A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny
[Bernt, Matthias; Middendorf, Martin] Univ Leipzig, Dept Comp Sci, Parallel Comp & Complex Syst Grp, D-04109 Leipzig, Germany; [Bleidorn, Christoph; Schlegel, Martin] Univ Leipzig, Inst Biol, D-04103 Leipzig, Germany; [Braband, Anke] LGC Genom GmbH, D-12459 Berlin, Germany; [Dambach, Johannes; Donath, Alexander; Golombek, Anja; Meusemann, Karen; Misof, Bernhard; Struck, Torsten H.] Zoolog Forschungsmuseum Alexander Koenig ZFMK, Ctr Mol Biodivers Res ZMB, D-53113 Bonn, Germany; [Fritzsch, Guido; Juehling, Frank; Stadler, Peter F.] Univ Leipzig, Interdisciplinary Ctr Bioinformat, Dept Comp Sci, Bioinformat Grp, D-04107 Leipzig, Germany; [Hadrys, Heike; Schierwater, Bernd] TiHo Hannover, ITZ, Ecol & Evolut, D-30559 Hannover, Germany; [Juehling, Frank] Univ Strasbourg, CNRS, IBMC, Architecture & Reactivite ARN, Strasbourg, France; [Perseke, Marleen] Chinese Acad Sci, South China Sea Inst Oceanol, Marine Biol Lab, Guangzhou 510301, Guangdong, Peoples R China; [Podsiadlowski, Lars] Univ Bonn, Inst Evolutionary Biol & Ecol, D-53121 Bonn, Germany; [von Reumont, Bjoern] Nat Hist Museum, Dept Life Sci, London SW7 5BD, England; [Schroedl, Michael; Stoeger, Isabella] Zoolog Staatssammlung Munchen, D-81247 Munich, Germany; [Simon, Sabrina] Amer Museum Nat Hist, Sackler Inst Comparat Gen, New York, NY 10024 USA; [Stadler, Peter F.] Max Planck Inst Math Sci, D-04103 Leipzig, Germany; [Stadler, Peter F.] Fraunhofer Inst Zelltherapie & Immunol, D-04103 Leipzig, Germany; [Stadler, Peter F.] Univ Vienna, Dept Theoret Chem, A-1090 Vienna, Austria; [Stadler, Peter F.] Univ Copenhagen, Ctr Non Coding RNA Technol & Hlth, DK-1870 Frederiksberg, Denmark; [Stadler, Peter F.] Santa Fe Inst, Santa Fe, NM 87501 USA; bernt@informatik.uni-leipzig.de; lars@cgae.de
2013
发表期刊MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN1055-7903
卷号69期号:2页码:352-364
摘要About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches. (C) 2013 Elsevier Inc. All rights reserved.
部门归属LMB
关键词Mitochondrial Genomes Animal Phylogeny
学科领域Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
资助者We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg. ; We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg. ; We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg. ; We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg.
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资助者We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg. ; We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg. ; We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg. ; We thank Omar Rota-Stabelli and Franz Lang for contributing amino acidsequences of additional taxa. This study was supported by the following grants from German Science foundation (DFG) priority programme "Deep Metazoan Phylogeny", SPP 1174: BL 787/2-1, 2 (CB); BA 1520/10-1, 2 (LP); SCHO 442/8-1, 2 (AB); PO 765/4-3 (LP); STA 850/3-2; STA 850/2 (MB, AD, GF, FJ, MM, PFS); STR-683/5-2, 6-1 (THS); SCHL 229/14-1 (MP, M. Schlegel); HA 1947/5 (HH, SSi); SCHR 667/9-1 (IS, M. Schroedl); WA530/34 (BvR); MI 649/7 (BM, KM); Schi-227/20, Schi-227/26-1 (BS). Bv12 received additional support from DFG Grant RE-3454/1-1. SSi received additional support from a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD). FJ was funded by French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]; French-German University (DFH-UFA, Cotutelle de these CT-08-10); a doctoral fellowship of the German Academic Exchange Service [DAAD D/10/43622]; and a bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg.
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条目标识符http://ir.scsio.ac.cn/handle/344004/10977
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通讯作者bernt@informatik.uni-leipzig.de; lars@cgae.de
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[Bernt, Matthias,Middendorf, Martin] Univ Leipzig, Dept Comp Sci, Parallel Comp & Complex Syst Grp, D-04109 Leipzig, Germany,[Bleidorn, Christoph,et al. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2013,69(2):352-364.
APA [Bernt, Matthias.,Middendorf, Martin] Univ Leipzig, Dept Comp Sci, Parallel Comp & Complex Syst Grp, D-04109 Leipzig, Germany.,[Bleidorn, Christoph.,Schlegel, Martin] Univ Leipzig, Inst Biol, D-04103 Leipzig, Germany.,[Braband, Anke] LGC Genom GmbH, D-12459 Berlin, Germany.,...&lars@cgae.de.(2013).A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.MOLECULAR PHYLOGENETICS AND EVOLUTION,69(2),352-364.
MLA [Bernt, Matthias,et al."A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny".MOLECULAR PHYLOGENETICS AND EVOLUTION 69.2(2013):352-364.
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