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1.
We explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA sequences of eight teleosts (including three newly determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.  相似文献
2.
In a previous study based on 100 whole mitochondrial genome (mitogenome) sequences, we sought to provide a new perspective on the ordinal relationships of higher ray-finned fish (Actinopterygii). The study left unexplored the phylogenetic position of toadfishes (order Batrachoidiformes), as data were unavailable owing to technical difficulties. In the present study, we successfully determined mitogenomic sequences for two toadfish species ( Batrachomoeus trispinosus and Porichthys myriaster ) and found that the difficulties resulted from unusual gene arrangements and associated repetitive non-coding sequences. Unambiguously aligned, concatenated mitogenomic sequences (13 461 bp) from 102 higher actinopterygians (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd and 3rd codon positions of the protein-coding genes, tRNA genes and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenies strongly suggest that the toadfishes are not members of relatively primitive higher actinopterygians (Paracanthopterygii), but belong to a crown group of actinopterygians (Percomorpha), as was demonstrated for ophidiiform eels (Ophidiiformes) and anglerfishes (Lophiiformes) in the previous study. We propose revised limits of major unranked categories for higher actinopterygians and a new name (Berycomorpha) for a clade comprising two reciprocally paraphyletic orders (Beryciformes and Stephanoberyciformes) based on the present mitogenomic phylogenies.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 289–306.  相似文献
3.
Higher-level relationships of the basal Euteleostei (=Protacanthopterygii) are so complex and controversial that at least nine different morphology-based phylogenetic hypotheses have been proposed during the last 30 years. Relationships of the Protacanthopterygii were investigated using mitochondrial genomic (mitogenomic) data from 34 purposefully chosen species (data for 12 species being newly determined during the study) that fully represented major basal euteleostean lineages and some basal teleosts plus neoteleosts as outgroups. Unweighted and weighted maximum parsimony (MP) and maximum likelihood (ML) analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and 3rd codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) from the 34 species. The resultant trees were well resolved and largely congruent, with most internal branches being supported by high statistical values. Monophyly of the protacanthopterygians was confidently rejected by the mitogenomic data. Of the five major monophyletic groups that received high statistical support within the protacanthopterygians, a clade comprising members of the alepocephaloids was unexpectedly nested within the Otocephala, sister-group of the euteleosts. The remaining four major monophyletic groups, on the other hand, occupied phylogenetic positions intermediate between the otocephalans and neoteleosts, with a clade comprising esociforms + salmoniforms being more basal to the argentinoids and osmeroids. Although interrelationships of the latter two clades (argentinoids and osmeroids) with the neoteleosts remained ambiguous, the present results indicated explicitly that the protacanthopterygians as currently defined merely represent a collective, polyphyletic group of the basal euteleosts, located between the basal teleosts (elopomorphs and below) and neoteleosts (stomiiforms and above).  相似文献
4.
Mitogenomic analyses of caniform relationships   总被引:5,自引:0,他引:5  
Extant members of the order Carnivora split into two basal groups, Caniformia (dog-like carnivorans) and Feliformia (cat-like carnivorans). In this study we address phylogenetic relationships within Caniformia applying various methodological approaches to analyses of complete mitochondrial genomes. Pinnipeds are currently well represented with respect to mitogenomic data and here we add seven mt genomes to the non-pinniped caniform collection. The analyses identified a basal caniform divergence between Cynoidea and Arctoidea. Arctoidea split into three primary groups, Ursidae (including the giant panda), Pinnipedia, and a branch, Musteloidea, which encompassed Ailuridae (red panda), Mephitidae (skunks), Procyonidae (raccoons) and Mustelidae (mustelids). The analyses favored a basal arctoid split between Ursidae and a branch containing Pinnipedia and Musteloidea. Within the Musteloidea there was a preference for a basal divergence between Ailuridae and remaining families. Among the latter, the analyses identified a sister group relationship between Mephitidae and a branch that contained Procyonidae and Mustelidae. The mitogenomic distance between the wolf and the dog was shown to be at the same level as that of basal human divergences. The wolf and the dog are commonly considered as separate species in the popular literature. The mitogenomic result is inconsistent with that understanding at the same time as it provides insight into the time of the domestication of the dog relative to basal human mitogenomic divergences.  相似文献
5.
The complete 15,831 bp nucleotide sequence of the mitochondrial genome from Elimaea cheni(Phaneropterinae)was determined.The putative initiation codon for cox1 was TTA.The phylogeny of Orthoptera based on different mtDNA datasets were analyzed with maximum likelihood(ML)and Bayesian inference(BI).When all 37 genes(mtDNA)were analyzed simultaneously,the monophyly of Caelifera and Ensifera were recovered in the context of our taxon sampling.The phylogeny of Orthoptera was largely consistent with previous phylogenetie hypotheses.Rhaphidophoridae to be a sister group of Tettigoniidae,and the relationships among four subfamilies of Tettigoniidae were(Phaneropterinae+(Conocephalinae+(Bradyporinae+Tettigoniinae))).Pyrgomorphidae was the most basal group of Caelifera.The relationships among six acridid subfamilies were(Oedipodinae+(Acridinae+(Gomphocerinae+(Oxyinae+(Calliptaminae +Cyrtacanthaeridinae))))).However,we did not recover a monophyletic Grylloidea.Myrmecophilidae clustered into one clade with Gryllotalpidae instead of with Gryllidae.ML and BI analyses of all protein coding genes(using all nucleotide sequence data or excluding the third codon position,and amino acid sequences)revealed a topology identical to that of the entire mtDNA genome dataset.However,22 tRNAs genes excluding the DHU loop and T()C loop(TRNA),and two rRNA genes(RRNA)perform poorly when analyzed as single dataset.Our results suggest that the best phylogenetie inferences were ML and BI methods based on total mtDNA.Excluding tRNA genes,rRNA genes and the third codon position of protein coding genes from dataset and converting nucleotide sequences to amino acid sequences do not positively affect phylogenetic reconstruction.  相似文献
6.
For the first step toward resolution of the higher-level relationships of the order Aulopiformes (Teleostei: Eurypterygii) using longer DNA sequences, we determined the complete mitochondrial DNA sequence for Aulopus japonicus (Aulopodidae). The entire genome was purified by gene amplification using a long PCR technique, and the products were subsequently used as templates for PCR with 63 fish-versatile and 3 species-specific primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products demonstrated that the genome (16 653 base pairs [bp]) contained the same 37 mitochondrial genes (2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as found in other vertebrates, with the gene order identical to that in typical vertebrates. Maximum-parsimony analysis using nucleotide sequences from the concatenated 12 protein-coding genes (no third codon positions and excluding the ND6 gene) plus 22 tRNA genes (stem regions only) from eight teleosts placed A. japonicus in a reasonable phylogenetic position; those from individual protein-coding genes and the concatenated 22 tRNA genes alone, however, did not reproduce the expected phylogeny with few exceptions, probably owing to insufficient phylogenetic information in these smaller data sets. This result suggests that further taxonomic sampling and sequencing efforts may clarify limits and intra- and interrelationships of this morphologically and ecologically diverse group of fishes using mitochondrial genomic (mitogenomic) data. Received: August 31, 2000 / Revised: December 20, 2000 / Accepted: January 23, 2001  相似文献
7.
Recent studies have demonstrated that deviations from the typical vertebrate mitochondrial gene order are more frequent than initially thought. Such deviations, however, are minor, with inversions and/or translocations of a few genes being involved and tandem duplication of the gene regions followed by deletions of genes having been invoked as mechanisms originating in such novel gene order. During the course of molecular phylogenetic studies on the Elopomorpha (eels and their allies), we found that mitochondrial genomes (mitogenomes) from the two deep-sea gulper eels, Eurypharynx pelecanoides (Eurypharyngidae) and Saccopharynx lavenbergi (Saccopharyngidae), exhibit an identical gene order which greatly differs from that of any other vertebrates. Phylogenetic analysis using the mitogenomic data from 59 species of fish not only confirmed a single origin of such a gene order with confidence but also indicated that it had been derived from the typical vertebrate gene order. Detailed comparisons of the gulper eel gene order with that of typical vertebrates suggested that occurrence of a single step, large-scale duplication of gene region extending >12 kb, followed by deletions of genes in a common ancestor of the two species, most parsimoniously accounts for this unusual gene arrangement.  相似文献
8.
An approach for sequencing the entire mitochondrial genomes (mitogenomes) of decapod crustaceans using 79 newly designed and 7 published polymerase chain reaction (PCR) primers is described. The approach comprises the following steps: (1) the entire mitogenome is amplified in 2 or 3 long PCRs; (2) the 86 primers are used in different combinations to amplify contiguous, overlapping short segments of the entire mitogenome with the diluted long PCR products as templates; (3) direct cycle sequencing is conducted using the short PCR products. This strategy allows a more rapid determination of decapod mitogenomic sequences than a traditional method using cloned mitochondrial DNA and primer walking strategy. As a practical example, the mitogenomic sequence for a kuruma prawn Marsupenaeus japonicus (Crustacea: Decapoda), was determined using the PCR-based approach.  相似文献
9.
Partitioned Bayesian analysis of whole mitochondrial genome sequences from 30 basal teleosts confidently placed Sundasalanx (Sundasalangidae) within the Clupeiformes, not Osmeriformes as originally thought. This study represents the first demonstration of the phylogenetic position of Sundasalanx on a phylogenetic tree.  相似文献
10.
The complete sequence of the mitochondrial genome of Leptorhynchoides thecatus (Acanthocephala) was determined, and a phylogenetic analysis was carried out to determine its placement within Metazoa. The genome is circular, 13,888 bp, and contains at least 36 of the 37 genes typically found in animal mitochondrial genomes. The genes for the large and small ribosomal RNA subunits are shorter than those of most metazoans, and the structures of most of the tRNA genes are atypical. There are two significant noncoding regions (377 and 294 bp), which are the best candidates for a control region; however, these regions do not appear similar to any of the control regions of other animals studied to date. The amino acid and nucleotide sequences of the protein coding genes of L. thecatus and 25 other metazoan taxa were used in both maximum likelihood and maximum parsimony phylogenetic analyses. Results indicate that among taxa with available mitochondrial genome sequences, Platyhelminthes is the closest relative to L. thecatus, which together are the sister taxon of Nematoda; however, long branches and/or base composition bias could be responsible for this result. The monophyly of Ecdysozoa, molting organisms, was not supported by any of the analyses. This study represents the first mitochondrial genome of an acanthocephalan to be sequenced and will allow further studies of systematics, population genetics, and genome evolution.Reviewing Editor: Dr. Rafael Zardoya The entire genome sequence has been deposited with the GenBank Data Libraries under-accession number AY562383.  相似文献
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