Interrelationships of the subgenera of Coryphaenoides (Teleostei: Gadiformes: Macrouridae): synthesis of allozyme,peptide mapping,and DNA sequence data

DNA sequences of the 12s rRNA mitochondrial gene from 12 species key to the question of the monophyly of the deep-sea fish genus Coryphaenoides (Macrouridae) were analyzed phylogenetically using maximum parsimony and maximum likelihood. The results were compared with those of three previous studies in which allozyme, peptide mapping, and DNA sequence data were similarly analyzed. The allozyme and DNA sequence data suggested that the largest subgenus (Coryphaenoides), which contained most of the species inhabiting continental slopes between approximately 600 and 2000m depth, is monophyletic. Two of the three subgenera containing the species inhabiting abyssal ocean basins below approximately 2000m together formed a sister group to subgenus Coryphaenoides. The macrourids of the abyssal basins and those of the continental slopes thus appear to have experienced separate radiations from a common ancestor.     

The complete mitogenome of the snakehead Channa argus (Perciformes: Channoidei): genome characterization and phylogenetic implications

To better understand the phylogenetic status of the snakehead, Channa argus, we determined its complete mitogenome sequence using long-polymerase chain reaction and the direct sequencing method. The complete mitogenome sequence was 16,559?bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. This was the first report of the mitogenome sequence in suborder Channoidei. Phylogenetic relationships of 14 perciform suborders based on mitogenome sequences were reconstructed using Bayesian inference and maximum likelihood methods. The results strongly supported the monophyly of Perciformes and the snakehead, as a representative species of suborder Channoidei, formed the most basal branch having sister relationship with the clade containing all other analyzed perciform fishes. The further phylogenetic analyses of six channid species, based on cytochrome b gene, suggested that two channid genera constituted reciprocally monophyletic clades. In addition, the relaxed molecular clock method was used to estimate divergence dates among major suborders of Perciformes and major species in Channoidei.     

Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts

The fishes currently recognized as members of the order Gasterosteiformes (sticklebacks, pipefishes, and their relatives) number 278 species, classified into two suborders (Gasterosteoidei and Syngnathoidei), 11 families and 71 genera. Members of this group exhibit unique appearances, many of which are derived from armored bodies with bony plates in various forms. Although recent molecular phylogenetic studies have repeatedly questioned the monophyly of this order, none of the studies examined all of the representative families and the phylogenetic reality of the group has remained unclear. In this study, we examined whole mitochondrial genome (mitogenome) sequences from 13 gasterosteiform species representing all 11 families in the order, and subjected them to partitioned maximum likelihood and Bayesian analyses, with additional data from other percomorphs and outgroups (75 mitogenome sequences considered overall, including 10 newly determined). The resultant phylogenies indicated explicitly that previously recognized members of Gasterosteiformes had diverged basally within the Percomorpha into three different clades with the following subgroups: Syngnathoidei, Gasterosteoidei (minus Indostomidae), and Indostomidae. Monophyly of the order Gasterosteiformes and any combinations of the three subgroups were confidently rejected by statistical tests. Syngnathoidei (together with Dactylopteroidei) formed a monophyletic group, a sister-group relationship between Gasterosteoidei (minus Indostomidae) and Zoarcoidei was reconfirmed and Indostomidae was nested within the Synbranchiformes, rendering the latter group paraphyletic. Our study demonstrates a new perspective of gasterosteiform phylogeny, which will provide fundamental information for future studies of phylogeny, systematics, and evolution.     

Intra- and interfamily relationships of Vespertilionidae inferred by various molecular markers including SINE insertion data

The family Vespertilionidae comprises the largest number of species in the order Chiroptera, and its members are distributed over most of the world. We collected sequences of the mitochondrial NDI (NADH dehydrogenase subunit 1) gene from 38 species as well as 20 sequences of exon28 of the vWF (von Willebrand Factor) gene and analyzed phylogenetic relationships in Vespertilionidae using maximum-likelihood analyses and SINE (short interspersed elements) insertions. Our data strongly suggest the following: (1) Murininae and Myotis, each of which is classified into different subfamilies, are monophyletic; (2) the monophyly of Murininae, Myotis, Pipistrellini, and Plecotini is supported by our analyses of the NDI and nuclear vWF as well as data from SINE insertions, while Miniopterinae was not included in this group; and (3) Rhinolophoidea (microchiroptera) is separated from all the other microchiropteran species. Our study represents the most comprehensive phylogenetic model of Vespertilionidae to date.     

Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages.     

27种瓢虫mtDNA-COI基因序列分析及系统发育研究(鞘翅目:瓢虫科)

将自测的瓢虫科4亚科16种和从GenBank中检索到相关物种的mtDNA-COI基因编码区序列片断进行同源性比较,计算核苷酸使用频率,并构建分子系统树。在获得的471bp序列中,共有227个变异位点,195个简约信息位点,A T约占66.7%,转换发生比颠换更频繁。分子系统树表明:同种和同属的瓢虫均以较高置信值聚在一起,4个亚科都能恢复为单系;食植瓢虫亚科从系统树的基部最早分出,是瓢虫科最为原始的类群,小毛瓢虫亚科和盔唇瓢虫亚科首先聚为一支,显示二者具有较近的亲缘关系,然后再与瓢虫亚科相聚,食植瓢虫亚科的食植瓢虫属和裂臀瓢虫属均不是单系群。     

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740 bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.     

Molecular Systematics of Selene (Perciformes: Carangidae) Based on Cytochrome b Sequences

The marine fishes of the genus Selene are morphologically unique, although little is known about how these species are related to other members of the family Carangidae (Perciformes). In addition, questions remain about the potential validity of two putative species and how species groups with unique body forms within Selene are related. We used DNA sequences of the mitochondrial cytochrome b gene to reconstruct the phylogeny of the seven species of Selene along with five additional species of carangids. Maximum-likelihood and maximum-parsimony analyses were used to examine the sequence data and both phylogenetic methods were compared. Maximum-likelihood produced a monophyletic Selene, whereas parsimony analyses did not. Both maximum-likelihood and maximum-parsimony produced similar support for species groups within Selene. Maximum-likelihood produced two monophyletic subgroups within the genus Selene, the "long-finned" and "short-finned" Selene. Maximum-parsimony produced the same monophyletic "long-finned" group but a paraphyletic "short-finned" group. Both analyses confirm that S. brownii and S. setapinnis are distinct species, expunging the question of conspecificity. The phylogenetic placement of the most basal taxon within Selene, S. orstedii, was problematic and differed among analyses. More data are needed to resolve with confidence its correct phylogenetic placement and, thus, the monophyly of the genus Selene.     

Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences

The relationships among and within the main lineages of the order Clupeiformes have been explored in few morphological studies and still remain poorly understood. Using whole mitogenome sequences, we inferred the relationships among 25 clupeiform species, sampled from each clupeiform family and subfamily, and a large selection of non-clupeiform teleosts. Our character sets, including unambiguously aligned, concatenated mitogenome sequences that we have divided into four (1st and 2nd codon positions, tRNA genes, and rRNA genes) or five partitions (same as before plus the transversions at 3rd codon positions, using 'RY' coding), were analyzed by the partitioned Bayesian method. The result strongly supported the monophyly of the Clupeiformes within the Otocephala, with Denticeps clupeoides as the sister group of a clade comprising all the remaining clupeiforms species (= suborder Clupeoidei). Within the Clupeoidei, the family Engraulidae was the sister group of the remaining taxa, comprising members of Sundasalangidae, Pristigasteridae, Clupeidae and Chirocentridae. Relationships among the latter four families remained ambiguous. In particular, the position of the Chirocentridae was difficult to estimate possibly owing to its higher molecular evolutionary rate. Of the five subfamilies in the family Clupeidae, monophylies of three (Alosinae, Clupeinae and Dorosomatinae) were statistically rejected. Instead, our mitogenomic data provide strong support for new clades within the Clupeidae, some of which are composed of members of more than one of the previously accepted subfamilies.     

Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae

Genome comparison has shed light on many fields of both basic and applied research, including the study of species phylogeny. Grass carp (Ctenopharyngodon idella) belongs to Cyprinidae, the largest freshwater fish family; but which subfamily it belongs to remains a controversial issue. In this study, the complete mitochondrial genome (mitogenome) sequence of grass carp was determined and phylogenetic analyses of all mitochondrial protein-coding genes and a nuclear gene (RAG 2) were conducted to explore the evolutionary relationship of grass carp with other cyprinid species. The mitogenome of grass carp is 16,609 bp in length. As with most other vertebrates, it contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one putative control region. Phylogenetic analyses using two different datasets (mitochondrial and nuclear) and three different computational algorithms (Bayesian, MP and ML) all revealed two distinct groups with high statistical support, indicating that Cyprininae and Leuciscinae are two separate, valid subfamilies. Importantly, our phylogenetic result provides strong molecular evidence in support of the placement of Ctenopharyngodon in Leuciscinae rather than in Cyprininae.     

Monophyly of Endosymbiont Containing Trypanosomatids: Phylogeny versus Taxonomy

To obtain additional information on the phylogenetic relationships within the family Trypanosomatidae (order Kinetoplastida), we have sequenced the small subunit ribosomal RNA genes from the endosymbiont containing species Herpetomonas roitmani TCC080, Herpetomonas sp. TCC263, Crithidia oncopelti ATCC 12982 and a partial large subunit rRNA gene from H. roitmani. The small subunit sequences in the two isolates of Herpetomonas are very similar but not identical, and so are their restriction digest profiles of kinetoplast DNA. The size of minicircles in both isolates is 4.2 kilobases. The inferred ribosomal RNA phylogenetic trees shows the genera Herpetomonas and Crithidia as polyphyletic. Endosymbiont-bearing herpetomonads cluster with the endosymbiont-bearing crithidias and a blastocrithidia to form a monophyletic clade, whereas the endosymbiont-free members of these genera are found elsewhere in the tree. These data support the hypothesis of a monophyletic origin of endosymbiosis in trypanosomatid evolution and also suggest that a taxonomic revision is needed in order to better describe the natural affinities in this family.     

Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala

Although the order Gonorynchiformes includes only 31 species assigned to seven genera and four families, it exhibits a large variety of anatomical structures, making difficult the reconstruction of phylogenetic relationships among its representatives. Within the basal teleosts, the Gonorynchiformes belong to the Otocephala where they have been alternatively placed as the sister group of the Otophysi and of the Clupeiformes. In this context, we investigated the phylogeny of the Gonorynchiformes using whole mitogenome sequences from 40 species (six being newly determined for this study). Our taxonomic sampling included at least one species of each gonorynchiform genus and of each other major otocephalan lineage. Unambiguously aligned, concatenated mitogenomic sequences (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd, and 3rd codon positions, tRNA genes, and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenetic trees were fully resolved, with most of the nodes well supported by the high posterior probabilities. As expected, the Otocephala were recovered as monophyletic. Within this group, the mitogenome data supported the monophyly of Alepocephaloidei, Gonorynchiformes, Otophysi, and Clupeiformes. The Gonorynchiformes and the Otophysi formed a sister group, rending the Ostariophysi monophyletic. This result conflicts with previous mitogenomic phylogenetic studies, in which a sister relationship was found between Clupeiformes and Gonorynchiformes. We discussed the possible causes of this incongruence. Within the Gonorynchiformes, the following original topology was found: (Gonorynchus (Chanos (Phractolaemus (Cromeria (Grasseichthys (Kneria, Parakneria)))))). We confirmed that the paedomorphic species Cromeria nilotica and Grasseichthys gabonensis belong to the family Kneriidae; however, the two species together did not form a monophyletic group. This result challenges the value of reductive or absent characters as synapomorphies in this group.     

A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?

Background  

The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecules, there has been no clear resolution except for monophyly of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084).     

虾虎鱼类线粒体全基因组序列结构特征分析及系统发育关系探讨

虾虎鱼类体态变异大、体型小、种类多, 形态鉴定及谱系分类较为困难。为深入开展虾虎鱼类的鉴定、分类及遗传进化等研究, 文章对已获得的26种虾虎鱼线粒体全基因组进行分析。结果发现, 虾虎鱼类线粒体基因组的基因组成及排列模式与大多数脊椎动物线粒体基因组特征基本一致; 由于不同物种的控制区存在不同数量的重复序列而导致基因组序列长度存在明显的差异; 26种虾虎鱼线粒体全基因组序列及不同基因中A+T的含量均超过50%, 并存在碱基G偏倚现象。基于37个编码基因序列, 利用Kimura双参数法计算遗传距离, 发现矛尾刺虾虎鱼与斑尾刺虾虎鱼、斑纹舌虾虎鱼与钝吻舌虾虎鱼分别为同种异名。通过对26种虾虎鱼线粒体基因组控制区序列的比较, 识别了终止结合序列区、中央保守区及保守序列区。利用26种虾虎鱼线粒体基因组的36个编码基因序列构建系统发育树, 发现部分聚类结果不同于传统的形态学分类方式, 虾虎鱼科中的5个亚科出现了明显的分化, 近盲虾虎鱼亚科、背眼虾虎鱼亚科、瓢虾虎鱼亚科亲缘关系较近而聚成一大支, 然后与拟虾虎鱼亚科种类形成姐妹类群, 虾虎鱼亚科与其它的4个亚科亲缘关系较远, 单独成为一个类群。根据分子钟估算结果推测虾虎鱼科物种可能起源于始新世晚期至渐新世时段, 在中新世进一步分化为具有现代表征的虾虎鱼种类。     

Gene rearrangement and sequence analysis of mitogenomes suggest polyphyly of Archaeobalanid and Balanid barnacles (Cirripedia: Balanomorpha)

The acorn barnacles (Cirripedia, Thoracica, Balanomorpha) are a diverse group of crustaceans found in virtually all marine and estuarine habitats. Barnacles are important model species in various biological researches, including evolution, intertidal ecology, larval biology and antifouling. However, there remains a lack of a thorough understanding of the phylogeny for this group of animals, particularly at higher taxonomic levels. In this study, we attempt to determine the phylogenetic relationships among balanomorphan families based on analysis of complete mitochondrial genome from various barnacle families and investigate the evolution of mitogenome in barnacles. Whole mitogenomes of six barnacles were newly sequenced, including Acasta sulcata (Archaeobalanidae), Armatobalanus allium (Archaeobalanidae), Chelonibia testudinaria (Chelonibiidae), Octomeris sp. (Chthamalidae), Savignium biporata (Pyrgomatidae) and Tetraclitella divisa (Tetraclitidae), which exhibit five different gene arrangements. Phylogenetic analysis on 15 complete mitochondrial genome sequences from major barnacle families supported Chthamalidae, Pyrgomatidae and Tetraclitidae formed monophyletic units, but suggested polyphyly of both Archaeobalanidae and Balanidae. Chthamalidae was the earliest diverged lineage in Balanomorpha. Chelonibiidae + Tetraclitidae formed the sister taxon to the monophyletic superfamily Balanoidea (Archaeobalanidae + Balanidae + Pyrgomatidae). The members of Archaeobalanidae and Balanidae intermingled in the inferred topology with the monophyletic Pyrgomatidae deeply nested within. Two Megabalanus species from the family Balanidae and A. sulcata from the family Archaeobalanidae share the same six‐gene‐cluster inversion as compared to the other ten balanomorphan barnacles, providing further evidence for the non‐monophyly for the two families. We showed here that the informativeness of the complete mitogenome sequence and rare genomic events in resolving various questions concerning Balanomorpha relationships. The non‐monophyletic status of Archaeobalanidae and Balanidae falsified many previous hypotheses concerning the complex evolution of Balanomorpha and call for further investigations and careful revision on the taxonomy of the group. Future study focusing on the enigmatic and tentatively basal lineages, for example, Chionelasmatoidea Pachylasmatoidea and Catophragmidae, would be most helpful in fully resolving the phylogeny and mitogenome evolutionary history of acorn barnacles.     

The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae)

The complete nucleotide sequences of the mitochondrial genome (mitogenome) of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae), were determined. The 15,521-bp-long G. orientalis mitogenome contains typical gene complement, base composition, and codon usage found in metazoan mitogenomes. The G. orientalis mitogenome contains the third lowest A+T content (70.5%) among the complete insects mt genome sequences. The initiation codon for the G. orientalis COI gene appears to be ATG, instead of the tetranucleotides, which have been postulated to act as initiation codon for Locusta migratoria and some lepidopteran COI genes. The initiation codon for ND2 appears to be GTG, which is rare, but has been designated as an initiator of Tricholepidion gertschi ND2. All anticodons of G. orientalis tRNAs were identical to Drosophila yakuba and L. migratoria. The tRNA(Ser)(AGN) could not form a stable stem loop structure in the DHU arm as shown in many other insect tRNA(Ser)(AGN). Phylogenetic analysis of nucleotide sequence information from all mt genes supported a monophyletic Diptera, a monophyletic Lepidoptera, a monophyletic Coleoptera, a monophyletic Mecopterida (Diptera+Lepidoptera), and a monophyletic Endopterygota (Diptera+Lepidoptera+Coleoptera), suggesting that the complete insect mitogenome sequence has a resolving power to the diversification events within Endopterygota. However, the relationships of ancient insect orders were unstable, indicating the limited use of mitogenome information at deeper phylogenetic depth.     

Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes

Systematics of the red algal order Corallinales has a long and convoluted history. In the present study, molecular approaches were used to assess the phylogenetic relationships based on the analyses of two datasets: a large dataset of SSU sequences including mainly sequences from GenBank; and a combined dataset including four molecular markers (two nuclear: SSU, LSU; one plastidial: psbA; and one mitochondrial: COI). Phylogenetic analyses of both datasets re-affirmed the monophyly of the Corallinales as well as the two families (Corallinaceae and Hapalidiaceae) currently recognized within the order. Three of the four subfamilies of the Corallinaceae (Corallinoideae, Lithophylloideae, Metagoniolithoideae) were also resolved as a monophyletic lineage whereas members of the Mastophoroideae were resolved as four distinct lineages. We therefore propose to restrict the Mastophoroideae to the genera Mastophora, Metamastophora, and possibly Lithoporella in the aim of rendering this subfamily monophyletic. In addition, our phylogenies resolved the genus Hydrolithon in two unrelated lineages, one containing the generitype Hydrolithon reinboldii and the second containing Hydrolithon onkodes, which used to be the generitype of the now defunct genus Porolithon. We therefore propose to resurrect the genus Porolithon for the second lineage encompassing those species with primarily monomerous thalli, and trichocyte arrangements in large pustulate horizontal rows. Moreover, our phylogenetic analyses revealed the presence of cryptic diversity in several taxa, shedding light on the need for further studies to better circumscribe species frontiers within the diverse order Corallinales, especially in the genera Mesophyllum and Neogoniolithon.     

Monophyly of the family Desmoscolecidae (Nematoda,Demoscolecida) and Its Phylogenetic position inferred from 18S rDNA sequences

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia longicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct sub-groups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].     

The first complete mitogenome of Picumnus innominatus (Aves,Piciformes, Picidae) and phylogenetic inference within the Picidae

The avian family Picidae, which is nearly global in distribution, contains the piculets (Picumninae and Nesoctitinae), the woodpeckers (Picinae), and the wrynecks (Jynginae). However, the phylogenetic relationships within the Picidae remain obscure for most genera. In the present study, the complete mitochondrial genome of Picumnus innominatus was determined and described, which was the first complete mitogenome reported in the Picumnus. The circular mitogenome of P. innominatus was 17,180 bp in size and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNA genes, a control region (CR), and a noncoding region. The gene order and arrangement of the P. innominatus mitogenome were identical to other mitogenomes of the Picidae. Moreover, strikingly large tandem repeats were found in the noncoding region of the P. innominatus mitogenome, which have not yet been covered in other picid species to date. At the family level (Picidae), the highest dN/dS ratio was detected for the ND1 gene (1.38726) among 13 PCGs, indicating that positive selection was powerful for this gene. Bayesian and Maximum Likelihood phylogenetic analyses based on the combination of 12S rRNA and CYTB gene supported strongly that the Picumninae is monophyletic.     

The complete mitochondrial genome sequence of the little grebe (<Emphasis Type="Italic">Tachybaptus ruficollis</Emphasis>)

Podicipediformes comprises one family (Podicipedidae) including 6 genera, 22 species, and the phylogenetic placement of this order was still in debate. In this study, we sequenced the complete mitochondrial genome (mitogenome) of little grebe (Tachybaptus ruficollis) in Podicipediformes, and explored the phylogenetic position of this order with mitogenome sequences of 21 species from ten families in seven orders. The genome was 16,688 bp in length, and contained 37 genes typical to avian mitogenomes and one control region. The gene organization and characters were similar with other two mitogenomes available in Podicipediformes to date. Phylogenetic tree was constructed with Bayesian method based on mitogenome sequences excluding the control regions. The results supported the closest relationship between Podicipediformes and Phoenicopteriformes, and the topology of our tree was generally similar with the conclusions of previous molecular systematic investigations. Our results furtherly proved the validity of mitogenome data in taxonomic and phylogenetic studies.