基于线粒体细胞色素b基因序列的虹雉属鸟类的系统发育关系

通过雉科虹雉属(Lophophorus)、角雉属(Tragopan)、勺鸡属(Pucrasia)和血雉属(Ithaginis)7种鸟类的细胞色素b(cyt b)基因序列比较,构建的虹雉属及其近缘属的分子系统树表明：①3种虹雉构成一个单系群(monophyletic group),虹雉属与角雉属、勺鸡属构成一个单系群;②虹雉属内分为白尾梢虹雉,以及棕尾虹雉和绿尾虹雉两个演化枝。综合分子系统学、地理分布格局和形态学的证据,推测虹雉属鸟类起源于中国的横断山脉,其中繁衍生活在原地的一枝演化为白尾梢虹雉;另一枝则分别进入喜马拉雅山区(西)和中国西南部(东),向西的演化为棕尾虹雉,向东的则为绿尾虹雉。     

Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes)

It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenetic relationship of the Cobitoidea was ((Catostomidae+Gyrinocheilidae)+(Botiinae+(Balitorinae+(Cobitinae+Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae.     

A mitogenome of the Chevrier's field mouse (Apodemus chevrieri) and genetic variations inferred from the cytochrome b gene

The Chevrier's field mouse (Apodemus chevrieri) is an endemic species to China and is an important pest in agriculture and human diseases. In this study, the complete mitochondrial genome of this species was sequenced and its size was 16,298 bases (accession no.: HQ896683). The mitogenome structure was similar compared with other reported rodent mitochondrial genomes and includes 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and 1 control region. This was the first complete mitogenome sequenced in genus Apodemus. The phylogenetic analyses based on the sequences of 12 heavy-strand protein-coding genes demonstrated that A. chevrieri clustered together with genus Mus. Additionally, extremely high haplotype and nucleotide diversities (h=0.978, π=2.6%) were observed based on 44 mitochondrial cytochrome b (cyt b) gene sequences. This suggests adaptive divergence of this species to a variety of living habitats and potential refuges in the eastern margin of the Hengduan Mountains during the Quaternary ice ages. No population expansions or genetic bottlenecks were observed in demographic analyses. The phylogenetic analysis of cyt b sequences and haplotypes revealed a genetic differentiation between north and south populations. The divergence between north clade and south clade occurred probably in the middle Pleistocene 1.1815 million years ago (Mya) (95% highest posterior density 2.3189-0.2737 Mya), which was congruent with the periods of the most tense uplift events in the Tibetan Plateau.     

Phylogeny of the Colubroidea (Serpentes): new evidence from mitochondrial and nuclear genes

The Colubroidea contains over 85% of all the extant species of snakes and is recognized as monophyletic based on morphological and molecular data. Using DNA sequences (cyt b, c-mos) from 100 species we inferred the phylogeny of colubroids with special reference to the largest family, the Colubridae. Tree inference was obtained using Bayesian, likelihood, and parsimony methods. All analyses produced five major groups, the Pareatidae, Viperidae, Homalopsidae, the Elapidae, and the Colubridae. The specific content of the latter two groups has been altered to accommodate evolutionary history and to yield a more stable taxonomy. We propose an updated classification based on the reallocation of species as indicated by our inferred phylogeny.     

Phylogeography of Balkan wall lizard (Podarcis taurica) and its relatives inferred from mitochondrial DNA sequences

Wall lizards of the genus Podarcis (Sauria, Lacertidae) comprise 17 currently recognized species in southern Europe, where they are the predominant reptile group. The taxonomy of Podarcis is complex and unstable. Based on DNA sequence data the species of Podarcis falls into four main groups that have substantial geographical conherence (western island group, southwestern group, Italian group and Balkan group). The Balkan species are divided in two subgroups: the subgroup of Podarcis taurica (P. taurica, P. milensis, P. gaigeae and perhaps P. melisellensis), and the subgroup of Podarcis erhardii (P. erhardii and P. peloponnesiaca). We addressed the question of phylogenetic relations among the species of the P. taurica subgroup encountered in Greece, as they can be inferred from partial mtDNA (cyt b and 16S) sequences. Our data support the monophyly of P. taurica subgroup and suggest that P. gaigeae, P. milensis and P. melisellensis form a clade, which thereinafter connects to P. taurica. Within the previous clade, P. gaigeae is more closely related to P. milensis than to P. melisellensis. However, the specimens of P. taurica were subdivided in two different groups. The first one includes the specimens from northeastern Greece, and the other group includes the specimens from the rest of continental Greece and Ionian islands. Because the molecular clock of the cyt b and 16 rRNA genes was not rejected in our model test, it is possible to estimate times of speciation events. Based on the splitting of the island of Crete from Peloponnisos [c. 5 million years ago (Ma)], the evolutionary rate for the cyt b is 1.55% per million years (Myr) and for the 16S rRNA is 0.46% per Myr. These results suggest that the evolutionary history of P. taurica in Greece is more complex than a single evolutionary invasion. The data analysed, stress the need for a reconsideration of the evolutionary history of Greek Podarcis species and help overcome difficulties that classical taxonomy has encountered at both the species level.     

A molecular phylogeny of Equatorial African Lacertidae, with the description of a new genus and species from eastern Democratic Republic of the Congo

Currently, four species of the lacertid lizard genus Adolfus are known from Central and East Africa. We sequenced up to 2,825 bp of two mitochondrial (16S and cyt b) and two nuclear (c-mos and RAG1) genes from 41 samples of Adolfus (representing every species), two species each of Gastropholis and Holaspis, and in separate analyses combined this data with GenBank sequences of all other Eremiadini genera and four Lacertini outgroups. Data from DNA sequences were analyzed with maximum parsimony (PAUP), maximum-likelihood (RAxML) and Bayesian inference (MrBayes) criteria. Results demonstrated that Adolfus is not monophyletic: A. africanus (type species), A. alleni and A. jacksoni are sister taxa, whereas A. vauereselli and a new species from the Itombwe Plateau of Democratic Republic of the Congo are in a separate lineage. Holaspis and Gastropholis were recovered in separate clades. Based on this molecular data, relatively substantial sequence divergence and multiple morphological differences, we describe a new genus of lacertid for the lineage including A. vauereselli and the new Itombwe species. The recognition of this new, endemic genus underscores the conservation importance of the Albertine Rift, especially the Itombwe Plateau, a unique region that is severely threatened by unchecked deforestation, mining and poaching.     

Molecular evolutionary relationships in the avian genus Anthus (Pipits: Motacillidae)

Nucleotide sequences for 1035 bp of the mitochondrial cytochrome b gene were used to determine the molecular evolutionary relationships of species in the cosmopolitan avian genus Anthus. Phylogenetic analysis of these mtDNA sequences supported four major clades within the genus: (1) the small-bodied African pipits, (2) a largely Palearctic clade, (3) a largely South American clade, and (4) an African-Eurasian-Australian clade. Anthus hellmayri, A. correndera, and A. rubescens are shown to be paraphyletic. The possibility of paraphyly within A. similis is instead inferred to be the discovery of a new species and supported by reference to the museum voucher specimen. Sequence divergence suggests a Pliocene/Miocene origin for the genus. Although Anthus cytochrome b is found not to be behaving in a clocklike fashion across all taxa, speciation during the Pleistocene epoch can be reasonably inferred for the 66% of sister pairs that are diverging in a clocklike manner. Base compositions at each codon position are similar to those found across a growing number of avian lineages. The resulting phylogenetic hypothesis is compared to previous hypotheses of Anthus relationships, all of which deal with relationships of a particular species or a particular species complex; roughly half of these previous hypotheses are supported.     

Molecular phylogeny and systematics of the pseudoxyrhophiine snake genus Liopholidophis (Reptilia, Colubridae): evolution of its exceptional sexual dimorphism and descriptions of new taxa

The pseudoxyrhophiine snake genus Liopholidophis Mocquard, 1904 is endemic to Madagascar and consists of two distinct species groups. We performed molecular phylogenetic analyses using nucleotide sequences of c . 2200 bp from two mitochondrial genes (16S rRNA, cyt b ) and one nuclear gene (c-mos) to test the monophyly of the genus Liopholidophis and to investigate the relationships of the known species and an unidentified Liopholidophis population. Our phylogeny strongly supports the polyphyly of the genus Liopholidophis , confirms the monophyly of both species groups, and reveals that the unidentified population belongs to a new species. We therefore transfer the species of the former L. stumpffi group ( L. epistibes , L. infrasignatus , L. lateralis , L. martae , and L. stumpffi ) to a new genus Bibilava gen. n. and describe Liopholidophis dimorphus sp. n. from the rainforests of Montagne d'Ambre National Park in northern Madagascar. Finally, we compare our phylogeny with previous hypotheses and discuss the evolution of the extreme sexual dimorphism in tail length of Liopholidophis s. str.     

Phylogeography of the finless porpoise and potential implications for the taxonomy of Neophocaena spp.

The finless porpoise (genus Neophocaena) is a poorly known cetacean of great conservation concern. Within its range, from western Pacific to northwestern Indian Ocean, there are currently two species recognized (N. asiaeorientalis and N. phocaenoides), thought to be reproductively isolated since last glacial maximum, with the only sympatric overlap zone in Taiwan Strait. However, the genetic variation across the genus’ distribution has not yet been extensively studied, especially in the Indian Ocean. We performed an exhaustive review of molecular data of the finless porpoise across its range. Neighbor-net networks analyses based on two mitochondrial loci (control region/CR and cytochrome b/cyt b) suggest that finless porpoises from the Indian and Pacific Ocean constitute two distinct clades, well-defined by fixed mutations at both loci. A molecular clock analyses indicate early split (CR: 13.1 Ma, cyt b: 12.9 Ma) between these two oceanic lineages, while spatial genetic analyses further suggest that in the Pacific the divergence was primarily due to the taxon from Japanese waters rather than inter-species divergence across the Taiwan Strait. As extinction risks can be substantially underestimated if threatened species are pooled together with non-threatened, especially in the absence of long-distance migration, we suggest that the present 2-species taxonomy of the genus Neophocaena should be given further examination, with concerted sampling effort in the Western Indian Ocean. More research effort and genomic information is needed before taxonomic revisions can be considered; such further studies are strongly recommended as they may affect the current status classification of the species constituting the genus Neophocaena. Most notably, the narrow-ridged finless porpoise off Japan merits urgent conservation attention.     

Cytochrome b sequences reveal Acomys minous (Rodentia, Muridae) paraphyly and answer the question about the ancestral karyotype of Acomys dimidiatus

Sequences of the cytochrome b (cyt b) mitochondrial gene show that the spiny mouse Acomys from Crete, known as the endemic species A. minous, is composed of two distinct maternal lineages ("A" and "B"). Group "A" sequences cluster with A. nesiotes (Cyprus) and group "B" sequences cluster with A. cilicicus (Turkey), which is evidence of paraphyly of A. minous in regard to these two species. From cyt b sequences, the three taxa are very closely related to A. cahirinus (Egypt): the maximum divergence found among these sequences is 1.6%, which is equivalent to the intraspecific diversity observed in other Acomys species. Paleozoology evidenced that man unintentionally introduced Acomys into Crete and Cyprus during antiquity. The divergence time between Acomys cyt b sequences found in Crete was estimated at 0.4 Myr, which means that the diversity observed did not appear after the introduction but reflects a much more ancient polymorphism. Cytochrome b phylogeny and cytogenetic data together comprise evidence that, within the species A. dimidiatus (Saudi Arabia, Israel, Egypt), it is the karyotypic form with 36 chromosomes that derives from the form with 38 chromosomes, due to a single acrocentric fusion.     

Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes

Nucleotide sequences of the mitochondrial protein coding cytochrome b (cyt b; 650 bp) and small-subunit 12S ribosomal RNA (approximately 350 bp) genes were used in analyses of phylogenetic relationships among extant phrynosomatid sand lizards, including an examination of competing hypotheses regarding the evolution of "earlessness." Sequences were obtained from all currently recognized species of sand lizards as well as representatives of the first and second outgroups and analyzed using both parsimony and likelihood methods. The cyt b data offer strong support for relationships that correspond with relatively recent divergences and moderate to low support for relationships reflecting more ancient divergences within the clade. These data support monophyly of the "earless" taxa, the placement of Uma as the sister taxon to the other sand lizards, and monophyly of all four taxa traditionally ranked as genera. All well-supported relationships in the 12S phylogeny are completely congruent with well-supported relationships in the cyt b phylogeny; however, the 12S data alone provide very little support for deeper divergences. Phylogenetic relationships within species are concordant with geography and suggest patterns of phylogeographic differentiation, including the conclusion that at least one currently recognized species (Holbrookia maculata) actually consists of more than one species. By independently optimizing likelihood model parameters for various subsets of the data, we found that nucleotide substitution processes vary widely between genes and among the structural and functional regions or classes of sites within each gene. Therefore, we compared competing phylogenetic hypotheses, using parameter estimates specific to those subsets, analyzing the subsets separately and in various combinations. The hypothesis supported by the cyt b data was favored over rival hypotheses in all but one of the five comparisons made with the entire data set, including the set of partitions that best explained the data, although we were unable to confidently reject (P < 0.05) alternative hypotheses. Our results highlight the importance of optimizing models and parameter estimates for different genes or parts thereof--a strategy that takes advantages of the strengths of both combining and partitioning data.     

Comparison of complete mitochondrial DNA control regions among five Asian freshwater turtle species and their phylogenetic relationships

The complete mitochondrial DNA (mtDNA) control regions (CR), cytochrome b (Cyt b), NADH dehydrogenase subunit 4 (ND4) and cytochrome coxidase subunit I (CO I) genes of four Asian freshwater turtles, Mauremys japonica, Ocadia sinensis, M. mutica, and Annamemys annamensis, were sequenced using universal PCR and long-PCR techniques. Combined with CR sequences of Chinemys reevesii, the composition and structure of CR of the five species were compared and analyzed. Three functional domains (TAS, CD and CSB) in CR and their conserved sequences (TAS, CSB-F, CSB-1, CSB-2, and CSB-3) were identified based on sequence similarity to those of other turtles. At the 3' end of CSB, six type motifs of variable number of tandem repeats (VNTRs) of five species were recognized, in which the TTATATTA motif may be the VNTR motif of the ancestral species of these five turtles. Comparison of nucleotide divergences among Cyt b, ND4, CO I, and CR of 11 turtle species using transitions + transversions and transversions-only methods supported the conclusion that CR evolved 2.6- to 5.7-fold faster than the other mtDNA genes. After excluding VNTRs of CR, molecular phylogenetic trees were constructed with maximum parsimony, maximum likelihood and Bayesian inference methods. The results supported an expanded clade of Mauremys, which included species formerly in Ocadia, Chinemys, Mauremys, and Annamemys; this was also reflected in the results of VNTR analysis.     

Comparative evolution of the mitochondrial cytochrome b gene and nuclear beta-fibrinogen intron 7 in woodpeckers

Most molecular phylogenetic studies of vertebrates have been based on DNA sequences of mitochondrial-encoded genes. MtDNA evolves rapidly and is thus particularly useful for resolving relationships among recently evolved groups. However, it has the disadvantage that all of the mitochondrial genes are inherited as a single linkage group so that only one independent gene tree can be inferred regardless of the number of genes sequenced. Introns of nuclear genes are attractive candidates for independent sources of rapidly evolving DNA: they are pervasive, most of their nucleotides appear to be unconstrained by selection, and PCR primers can be designed for sequences in adjacent exons where nucleotide sequences are conserved. We sequenced intron 7 of the beta-fibrinogen gene (beta-fibint7) for a diversity of woodpeckers and compared the phylogenetic signal and nucleotide substitution properties of this DNA sequence with that of mitochondrial-encoded cytochrome b (cyt b) from a previous study. A few indels (insertions and deletions) were found in the beta-fibint7 sequences, but alignment was not difficult, and the indels were phylogentically informative. The beta-fibint7 and cyt b gene trees were nearly identical to each other but differed in significant ways from the traditional woodpecker classification. Cyt b evolves 2.8 times as fast as beta-fibint7 (14. 0 times as fast at third codon positions). Despite its relatively slow substitution rate, the phylogenetic signal in beta-fibint7 is comparable to that in cyt b for woodpeckers, because beta-fibint7 has less base composition bias and more uniform nucleotide substitution probabilities. As a consequence, compared with cyt b, beta-fibint7 nucleotide sites are expected to enter more distinct character states over the course of evolution and have fewer multiple substitutions and lower levels of homoplasy. Moreover, in contrast to cyt b, in which nearly two thirds of nucleotide sites rarely vary among closely related taxa, virtually all beta-fibint7 nucleotide sites appear free of selective constraints, which increases informative sites per unit sequenced. However, the estimated gamma distribution used to model rate variation among sites suggests constraints on some beta-fibint7 sites. This study suggests that introns will be useful for phylogenetic studies of recently evolved groups.     

从细胞色素b 基因全序列分析岩羊和山羊、绵羊的系统发生关系

本文测定了来自四川和青海岩羊的细胞色素b 基因全序列(1 140 bp) , 结合从GenBank 中检索获得的山羊、北山羊、绵羊和盘羊4 个近缘种细胞色素b 核苷酸同源区序列进行比较, 分析了碱基组成和变异情况以及核苷酸序列差异。分别采用简约法和距离矩阵法构建分子系统树, 得到了基本相同的拓扑结构, 从分子水平初步探讨了岩羊的系统起源问题。岩羊与山羊属的山羊、北山羊有着比绵羊属的绵羊、盘羊更近的亲缘关系。岩羊与山羊、北山羊的分歧时间大约在3～6 百万年, 而与盘羊、绵羊的分歧时间大约在6～8 百万年。     

Molecular phylogenetic relationships of pond frogs distributed in the Palearctic region inferred from DNA sequences of mitochondrial 12S ribosomal RNA and cytochrome b genes

The evolutionary relationships of pond frogs distributed in the Far East and Europe were investigated by analyses of nucleotide sequences of mitochondrial 12S ribosomal RNA (12S rRNA) and cytochrome b (cyt b) genes. The nucleotide sequences of a 412-bp segment of the 12S rRNA gene and a 534-bp segment of the cyt b gene were determined by the PCR-direct sequencing method using 19 frogs belonging to six species and one subspecies distributed in the Palearctic region. Phylogenetic trees were constructed by the neighbor-joining and maximum-likelihood methods using Rana catesbeiana or Xenopus laevis as an outgroup. The 412-bp segment of the 12S rRNA gene contained 65 variable sites including gap sites, and the 534-bp segment of the cyt b gene contained 160 variable sites. The nucleotide sequence divergences of the 12S rRNA gene were 0.25-4.83% within the Far Eastern frogs, 0.25-6.22% within the European frogs, and 8.74-11.24% between the Far Eastern and the European frogs, whereas those of the cyt b gene were 3.64-14.73% within the Far Eastern frogs, 0.38-14.42% within the European frogs, and 16.53-23.58% between the Far Eastern and the European frogs. Although most nucleotide substitutions were at the third codon position of the cyt b gene and were silent mutations, 4 amino acid replacements occurred within the Far Eastern frogs, 4 within the European frogs, and 11 between the Far Eastern and the European frogs. The phylogenetic trees constructed from the nucleotide sequence divergences showed slightly different topologies for the 12S rRNA and cyt b genes. R. esculenta from Ukraine was closely related to R. lessonae from Luxembourg in both the 12S rRNA and the cyt b gene sequences.     

Colonization of Ireland: revisiting 'the pygmy shrew syndrome' using mitochondrial, Y chromosomal and microsatellite markers

There is great uncertainty about how Ireland attained its current fauna and flora. Long-distance human-mediated colonization from southwestern Europe has been seen as a possible way that Ireland obtained many of its species; however, Britain has (surprisingly) been neglected as a source area for Ireland. The pygmy shrew has long been considered an illustrative model species, such that the uncertainty of the Irish colonization process has been dubbed 'the pygmy shrew syndrome'. Here, we used new genetic data consisting of 218 cytochrome (cyt) b sequences, 153 control region sequences, 17 Y-intron sequences and 335 microsatellite multilocus genotypes to distinguish between four possible hypotheses for the colonization of the British Isles, formulated in the context of previously published data. Cyt b sequences from western Europe were basal to those found in Ireland, but also to those found in the periphery of Britain and several offshore islands. Although the central cyt b haplotype in Ireland was found in northern Spain, we argue that it most likely occurred in Britain also, from where the pygmy shrew colonized Ireland as a human introduction during the Holocene. Y-intron and microsatellite data are consistent with this hypothesis, and the biological traits and distributional data of pygmy shrews argue against long-distance colonization from Spain. The compact starburst of the Irish cyt b expansion and the low genetic diversity across all markers strongly suggests a recent colonization. This detailed molecular study of the pygmy shrew provides a new perspective on an old colonization question.     

Molecular phylogeny of Turkish Trachurus species (Perciformes: Carangidae) inferred from mitochondrial DNA analyses

Genetic variation among three species of Trachurus (T. trachurus, T. mediterraneus and T. picturatus) from Turkey was investigated by phylogenetic analysis of the entire mtDNA control region (CR) (862 bp, n = 182) and partial cytochrome (cyt) b (239 bp, n = 174) sequences. Individuals were collected at nine stations in four geographic locations: North‐eastern Mediterranean Sea, Aegean Sea, Sea of Marmara and Black Sea. Polymerase chain reaction‐direct sequencing of the CR and the partial cyt b genes produced 28 and 131 distinct haplotypes, respectively. Maximum likelihood, neighbour‐joining and maximum parsimony methods produced similar tree topologies. The results of both CR and cyt b sequence analyses revealed the existence of several species‐specific nucleotide sites that can be used to discriminate between the three species. Genetic distances indicated that T. mediterraneus and T. picturatus are more closely related to each other than either is to T. trachurus. Inter‐nucleotide and intra‐nucleotide diversities of T. picturatus were larger than those of T. mediterraneus and T. trachurus. There was no evidence of a geographical difference in haplotype frequencies of these two mtDNA regions to be clustered.     

基于18S rDNA遗传距离与GC含量对游走类纤毛虫的分子系统学研究

为了揭示游走类纤毛虫的系统发生,对寄生于淡水鱼类的车轮虫科中的6种车轮虫进行了18S rDNA的测序并获得了9个序列。采用了最大似然法(ML)与贝叶斯法(BI)对GenBank中所有游走类纤毛虫的18S rDNA序列进行了系统树的构建,并首次将SPSS与18S rDNA遗传距离结合分析了游走类纤毛虫的系统发生。研究结果进一步证实了车轮虫属(Trichodina)的非单系发生与小车轮虫属 (Trichodinella) 的有效性。此外,研究结合18S rDNA 的GC含量与遗传距离分析提出了游走类纤毛虫科属及种间新的鉴定依据: 18S rDNA 的GC含量可用于游走类纤毛虫的科属区分,且与游走类纤毛虫的分化密切相关; 18S rDNA的遗传距离在游走类纤毛虫的不同阶元中具有一定的阈值范围,即通常种内遗传距离阈值范围为0.000-0.005,属种间阈值范围为0.005-0.150,当遗传距离大于0.150时,则达到了科间水平。     

Evidence for phylogenetic congruence among sulfur-oxidizing chemoautotrophic bacterial endosymbionts and their bivalve hosts

Sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria are now known to occur as endosymbionts in phylogenetically diverse bivalve hosts found in a wide variety of marine environments. The evolutionary origins of these symbioses, however, have remained obscure. Comparative 16S rRNA sequence analysis was used to investigate whether thioautotrophic endosymbionts are monophyletic or polyphyletic in origin and to assess whether phylogenetic relationships inferred among these symbionts reflect those inferred among their hosts. 16S rRNA gene sequences determined for endosymbionts from nine newly examined bivalve species from three families (Vesicomyidae, Lucinidae, and Solemyidae) were compared with previously published 16S rRNA sequences of thioautotrophic symbionts and free-living bacteria. Distance and parsimony methods were used to infer phylogenetic relationships among these bacteria. All newly examined symbionts fall within the gamma subdivision of the Proteobacteria, in clusters containing previously examined symbiotic thioautotrophs. The closest free-living relatives of these symbionts are bacteria of the genus Thiomicrospira. Symbionts of the bivalve superfamily Lucinacea and the family Vesicomyidae each form distinct monophyletic lineages which are strongly supported by bootstrap analysis, demonstrating that host phylogenies inferred from morphological and fossil evidence are congruent with phylogenies inferred for their respective symbionts by molecular sequence analysis. The observed congruence between host and symbiont phylogenies indicates shared evolutionary history of hosts and symbiont lineages and suggests an ancient origin for these symbioses. Correspondence to: D.L. Distel