Eight new mtDNA sequences of glass sponges reveal an extensive usage of + 1 frameshifting in mitochondrial translation

Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of + 1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate the mechanism of frameshifting, we determined eight new complete or nearly complete mtDNA sequences from glass sponges and examined individual mitochondrial genes from three others. We found nine new instances of single nucleotide insertions in these sequences and analyzed them both comparatively and phylogenetically. The base insertions appear to have been gained and lost repeatedly in hexactinellid mt protein genes, suggesting no functional significance for the frameshifting sites. A high degree of sequence conservation, the presence of unusual tRNAs, and a distinct pattern of codon usage suggest the “out-of-frame pairing” model of translational frameshifting. Additionally, we provide evidence that relaxed selection pressure on glass sponge mtDNA – possibly a result of their low growth rates and deep-water lifestyle – has allowed frameshift insertions to be tolerated for hundreds of millions of years. Our study provides the first example of a phylogenetically diverse and extensive usage of translational frameshifting in animal mitochondrial coding sequences.     

Paraphyly of the Pseudophyllidea (Platyhelminthes: Cestoda): circumscription of monophyletic clades based on phylogenetic analysis of ribosomal RNA

Phylogenetic relationships of cestodes of the order Pseudophyllidea (Platyhelminthes: Cestoda) were examined using sequences of complete small subunit and partial (D1-D3 region) large subunit nuclear rDNA of members of all pseudophyllidean families. The results provide evidence of paraphyly of the order as indicated by previous molecular phylogenetic analyses based on a much lower number of species sequenced. Pseudophyllidean tapeworms represent an artificial assemblage comprising two unrelated clades. “Bothriocephalidea” is formed by four families sensu Bray et al. (1994), namely Bothriocephalidae, Echinophallidae, Philobythiidae and Triaenophoridae, whereas two other families, Diphyllobothriidae and Cephalochlamydidae, give rise to the “Diphyllobothriidea”. The present results indicate that “Bothriocephalidea” forms the most derived clade of all difossate and tetrafossate/bothriate tapeworm lineages which are considered to be basal relative to the rest of tetrafossate/bothridiate and acetabulate cestodes. By contrast, “Diphyllobothriidea”, which includes medically important parasites (Diphyllobothrium and Spirometra), appeared more basal, without a clearly resolved position within other difossate tapeworm lineages.     

Origin and evolution of Schistosoma japonicum

In his hypothesis on the coevolution of Asian schistosomes and snails, Davis implies that the ancestors of the Schistosoma japonicum and S. indicum species group were African and arrived in Asia via the Indian plate. This paper briefly reviews molecular phylogenetic relationships among species of the genus Schistosoma to test Davis’ theory about the origin and evolution of S. japonicum. All analyses using DNA base sequences, mitochondrial genome gene order and C-banding patterns suggest that Schistosoma originated in Asia and not Africa.     

The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): great difference in the A+T-rich region compared to Liriomyza trifolii

The complete mitochondrial genome sequence of Liriomyza sativae Blanchard (15,551 bp) was determined and analyzed in this study. The circular genome contained 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and an A + T-rich region. The initiation codons of COI and ND1 were ‘ATCA’ and ‘GTG’, respectively. ND2 gene used the truncated termination codon ‘T’. All the tRNA genes had the typical cloverleaf secondary structures except for tRNA^Ser(AGN) gene, which was found with the absence of a DHU arm. In addition, a tRNA-like secondary structure (tRNA^Met) was found in the A + T-rich region. The great difference was that the length of L. sativae A + T-rich region was 597 bp shorter than that of Liriomyza trifolii (Burgess). Meanwhile, some minor differences such as ‘TATA’ block were also observed in L. sativae in contrast to ‘TACA’ block in L. trifolii. There were also some essential structure elements such as ‘TATA’ block, ‘G(A)_nT’ block, poly-T stretch and stem-and-loop structure in the A + T-rich region of L. sativae mitochondrial genome.     

Evolutionary history of Calosomina ground beetles (Coleoptera, Carabidae, Carabinae) of the world as deduced from sequence comparisons of the mitochondrial ND 5 gene

We deduced the phylogenetic relationships of 54 individuals representing 27 species of the Calosomina (Coleoptera, Carabidae) from various regions of the world from the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences. The results suggest that these Calosomina radiated into 17 lineages within a short time about 30 million years ago (Mya). Most of the lineages are composed of a single genus containing only one or a few species. In some cases, several species classified into the same genus (e.g., Calosoma maximowiczi, Calos. inquisitor and Calos. frigidum) appear separately in independent lineages, while in others a series of species classified into different genera fall into one lineage (e.g., Chrysostigma calidum, Blaptosoma chihuahua, Microcallisthenes wilkesi and Callisthenes spp.). Based on this molecular phylogeny and morphological data, the probable evolutionary history and mode of morphological differentiation of the Calosomina are discussed.     

Morphological, mitochondrial DNA and allozyme evolution in representative amphibians and reptiles inhabiting each side of the Strait of Gibraltar

Patterns of differentiation in morphology, mitochondrial DNA and allozymes in amphibians and reptiles inhabiting northern and southern shores of the Strait of Gibraltar are not concordant, suggesting that each taxon was affected differently by events preceding or following the formation of the Strait of Gibraltar. Mitochondrial DNA and allozyme differentiation between Discoglossus jeanneae and Discoglossus scovazzi (Anura, Discoglossidae), Rana perezi and Rana saharica (Anura, Ranidae), and Blanus cinereus and Blanus tingitanus (Squamata, Amphisbaenia, Amphisbaenidae) is substantial, whereas morphological differentiation is moderate in Rana and Blanus , but is substantial in Discoglossus . Differentiation in mitochondrial DNA and morphology between Timon ( Lacerta ) lepidus and Timon ( Lacerta ) tangitanus (Squamata, Lacertoidea, Lacertidae) is considerable, but allozyme differentiation is low. In members of type-I and -II Podarcis vaucheri (Squamata, Lacertoidea, Lacertidae), morphology and mitochondrial DNA are moderately differentiated, but allozyme differentiation is low. Spanish and Moroccan populations of Hyla meridionalis (Anura, Hylidae), Mauremys leprosa (Testudines, Geoemydidae), and Macroprotodon brevis (Squamata, Serpentes, Colubridae) demonstrate little allozyme and mitochondrial DNA differentiation, but whereas morphological differentiation between Mauremys and Macroprotodon populations is moderate, Hyla demonstrate substantial morphological differentiation between continental populations. These data suggest that sex-limited mitochondrial markers are reflective of ancient phylogenetic history, whereas biparentally inherited allozyme markers and morphological characteristics reflect more recent population structure and movement.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 445–461.     

Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): New inferences about mitochondrial rate heterogeneity,neutral theory,and phylogenetic relationships within the order Passeriformes

We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald–Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.     

红花变豆菜叶绿体基因组结构及同属种间关系研究

红花变豆菜（Sanicula rubriflora F. Schmidt）是有药用价值的植物,全株干燥后与其他药用同属植物易混淆,种间关系存在争议,通过高通量测序技术对红花变豆菜叶绿体基因组测序,利用生物信息学方法对测序数据进行拼接、注释,首次报道红花变豆菜叶绿体基因组结构及特点,利用叶绿体基因组数据,提供种间分类新证据,并且分析相关类群的进化关系。S. rubriflora叶绿体基因组序列的长度为155 721 bp,其中包括一个85 981 bp的大单拷贝区（large single copy,LSC）和一个17 060 bp的小单拷贝区（small single-copy region,SSC）,它们被两个26 340 bp的反向重复区（inverted repeat sequence,IRs）隔开。红花变豆菜叶绿体基因组GC含量为38.20%,包含129个基因,其中84个蛋白质编码基因,37个tRNA基因和8个rRNA基因。红花变豆菜叶绿体基因组结构具有高度保守性,其中编码基因共有51 907个密码子,最多编码5 095个亮氨酸,最少编码689个色氨酸,简单重复序列分析共发现32个位点,大多数是单碱基重复的A/T类型。叶绿体基因组聚类结果支持天胡荽亚科（Hydrocotyloideae）是伞形科（Umbelliferae）内比较原始的类群;变豆菜亚科（Saniculoideae）和芹亚科（Apioideae）为姊妹类群,是伞形科较进化的类群;变豆菜属植物是一个相对自然的类群;红花变豆菜与黄花变豆菜（S. flavovirens）为近缘姊妹种,但是两者形态和地理分布差异较大。该研究结果为变豆菜属属下种间鉴定及其种间演化奠定基础。     

Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution

The superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the world's largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4+5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae+(Vaillantellidae+(Cobitidae+(Nemacheilidae+Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineage- or ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eye's optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had, as compared with other cobitoid lineages, significantly different dN/dS, dN and dS values for ND4 and IRBP genes. These significant differences are usually indicative of weaker selection pressure, and lineage-specific evolution on genes along the balitorid lineage. Furthermore, within Cobitoidea, excluding balitorids, species living in subtropics had significantly higher dN/dS values in RAG1 and IRBP genes than those living in temperate and tropical zones. Among tropical cobitoids, genes COI, ND5, EGR2B, IRBP and RH1, had a significantly higher mean dS value than those species in subtropical and temperate groups. These findings suggest that the evolution of these genes could also be ecological-group-specific and may have played an important role in the adaptive evolution and diversification of these groups. Thus, we hypothesize that the genes included in the present study were actively involved in lineage- and/or ecological-group-specific evolutionary processes of the highly diverse Cobitoidea. These two evolutionary patterns, both subject to further testing, are hypothesized as integral in the diversification with this major clade of the world's most diverse group of freshwater fishes.     

NADH dehydrogenase subunit 1 and cytochrome c oxidase subunit I sequences compared for members of the genus Taenia (Cestoda)

Nine members of the genus Taenia (Taenia taeniaeformis, Taenia hydatigena, Taenia pisiformis, Taenia ovis, Taenia multiceps, Taenia serialis, Taenia saginata, Taenia solium and the Asian Taenia) were characterised by their mitochondrial NADH dehydrogenase subunit 1 gene sequences and their genetic relationships were compared with those derived from the cytochrome c oxidase subunit I sequence data. The extent of inter-taxon sequence difference in NADH dehydrogenase subunit 1 (5.9–30.8%) was usually greater than in cytochrome c oxidase subunit I (2.5–18%). Although topology of the phenograms derived from NADH dehydrogenase subunit 1 and cytochrome c oxidase subunit I sequence data differed, there was concordance in that T. multiceps, T. serialis (of canids), T. saginata and the Asian Taenia (of humans) were genetically most similar, and those four members were genetically more similar to T. ovis and T. solium than they were to T. hydatigena and T. pisiformis (of canids) or T. taeniaeformis (of cats). The NADH dehydrogenase subunit 1 sequence data may prove useful in studies of the systematics and population genetic structure of the Taeniidae.     

三种蚜虫的线粒体基因组数据

完整的线粒体基因组已被广泛应用于分子进化、基因组学、系统发育等方面的研究。蚜虫是一类重要的农林业害虫, 但目前公开报道的蚜虫完整线粒体基因组非常有限, 因此获得更多的基因组数据对相关研究具有重要价值。本文报道了榕毛管蚜(Greenidea ficicola)、橘二叉蚜(Aphis aurantia)和油杉纩蚜(Mindarus keteleerifoliae) 3种蚜虫的完整线粒体基因组的序列、详细注释信息、基因结构图、密码子使用情况等。该数据集可为昆虫系统发育关系、种群分化格局、害虫防治等方面的工作提供帮助。     

Mitochondrial phylogeny and systematics of baboons (Papio)

Baboons (Papio, s.s.) comprise a series of parapatric allotaxa (subspecies or closely related species) widely distributed in sub-Saharan Africa. Despite extensive studies of their ecology, morphology, and behavior, disagreement about their phylogenetic relationships continues, as expressed in the current coexistence of at least three major, competing taxonomic treatments. To help resolve this situation, we sequenced approximately 900 bases of mitochondrial DNA of 40 individuals from five of the widely recognized "major" allotaxa. Total sequence diversity (>5%) is high compared to most primate species. Major mitochondrial clades correspond to recognized allotaxa, with the important exception that haplotypes from yellow and olive baboons form a single, monophyletic clade within which the two allotaxa do not comprise mutually exclusive clusters. The major clades fall unambiguously into the pattern: (chacma (Guinea (hamadryas (yellow + olive)))). This phylogeny does not support taxonomies that oppose hamadryas to all other baboons ("desert" vs. "savanna"), but is compatible with the view that all definable allotaxa should be recognized as coordinates, either as "phylogenetic" species or "biological" subspecies. The close relationship and unsegregated distribution of haplotypes from Kenyan and Tanzanian yellow and olive baboons are unexplained, but may reflect introgression across the documented hybrid zone. The overall phylogeny, when combined with paleontological data, suggests a southern African origin for extant Papio baboons, with all extant lineages sharing a common mitochondrial ancestor at approximately 1.8 Ma.     

子囊菌交配型基因MAT1-1的系统发育

子囊菌具有无性态与有性态的复杂性,以及人们对其系统发育和亲缘关系了解的局限性,进而导致菌物学家对子囊菌分类尚持不同意见。子囊菌的交配型基因（MAT）进化保守,且编码的蛋白质调控子囊菌的有性生殖过程。核盘菌Sclerotinia sclerotiorum (Lib.) de Bary隶属于子囊菌门Ascomycota、盘菌纲Discomycete,是一种典型丝状同宗配合真菌,控制该菌有性生殖的交配型基因MAT1-1和MAT1-2紧密连锁,且该菌并无有性态与无性态的复杂性。故此,本文根据所克隆的核盘菌交配型基因MAT1-1,利用PAUP*软件将82种含有Alpha-box交配型基因的子囊菌进行了系统进化分析,通过核苷酸及氨基酸水平的系统发育分析,并结合Ainsworth（1973）分类系统及最新的Deep Hyphae（2006）分类系统的对比研究,发现所构建的系统进化树与传统分类所表现的进化关系基本一致,且核盘菌交配型基因MAT1-1在进化过程中功能相对保守,该分析结果有助于对其他子囊菌交配型基因的克隆、系统分类与进化研究,同时对核盘菌的亲缘关系、病害预测及防治等具有重要意义。     

The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S), 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny.     

Genetic relationship between Salix exigua and other North American willows (Salix L.): Evidence from allozyme variation

Starch gel electrophoresis was used to examine the allozyme variation and the genetic relationship between Salix exigua and other North American willows. A total of 149 clonal collections comprising six willow species were analyzed for 26 putative isozyme loci. Genetic distances between species were estimated and used for distance analysis of species relationships. Individual alleles were used as characters for cladistic analysis of phylogenetic inference. Distance analysis indicates that S. exigua has approximately equal divergence to both subgenus Salix and Vetrix. Results of cladistic analysis suggest that S. exigua may be a separate group isolated from all other willows. Based on evidence of allozyme variation, it is suggested that the taxonomic placement of S. exigua within subgenus Salix need to be revised.     

Multiple Lineages of the Mitochondrial Gene NADH Dehydrogenase Subunit 1 (ND1) in Parasitic Helminths: Implications for Molecular Evolutionary Studies of Facultatively Anaerobic Eukaryotes

The task of using partial ND1 sequences to infer a phylogeny for species of the genus Paragonimus (Trematoda: Digenea) was complicated by the discovery of at least two ND1 lineages within individual worms. The divergence of the ND1 lineages is shown by phylogenetic analysis not only to predate the divergence of the three Paragonimus species or species groups investigated but also the divergence of some trematode families. Some sequences are clearly pseudogenes as they contain single base deletions and/or premature termination codons. The presence of both pseudogenes and/or mitochondrial heteroplasmy are invoked to explain the presence of multiple and divergent ND1 lineages in these trematodes, which have two distinct cytochemical types of mitochondria. The implications for phylogenetic studies generally and of parasitic helminths specifically, using ND1 sequence data, are discussed. The ability of these organisms to adapt their metabolic processes to the variable availability of oxygen as an electron acceptor are proposed to explain some of the molecular diversity observed in parasitic helminths and possibly also in other anaerobically adapted eukaryotes. Received: 18 October 1999 / Accepted: 23 June 2000     

The radiation of the Seicercus burkii complex and its congeners (Aves: Sylviidae): molecular genetics and bioacoustics

Cryptic species of passerine birds lack notable morphological differentiation and can best be identified by molecular and bioacoustic markers. Here we investigate seven cryptic species of the golden-spectacled warbler (Seicercus burkii complex) with respect to territorial song and cytochrome-b (cyt-b) sequences. Their phylogenetic relations to other Seicercus species and to members of the genus Phylloscopus are inferred by the same methods. Three separate lineages of Seicercus are nested within different branches of the molecular Phylloscopus tree. The S. burkii complex is a monophyletic unit comprising seven species (S. burkii s. str., S. whistleri, S. valentini, S. soror, S. omeiensis, S. tephrocephalus and S. affinis). S. xanthoschistos turned out to be a close relative of Phylloscopus davisoni within the P. reguloides group. Two isolated sister taxa, S. grammiceps and S. castaniceps, also branch together with the P. reguloides group. Within the S. burkii complex the overall haplotype and nucleotide diversity is highest in taxa from the Chinese middle and upper mountain belt (S. valentini, S. omeiensis and S. soror), indicating at least partially restricted gene flow in these species. This is explained by the fragmentation of high-altitude habitats in China while in the Himalayas the vicariant species S. whistleri inhabits a more continuous mountain belt at the same altitude. For the Chinese species from medium and high altitudes, past range expansion is indicated by significantly negative Tajima Ds. According to pairwise genetic distances, most species of the S. burkii complex have diverged 5 myr ago, the most recent split between S. burkii and S. tephrocephalus is dated 2 myr ago. Coalescence times for haplotype lineages of the different species range from 9 up to 12 myr, and between 5 and 6 myr for S. burkii and S. tephrocephalus.

Within Seicercus divergence of song features such as frequency parameters and syntax structures correlate with genetic distances between taxa. The three cyt-b lineages of Seicercus correspond to different clusters in a discriminant analysis by acoustic parameters. Common syntax structures of territorial song in the Phylloscopus/Seicercus assemblage are: (1) an introductory element derived from specific calls and (2) a syntax of trills and repeated element groups or a combination of both. There are clear indications that these song structures have repeatedly emerged, were lost or were altered in different branches of the phylogenetic tree at different times. Absolute differences between taxa in frequency parameters or in an acoustic divergence index increase significantly with growing genetic distances. However, due to multiple parallel evolution phylogenetic information provided by single acoustic traits decreases with increasing numbers of taxa involved in the investigation.     

Mitochondrial DNA as effective molecular markers for the genetic variation and phylogeny of the family Osteoglossidae

The present study examined the genetic variation of the family Osteoglossidae from different geographical locations based on the mitochondrial NADH dehydrogenase subunit 2 (ND2) and ATPase subunit 6 (ATPase6) genes; we then re-constructed the phylogenetic relationships using the two sequences in combination. The results showed that the partial sequences of mitochondrial ND2 and ATPase6 of the family Osteoglossidae were 813 bp and 669 bp, respectively. A total of 42 species-specific nucleotide positions of the family Osteoglossidae were found to be useful for molecular identification. The sequence variation showed greater differences (8.3% ~ 28.1% for the combined sequences, 8.3% ~ 26.7% for the ND2 gene, and 9.3% ~ 28.7% for the ATPase6 gene) among the different species of Osteoglossidae, and there was a significant association between the genetic difference and geographical location. Phylogenetic analyses using neighbor-joining, Bayesian inference, and maximum parsimony (MP) methods based on the combined sequences of the two genes were able to distinguish the different species and were in agreement with the existing taxonomy based on morphological characters and in association with the geographical distribution among seven species of the family Osteoglossidae.     

The mitochondrial genome of Ifremeria nautilei and the phylogenetic position of the enigmatic deep-sea Abyssochrysoidea (Mollusca: Gastropoda)

The complete nucleotide sequence of the mitochondrial (mt) genome of the deep-sea vent snail Ifremeria nautilei (Gastropoda: Abyssochrysoidea) was determined. The double stranded circular molecule is 15,664 pb in length and encodes for the typical 37 metazoan mitochondrial genes. The gene arrangement of the Ifremeria mt genome is most similar to genome organization of caenogastropods and differs only on the relative position of the trnW gene. The deduced amino acid sequences of the mt protein coding genes of Ifremeria mt genome were aligned with orthologous sequences from representatives of the main lineages of gastropods and phylogenetic relationships were inferred. The reconstructed phylogeny supports that Ifremeria belongs to Caenogastropoda and that it is closely related to hypsogastropod superfamilies. Results were compared with a reconstructed nuclear-based phylogeny. Moreover, a relaxed molecular-clock timetree calibrated with fossils dated the divergence of Abyssochrysoidea in the Late Jurassic–Early Cretaceous indicating a relatively modern colonization of deep-sea environments by these snails.