒体基因组的进化差异.[方法]以15种榕小蜂的线粒体基因组(其中11种的线粒体基因组为新测定)数据为基础,采用比较线粒体基因组学方法,分析榕小蜂的线粒体基因组序列和进化特征.[结果]本研究新测定的11个榕小蜂物种的近全长线粒体...     

云斑车蝗线粒体基因组全序列测定与分析

采用长距 PCR 扩增及保守引物步移法并结合克隆测序测定并注释了云斑车蝗 Gastrimargus marmoratus （Thunberg）的线粒体基因组全序列。结果表明：云斑车蝗线粒体基因组全序列为15 904 bp（GenBank登录号为EU527334）,A+T含量略高于非洲飞蝗Locusta migratoria,为76.04%,包括13个蛋白质编码基因,22个tRNA 基因,2个rRNA基因和一段1 057 bp的A+T富集区。蛋白质基因的起始密码子中,除COⅠ和ND5为TTG以外,均为昆虫典型的起始密码子ATN。ND5基因使用了不完全终止密码子T,其余基因均为典型的TAA或TAG。预测了22个tRNA基因的二级结构,发现tRNA^Ser（AGN）缺少DHU臂, tRNA^Ser（UGY）的反密码子环上有9个碱基。预测了云斑车蝗12S和16S rRNA二级结构,分别包括3个结构域30个茎环和6个结构域44个茎环。A+T富集区含有3个串联重复序列。