DOI: 10.1093/gbe/evq071. Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method

Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method

10.1093/gbe/evq071

Crossref journal-article

Oxford University Press (OUP)

Genome Biology and Evolution (286)

Bibliography

Kamneva, O. K., Liberles, D. A., & Ward, N. L. (2010). Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method. Genome Biology and Evolution, 2, 870â886.

Authors 3

Olga K. Kamneva (first)
David A. Liberles (additional)
Naomi L. Ward (additional)

References 96 Referenced 19

10.1093/bioinformatics/bti263 / Bioinformatics / ProtTest: selection of best-fit models of protein evolution by Abascal (2005)
10.1002/prot.20550 / Proteins / Large-scale prediction of function shift in protein families with a focus on enzymatic function by Abhiman (2005)
10.1016/S0022-2836(05)80360-2 / J Mol Biol. / Basic local alignment search tool by Altschul (1990)
10.1038/sj.hdy.6801052 / Heredity / The quest for natural selection in the age of comparative genomics by Anisimova (2007)
10.1016/0065-2571(91)90012-B / Adv Enzyme Regul. / Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases by Benner (1991)
10.1016/S0065-2571(97)00019-8 / Adv Enzyme Regul. / Post-genomic science: converting primary structure into physiological function by Benner (1998)
10.1007/s00239-005-0096-1 / J Mol Evol. / Optimal gene trees from sequences and species trees using a soft interpretation of parsimony by Berglund-Sonnhammer (2006)
10.1093/nar/gkg151 / Nucleic Acids Res. / Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information by Blouin (2003)
10.1534/genetics.107.070805 / Genetics / The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: a high frequency of deletions in tandem duplicates by Brandstrom (2007)
10.1073/pnas.172510699 / Proc Natl Acad Sci U S A. / Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels by Britten (2002)
10.1073/pnas.0330964100 / Proc Natl Acad Sci U S A. / Majority of divergence between closely related DNA samples is due to indels by Britten (2003)
10.1186/1471-2105-8-227 / BMC Bioinformatics / Relationship between insertion/deletion (indel) frequency of proteins and essentiality by Chan (2007)
10.1016/j.jmb.2004.05.045 / J Mol Biol. / Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments by Chang (2004)
{'key': 'key\n\t\t\t\t20180618192339_bib14', 'first-page': '415', 'article-title': 'Scanning for the signatures of positive selection for human-specific insertions and deletions', 'volume': '2009', 'author': 'Chen', 'year': '2010', 'journal-title': 'Genome Biol Evol.'} / Genome Biol Evol. / Scanning for the signatures of positive selection for human-specific insertions and deletions by Chen (2010)
10.1111/j.1462-2920.2004.00614.x / Environ Microbiol. / Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae by Cho (2004)
10.1126/science.1088821 / Science / Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios by Clark (2003)
10.1021/bi026343m / Biochemistry / Structure and function of the C-terminal domain of methionyl-tRNA synthetase by Crepin (2002)
10.1021/bi0356247 / Biochemistry / Three-dimensional structure of methionyl-tRNA synthetase from Pyrococcus abyssi by Crepin (2004)
10.1007/s00239-001-0029-6 / J Mol Evol. / Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori by Davids (2002)
{'key': 'key\n\t\t\t\t20180618192339_bib20', 'first-page': '345', 'volume': '5', 'author': 'Dayhoff', 'year': '1978', 'journal-title': 'A model of evolutionary change in proteins. Atlas of protein sequence and structure. Washington (DC): National Biomedical Research Foundation'} / A model of evolutionary change in proteins. Atlas of protein sequence and structure. Washington (DC): National Biomedical Research Foundation by Dayhoff (1978)
{'key': 'key\n\t\t\t\t20180618192339_bib21', 'volume-title': 'The PyMOL user’s manual', 'author': 'DeLano', 'year': '2002'} / The PyMOL user’s manual by DeLano (2002)
{'issue': '1 Suppl', 'key': 'key\n\t\t\t\t20180618192339_bib22', 'article-title': 'Identifying dramatic selection shifts in phylogenetic trees', 'volume': '7', 'author': 'Dorman', 'year': '2007', 'journal-title': 'BMC Evol Biol.'} / BMC Evol Biol. / Identifying dramatic selection shifts in phylogenetic trees by Dorman (2007)
10.1093/nar/gkh340 / Nucleic Acids Res. / MUSCLE: multiple sequence alignment with high accuracy and high throughput by Edgar (2004)
10.1186/1471-2105-5-123 / BMC Bioinformatics / GASP: gapped ancestral sequence prediction for proteins by Edwards (2004)
10.1098/rstb.1994.0083 / Philos Trans R Soc Lond B Biol Sci. / Biodiversity at the molecular level: the domains, kingdoms and phyla of life by Embley (1994)
{'key': 'key\n\t\t\t\t20180618192339_bib26', 'first-page': '164', 'article-title': 'PHYLIP—phylogeny inference package (version 3.2)', 'volume': '5', 'author': 'Felsenstein', 'year': '1989', 'journal-title': 'Cladistics'} / Cladistics / PHYLIP—phylogeny inference package (version 3.2) by Felsenstein (1989)
10.1128/AEM.70.6.3724-3732.2004 / Appl Environ Microbiol. / Discovery of the novel candidate phylum “Poribacteria” in marine sponges by Fieseler (2004)
10.2307/2412116 / Syst Zool. / Toward defining the course of evolution: minimum change for a specific tree topology by Fitch (1971)
10.1146/annurev.micro.59.030804.121258 / Annu Rev Microbiol. / Intracellular compartmentation in planctomycetes by Fuerst (2005)
10.1073/pnas.88.18.8184 / Proc Natl Acad Sci U S A. / Membrane-bounded nucleoid in the eubacterium Gemmatata obscuriglobus by Fuerst (1991)
10.1126/science.1179709 / Science / The structure of the ribosome with elongation factor G trapped in the posttranslocational state by Gao (2009)
10.1016/j.gene.2003.09.030 / Gene / Insertion-deletion biases and the evolution of genome size by Gregory (2004)
10.1099/mic.0.2007/009118-0 / Microbiology / Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae by Griffiths (2007)
10.1093/oxfordjournals.molbev.a026080 / Mol Biol Evol. / Statistical methods for testing functional divergence after gene duplication by Gu (1999)
10.1093/oxfordjournals.molbev.a003824 / Mol Biol Evol. / Maximum-likelihood approach for gene family evolution under functional divergence by Gu (2001)
{'key': 'key\n\t\t\t\t20180618192339_bib36', 'first-page': '546', 'article-title': 'Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites', 'volume': '12', 'author': 'Gu', 'year': '1995', 'journal-title': 'Mol Biol Evol.'} / Mol Biol Evol. / Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites by Gu (1995)
10.1023/A:1000348616863 / Antonie van Leeuwenhoek / Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter by Hedlund (1997)
10.1073/pnas.89.22.10915 / Proc Natl Acad Sci U S A. / Amino acid substitution matrices from protein blocks by Henikoff (1992)
10.1146/annurev.micro.62.081307.162818 / Annu Rev Microbiol. / Chlamydiae as symbionts in eukaryotes by Horn (2008)
10.1093/molbev/msj030 / Mol Biol Evol. / Application of phylogenetic networks in evolutionary studies by Huson (2006)
10.1073/pnas.0711742105 / Proc Natl Acad Sci U S A. / Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB by Javelle (2008)
10.1007/s002390010170 / J Mol Evol. / Phylogenetic analysis of evolutionary relationships of the planctomycete division of the domain bacteria based on amino acid sequences of elongation factor Tu by Jenkins (2001)
10.1006/jmbi.1999.3091 / J Mol Biol. / Protein secondary structure prediction based on position-specific scoring matrices by Jones (1999)
{'key': 'key\n\t\t\t\t20180618192339_bib44', 'first-page': '275', 'article-title': 'The rapid generation of mutation data matrices from protein sequences', 'volume': '8', 'author': 'Jones', 'year': '1992', 'journal-title': 'Comput Appl Biosci.'} / Comput Appl Biosci. / The rapid generation of mutation data matrices from protein sequences by Jones (1992)
10.1093/nar/gkp896 / Nucleic Acids Res. / KEGG for representation and analysis of molecular networks involving diseases and drugs by Kanehisa (2010)
10.1073/pnas.251526398 / Proc Natl Acad Sci U S A. / A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins by Knudsen (2001)
10.1186/1471-2180-9-5 / BMC Microbiol. / Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum planctomycetes by Lee (2009)
10.1186/gb-2007-8-5-r71 / Genome Biol. / Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition by Lefébure (2007)
10.1101/gr.089250.108 / Genome Res. / Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter by Lefebure (2009)
10.1101/gr.1224503 / Genome Res. / OrthoMCL: identification of ortholog groups for eukaryotic genomes by Li (2003)
10.1093/oxfordjournals.molbev.a003745 / Mol Biol Evol. / Evaluation of methods for determination of a reconstructed history of gene sequence evolution by Liberles (2001)
10.1186/gb-2001-2-8-research0028 / Genome Biol. / The adaptive evolution database (TAED) by Liberles (2001)
10.1007/s002030100280 / Arch Microbiol. / Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell by Lindsay (2001)
10.1073/pnas.1001085107 / Proc Natl Acad Sci U S A. / Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus by Lonhienne (2010)
10.1073/pnas.0910756107 / Proc Natl Acad Sci U S A. / The structural and energetic basis for high selectivity in a high-affinity protein–protein interaction by Meenan (2010)
10.1038/385151a0 / Nature / Episodic adaptive evolution of primate lysozymes by Messier (1997)
10.1016/S0168-9525(01)02447-7 / Trends Genet. / Deletional bias and the evolution of bacterial genomes by Mira (2001)
10.1186/gb-2001-2-12-research0054 / Genome Biol. / The process of genome shrinkage in the obligate symbiont Buchnera aphidicola by Moran (2001)
10.1073/pnas.0503654102 / Proc Natl Acad Sci U S A. / Bacterial genome size reduction by experimental evolution by Nilsson (2005)
10.1186/1471-2148-8-233 / BMC Evol Biol. / Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes by Orsi (2008)
10.1093/genetics/161.1.299 / Genetics / Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time by Osterberg (2002)
10.1016/0022-2836(92)91008-D / J Mol Biol. / Analysis of insertions/deletions in protein structures by Pascarella (1992)
10.1371/journal.pcbi.1000214 / PLoS Comput Biol. / Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes by Penn (2008)
10.1101/gr.6254707 / Genome Res. / Genes under positive selection in Escherichia coli by Petersen (2007)
10.1023/A:1016076215168 / Genetica / DNA loss and evolution of genome size in Drosophila by Petrov (2002)
10.1128/JB.01797-07 / J Bacteriol. / Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla verrucomicrobia, lentisphaerae, chlamydiae, and planctomycetes and phylogenetic comparison with rRNA genes by Pilhofer (2008)
10.1093/molbev/msi178 / Mol Biol Evol. / Positive selection for indel substitutions in the rodent sperm protein Catsper1 by Podlaha (2005)
10.1073/pnas.2033555100 / Proc Natl Acad Sci U S A. / Positive selection on protein-length in the evolution of a primate sperm ion channel by Podlaha (2003)
10.1098/rspb.2002.2025 / Proc Biol Sci. / A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes by Pupko (2002)
10.1007/BF00160257 / J Mol Evol. / Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA by Reeves (1992)
10.1073/pnas.1001291107 / Proc Natl Acad Sci U S A. / Phylogenetic incongruence arising from fragmented speciation in enteric bacteria by Retchless (2010)
10.1073/pnas.95.11.6239 / Proc Natl Acad Sci U S A. / Genomic evidence for two functionally distinct gene classes by Rivera (1998)
{'key': 'key\n\t\t\t\t20180618192339_bib73', 'first-page': '219', 'article-title': 'Cloning and sequencing of a large fragment of the atpD gene of Pirellula marine—a contribution to the phylogeny of Planctomycetales', 'volume': '7', 'author': 'Roenner', 'year': '1991', 'journal-title': 'Endocyto Cell Res.'} / Endocyto Cell Res. / Cloning and sequencing of a large fragment of the atpD gene of Pirellula marine—a contribution to the phylogeny of Planctomycetales by Roenner (1991)
10.1038/nprot.2010.5 / Nat Protoc. / I-TASSER: a unified platform for automated protein structure and function prediction by Roy (2010)
10.1371/journal.pbio.1000281 / PLoS Biol. / The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins by Santarella-Mellwig (2010)
10.1128/MMBR.68.4.686-691.2004 / Microbiol Mol Biol Rev. / Status of the microbial census by Schloss (2004)
10.1007/s00239-005-0239-4 / J Mol Evol. / Positive selection on nucleotide substitutions and indels in accessory gland proteins of the Drosophila pseudoobscura subgroup by Schully (2006)
10.1093/genetics/142.3.1033 / Genetics / Synonymous nucleotide divergence: what is “saturation”? by Smith (1996)
10.1126/science.1147112 / Science / Genome-wide experimental determination of barriers to horizontal gene transfer by Sorek (2007)
10.1038/307735a0 / Nature / Molecular genetic evidence for early evolutionary origin of budding peptidoglycan-less eubacteria by Stackebrandt (1984)
10.1093/bioinformatics/btl446 / Bioinformatics / RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models by Stamatakis (2006)
10.1101/gr.1977804 / Genome Res. / Occurrence and consequences of coding sequence insertions and deletions in mammalian genomes by Taylor (2004)
10.1016/S0723-2020(11)80028-7 / Syst Appl Microbiol. / About the order of divergence of the major bacterial taxa during evolution by Van de Peer (1994)
10.1038/nsb1197-939 / Nat Struct Mol Biol. / Loop length, intramolecular diffusion and protein folding by Viguera (1997)
10.1016/j.copbio.2006.05.005 / Curr Opin Biotechnol. / The planctomycetes, verrucomicrobia, chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance by Wagner (2006)
10.1186/1471-2148-9-23 / BMC Evol Biol. / Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance by Wang (2009)
10.1099/00207713-50-6-1965 / Int J Syst Evol Microbiol. / Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny by Ward (2000)
{'key': 'key\n\t\t\t\t20180618192339_bib88', 'first-page': '757', 'article-title': 'The order Planctomycetales, including the genera Planctomyces, Pirellula, Gemmata and Isosphaera and the Candidatus genera Brocadia, Kuenenia and Scalindua', 'volume-title': 'The Prokaryotes: a Handbook on the Biology of Bacteria. New York: Springer', 'author': 'Ward', 'year': '2006'} / The Prokaryotes: a Handbook on the Biology of Bacteria. New York: Springer / The order Planctomycetales, including the genera Planctomyces, Pirellula, Gemmata and Isosphaera and the Candidatus genera Brocadia, Kuenenia and Scalindua by Ward (2006)
10.1093/oxfordjournals.molbev.a003851 / Mol Biol Evol. / A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach by Whelan (2001)
{'key': 'key\n\t\t\t\t20180618192339_bib90', 'first-page': '1396', 'article-title': 'Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites', 'volume': '10', 'author': 'Yang', 'year': '1993', 'journal-title': 'Mol Biol Evol.'} / Mol Biol Evol. / Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites by Yang (1993)
10.1093/acprof:oso/9780198567028.001.0001 / Computational molecular evolution by Yang (2006)
10.1093/molbev/msm088 / Mol Biol Evol / PAML 4: Phylogenetic Analysis by Maximum Likelihood by Yang (2007)
10.1093/oxfordjournals.molbev.a004148 / Mol Biol Evol. / Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages by Yang (2002)
10.1093/molbev/msi237 / Mol Biol Evol. / Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level by Zhang (2005)
10.1073/pnas.0406475101 / Proc Natl Acad Sci U S A. / The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli by Zheng (2004)
10.1093/molbev/msq077 / Mol Biol Evol / Detecting positive and purifying selection at synonymous sites in yeast and worm by Zhou (2010)

Dates

Type	When
Created	14 years, 9 months ago (Nov. 3, 2010, 10:27 p.m.)
Deposited	1 year, 5 months ago (March 31, 2024, 8:03 p.m.)
Indexed	1 year, 3 months ago (May 30, 2024, 11 p.m.)
Issued	15 years, 8 months ago (Jan. 1, 2010)
Published	15 years, 8 months ago (Jan. 1, 2010)
Published Online	14 years, 10 months ago (Nov. 3, 2010)
Published Print	15 years, 8 months ago (Jan. 1, 2010)

Funders 0

None

BibTeX

@article{Kamneva_2010, title={Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method}, volume={2}, ISSN={1759-6653}, url={http://dx.doi.org/10.1093/gbe/evq071}, DOI={10.1093/gbe/evq071}, journal={Genome Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Kamneva, Olga K. and Liberles, David A. and Ward, Naomi L.}, year={2010}, month=jan, pages={870–886} }

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      "volume": "31",
      "author": "Benner",
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      "first-page": "155",
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      "volume": "38",
      "author": "Benner",
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    {
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      "first-page": "240",
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      "article-title": "Optimal gene trees from sequences and species trees using a soft interpretation of parsimony",
      "volume": "63",
      "author": "Berglund-Sonnhammer",
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      "journal-title": "J Mol Evol."
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    {
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      "first-page": "790",
      "DOI": "10.1093/nar/gkg151",
      "article-title": "Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information",
      "volume": "31",
      "author": "Blouin",
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      "volume": "176",
      "author": "Brandstrom",
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      "journal-title": "Genetics"
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      "author": "Chan",
      "year": "2007",
      "journal-title": "BMC Bioinformatics"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib13",
      "doi-asserted-by": "crossref",
      "first-page": "617",
      "DOI": "10.1016/j.jmb.2004.05.045",
      "article-title": "Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments",
      "volume": "341",
      "author": "Chang",
      "year": "2004",
      "journal-title": "J Mol Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib14",
      "first-page": "415",
      "article-title": "Scanning for the signatures of positive selection for human-specific insertions and deletions",
      "volume": "2009",
      "author": "Chen",
      "year": "2010",
      "journal-title": "Genome Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib15",
      "doi-asserted-by": "crossref",
      "first-page": "611",
      "DOI": "10.1111/j.1462-2920.2004.00614.x",
      "article-title": "Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae",
      "volume": "6",
      "author": "Cho",
      "year": "2004",
      "journal-title": "Environ Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib16",
      "doi-asserted-by": "crossref",
      "first-page": "1960",
      "DOI": "10.1126/science.1088821",
      "article-title": "Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios",
      "volume": "302",
      "author": "Clark",
      "year": "2003",
      "journal-title": "Science"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib17",
      "doi-asserted-by": "crossref",
      "first-page": "13003",
      "DOI": "10.1021/bi026343m",
      "article-title": "Structure and function of the C-terminal domain of methionyl-tRNA synthetase",
      "volume": "41",
      "author": "Crepin",
      "year": "2002",
      "journal-title": "Biochemistry"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib18",
      "doi-asserted-by": "crossref",
      "first-page": "2635",
      "DOI": "10.1021/bi0356247",
      "article-title": "Three-dimensional structure of methionyl-tRNA synthetase from Pyrococcus abyssi",
      "volume": "43",
      "author": "Crepin",
      "year": "2004",
      "journal-title": "Biochemistry"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib19",
      "doi-asserted-by": "crossref",
      "first-page": "458",
      "DOI": "10.1007/s00239-001-0029-6",
      "article-title": "Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori",
      "volume": "54",
      "author": "Davids",
      "year": "2002",
      "journal-title": "J Mol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib20",
      "first-page": "345",
      "volume": "5",
      "author": "Dayhoff",
      "year": "1978",
      "journal-title": "A model of evolutionary change in proteins. Atlas of protein sequence and structure. Washington (DC): National Biomedical Research Foundation"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib21",
      "volume-title": "The PyMOL user\u2019s manual",
      "author": "DeLano",
      "year": "2002"
    },
    {
      "issue": "1 Suppl",
      "key": "key\n\t\t\t\t20180618192339_bib22",
      "article-title": "Identifying dramatic selection shifts in phylogenetic trees",
      "volume": "7",
      "author": "Dorman",
      "year": "2007",
      "journal-title": "BMC Evol Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib23",
      "doi-asserted-by": "crossref",
      "first-page": "1792",
      "DOI": "10.1093/nar/gkh340",
      "article-title": "MUSCLE: multiple sequence alignment with high accuracy and high throughput",
      "volume": "32",
      "author": "Edgar",
      "year": "2004",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib24",
      "doi-asserted-by": "crossref",
      "first-page": "123",
      "DOI": "10.1186/1471-2105-5-123",
      "article-title": "GASP: gapped ancestral sequence prediction for proteins",
      "volume": "5",
      "author": "Edwards",
      "year": "2004",
      "journal-title": "BMC Bioinformatics"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib25",
      "doi-asserted-by": "crossref",
      "first-page": "21",
      "DOI": "10.1098/rstb.1994.0083",
      "article-title": "Biodiversity at the molecular level: the domains, kingdoms and phyla of life",
      "volume": "345",
      "author": "Embley",
      "year": "1994",
      "journal-title": "Philos Trans R Soc Lond B Biol Sci."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib26",
      "first-page": "164",
      "article-title": "PHYLIP\u2014phylogeny inference package (version 3.2)",
      "volume": "5",
      "author": "Felsenstein",
      "year": "1989",
      "journal-title": "Cladistics"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib27",
      "doi-asserted-by": "crossref",
      "first-page": "3724",
      "DOI": "10.1128/AEM.70.6.3724-3732.2004",
      "article-title": "Discovery of the novel candidate phylum \u201cPoribacteria\u201d in marine sponges",
      "volume": "70",
      "author": "Fieseler",
      "year": "2004",
      "journal-title": "Appl Environ Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib28",
      "doi-asserted-by": "crossref",
      "first-page": "406",
      "DOI": "10.2307/2412116",
      "article-title": "Toward defining the course of evolution: minimum change for a specific tree topology",
      "volume": "20",
      "author": "Fitch",
      "year": "1971",
      "journal-title": "Syst Zool."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib29",
      "doi-asserted-by": "crossref",
      "first-page": "299",
      "DOI": "10.1146/annurev.micro.59.030804.121258",
      "article-title": "Intracellular compartmentation in planctomycetes",
      "volume": "59",
      "author": "Fuerst",
      "year": "2005",
      "journal-title": "Annu Rev Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib30",
      "doi-asserted-by": "crossref",
      "first-page": "8184",
      "DOI": "10.1073/pnas.88.18.8184",
      "article-title": "Membrane-bounded nucleoid in the eubacterium Gemmatata obscuriglobus",
      "volume": "88",
      "author": "Fuerst",
      "year": "1991",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib31",
      "doi-asserted-by": "crossref",
      "first-page": "694",
      "DOI": "10.1126/science.1179709",
      "article-title": "The structure of the ribosome with elongation factor G trapped in the posttranslocational state",
      "volume": "326",
      "author": "Gao",
      "year": "2009",
      "journal-title": "Science"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib32",
      "doi-asserted-by": "crossref",
      "first-page": "15",
      "DOI": "10.1016/j.gene.2003.09.030",
      "article-title": "Insertion-deletion biases and the evolution of genome size",
      "volume": "324",
      "author": "Gregory",
      "year": "2004",
      "journal-title": "Gene"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib33",
      "doi-asserted-by": "crossref",
      "first-page": "2648",
      "DOI": "10.1099/mic.0.2007/009118-0",
      "article-title": "Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae",
      "volume": "153",
      "author": "Griffiths",
      "year": "2007",
      "journal-title": "Microbiology"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib34",
      "doi-asserted-by": "crossref",
      "first-page": "1664",
      "DOI": "10.1093/oxfordjournals.molbev.a026080",
      "article-title": "Statistical methods for testing functional divergence after gene duplication",
      "volume": "16",
      "author": "Gu",
      "year": "1999",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib35",
      "doi-asserted-by": "crossref",
      "first-page": "453",
      "DOI": "10.1093/oxfordjournals.molbev.a003824",
      "article-title": "Maximum-likelihood approach for gene family evolution under functional divergence",
      "volume": "18",
      "author": "Gu",
      "year": "2001",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib36",
      "first-page": "546",
      "article-title": "Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites",
      "volume": "12",
      "author": "Gu",
      "year": "1995",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib37",
      "doi-asserted-by": "crossref",
      "first-page": "29",
      "DOI": "10.1023/A:1000348616863",
      "article-title": "Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter",
      "volume": "72",
      "author": "Hedlund",
      "year": "1997",
      "journal-title": "Antonie van Leeuwenhoek"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib38",
      "doi-asserted-by": "crossref",
      "first-page": "10915",
      "DOI": "10.1073/pnas.89.22.10915",
      "article-title": "Amino acid substitution matrices from protein blocks",
      "volume": "89",
      "author": "Henikoff",
      "year": "1992",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib39",
      "doi-asserted-by": "crossref",
      "first-page": "113",
      "DOI": "10.1146/annurev.micro.62.081307.162818",
      "article-title": "Chlamydiae as symbionts in eukaryotes",
      "volume": "62",
      "author": "Horn",
      "year": "2008",
      "journal-title": "Annu Rev Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib40",
      "doi-asserted-by": "crossref",
      "first-page": "254",
      "DOI": "10.1093/molbev/msj030",
      "article-title": "Application of phylogenetic networks in evolutionary studies",
      "volume": "23",
      "author": "Huson",
      "year": "2006",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib41",
      "doi-asserted-by": "crossref",
      "first-page": "5040",
      "DOI": "10.1073/pnas.0711742105",
      "article-title": "Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB",
      "volume": "105",
      "author": "Javelle",
      "year": "2008",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib42",
      "doi-asserted-by": "crossref",
      "first-page": "405",
      "DOI": "10.1007/s002390010170",
      "article-title": "Phylogenetic analysis of evolutionary relationships of the planctomycete division of the domain bacteria based on amino acid sequences of elongation factor Tu",
      "volume": "52",
      "author": "Jenkins",
      "year": "2001",
      "journal-title": "J Mol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib43",
      "doi-asserted-by": "crossref",
      "first-page": "195",
      "DOI": "10.1006/jmbi.1999.3091",
      "article-title": "Protein secondary structure prediction based on position-specific scoring matrices",
      "volume": "292",
      "author": "Jones",
      "year": "1999",
      "journal-title": "J Mol Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib44",
      "first-page": "275",
      "article-title": "The rapid generation of mutation data matrices from protein sequences",
      "volume": "8",
      "author": "Jones",
      "year": "1992",
      "journal-title": "Comput Appl Biosci."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib45",
      "doi-asserted-by": "crossref",
      "first-page": "D355",
      "DOI": "10.1093/nar/gkp896",
      "article-title": "KEGG for representation and analysis of molecular networks involving diseases and drugs",
      "volume": "38",
      "author": "Kanehisa",
      "year": "2010",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib46",
      "doi-asserted-by": "crossref",
      "first-page": "14512",
      "DOI": "10.1073/pnas.251526398",
      "article-title": "A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins",
      "volume": "98",
      "author": "Knudsen",
      "year": "2001",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib47",
      "doi-asserted-by": "crossref",
      "first-page": "5",
      "DOI": "10.1186/1471-2180-9-5",
      "article-title": "Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum planctomycetes",
      "volume": "9",
      "author": "Lee",
      "year": "2009",
      "journal-title": "BMC Microbiol."
    },
    {
      "issue": "5",
      "key": "key\n\t\t\t\t20180618192339_bib48",
      "doi-asserted-by": "crossref",
      "first-page": "R71",
      "DOI": "10.1186/gb-2007-8-5-r71",
      "article-title": "Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition",
      "volume": "8",
      "author": "Lef\u00e9bure",
      "year": "2007",
      "journal-title": "Genome Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib49",
      "doi-asserted-by": "crossref",
      "first-page": "1224",
      "DOI": "10.1101/gr.089250.108",
      "article-title": "Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter",
      "volume": "19",
      "author": "Lefebure",
      "year": "2009",
      "journal-title": "Genome Res."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib50",
      "doi-asserted-by": "crossref",
      "first-page": "2178",
      "DOI": "10.1101/gr.1224503",
      "article-title": "OrthoMCL: identification of ortholog groups for eukaryotic genomes",
      "volume": "13",
      "author": "Li",
      "year": "2003",
      "journal-title": "Genome Res."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib51",
      "doi-asserted-by": "crossref",
      "first-page": "2040",
      "DOI": "10.1093/oxfordjournals.molbev.a003745",
      "article-title": "Evaluation of methods for determination of a reconstructed history of gene sequence evolution",
      "volume": "18",
      "author": "Liberles",
      "year": "2001",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib52",
      "doi-asserted-by": "crossref",
      "first-page": "research0028.1",
      "DOI": "10.1186/gb-2001-2-8-research0028",
      "article-title": "The adaptive evolution database (TAED)",
      "volume": "2",
      "author": "Liberles",
      "year": "2001",
      "journal-title": "Genome Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib53",
      "doi-asserted-by": "crossref",
      "first-page": "413",
      "DOI": "10.1007/s002030100280",
      "article-title": "Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell",
      "volume": "175",
      "author": "Lindsay",
      "year": "2001",
      "journal-title": "Arch Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib54",
      "doi-asserted-by": "crossref",
      "first-page": "12883",
      "DOI": "10.1073/pnas.1001085107",
      "article-title": "Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus",
      "volume": "107",
      "author": "Lonhienne",
      "year": "2010",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib55",
      "doi-asserted-by": "crossref",
      "first-page": "10080",
      "DOI": "10.1073/pnas.0910756107",
      "article-title": "The structural and energetic basis for high selectivity in a high-affinity protein\u2013protein interaction",
      "volume": "107",
      "author": "Meenan",
      "year": "2010",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib56",
      "doi-asserted-by": "crossref",
      "first-page": "151",
      "DOI": "10.1038/385151a0",
      "article-title": "Episodic adaptive evolution of primate lysozymes",
      "volume": "385",
      "author": "Messier",
      "year": "1997",
      "journal-title": "Nature"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib57",
      "doi-asserted-by": "crossref",
      "first-page": "589",
      "DOI": "10.1016/S0168-9525(01)02447-7",
      "article-title": "Deletional bias and the evolution of bacterial genomes",
      "volume": "17",
      "author": "Mira",
      "year": "2001",
      "journal-title": "Trends Genet."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib58",
      "doi-asserted-by": "crossref",
      "first-page": "research0054.1",
      "DOI": "10.1186/gb-2001-2-12-research0054",
      "article-title": "The process of genome shrinkage in the obligate symbiont Buchnera aphidicola",
      "volume": "2",
      "author": "Moran",
      "year": "2001",
      "journal-title": "Genome Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib59",
      "doi-asserted-by": "crossref",
      "first-page": "12112",
      "DOI": "10.1073/pnas.0503654102",
      "article-title": "Bacterial genome size reduction by experimental evolution",
      "volume": "102",
      "author": "Nilsson",
      "year": "2005",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib60",
      "doi-asserted-by": "crossref",
      "first-page": "233",
      "DOI": "10.1186/1471-2148-8-233",
      "article-title": "Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes",
      "volume": "8",
      "author": "Orsi",
      "year": "2008",
      "journal-title": "BMC Evol Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib61",
      "doi-asserted-by": "crossref",
      "first-page": "299",
      "DOI": "10.1093/genetics/161.1.299",
      "article-title": "Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time",
      "volume": "161",
      "author": "Osterberg",
      "year": "2002",
      "journal-title": "Genetics"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib62",
      "doi-asserted-by": "crossref",
      "first-page": "461",
      "DOI": "10.1016/0022-2836(92)91008-D",
      "article-title": "Analysis of insertions/deletions in protein structures",
      "volume": "224",
      "author": "Pascarella",
      "year": "1992",
      "journal-title": "J Mol Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib63",
      "doi-asserted-by": "crossref",
      "first-page": "e1000214",
      "DOI": "10.1371/journal.pcbi.1000214",
      "article-title": "Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes",
      "volume": "4",
      "author": "Penn",
      "year": "2008",
      "journal-title": "PLoS Comput Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib64",
      "doi-asserted-by": "crossref",
      "first-page": "1336",
      "DOI": "10.1101/gr.6254707",
      "article-title": "Genes under positive selection in Escherichia coli",
      "volume": "17",
      "author": "Petersen",
      "year": "2007",
      "journal-title": "Genome Res."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib65",
      "doi-asserted-by": "crossref",
      "first-page": "81",
      "DOI": "10.1023/A:1016076215168",
      "article-title": "DNA loss and evolution of genome size in Drosophila",
      "volume": "115",
      "author": "Petrov",
      "year": "2002",
      "journal-title": "Genetica"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib66",
      "doi-asserted-by": "crossref",
      "first-page": "3192",
      "DOI": "10.1128/JB.01797-07",
      "article-title": "Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla verrucomicrobia, lentisphaerae, chlamydiae, and planctomycetes and phylogenetic comparison with rRNA genes",
      "volume": "190",
      "author": "Pilhofer",
      "year": "2008",
      "journal-title": "J Bacteriol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib67",
      "doi-asserted-by": "crossref",
      "first-page": "1845",
      "DOI": "10.1093/molbev/msi178",
      "article-title": "Positive selection for indel substitutions in the rodent sperm protein Catsper1",
      "volume": "22",
      "author": "Podlaha",
      "year": "2005",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib68",
      "doi-asserted-by": "crossref",
      "first-page": "12241",
      "DOI": "10.1073/pnas.2033555100",
      "article-title": "Positive selection on protein-length in the evolution of a primate sperm ion channel",
      "volume": "100",
      "author": "Podlaha",
      "year": "2003",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib69",
      "doi-asserted-by": "crossref",
      "first-page": "1313",
      "DOI": "10.1098/rspb.2002.2025",
      "article-title": "A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes",
      "volume": "269",
      "author": "Pupko",
      "year": "2002",
      "journal-title": "Proc Biol Sci."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib70",
      "doi-asserted-by": "crossref",
      "first-page": "17",
      "DOI": "10.1007/BF00160257",
      "article-title": "Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA",
      "volume": "35",
      "author": "Reeves",
      "year": "1992",
      "journal-title": "J Mol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib71",
      "doi-asserted-by": "crossref",
      "first-page": "11453",
      "DOI": "10.1073/pnas.1001291107",
      "article-title": "Phylogenetic incongruence arising from fragmented speciation in enteric bacteria",
      "volume": "107",
      "author": "Retchless",
      "year": "2010",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib72",
      "doi-asserted-by": "crossref",
      "first-page": "6239",
      "DOI": "10.1073/pnas.95.11.6239",
      "article-title": "Genomic evidence for two functionally distinct gene classes",
      "volume": "95",
      "author": "Rivera",
      "year": "1998",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib73",
      "first-page": "219",
      "article-title": "Cloning and sequencing of a large fragment of the atpD gene of Pirellula marine\u2014a contribution to the phylogeny of Planctomycetales",
      "volume": "7",
      "author": "Roenner",
      "year": "1991",
      "journal-title": "Endocyto Cell Res."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib74",
      "doi-asserted-by": "crossref",
      "first-page": "725",
      "DOI": "10.1038/nprot.2010.5",
      "article-title": "I-TASSER: a unified platform for automated protein structure and function prediction",
      "volume": "5",
      "author": "Roy",
      "year": "2010",
      "journal-title": "Nat Protoc."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib75",
      "doi-asserted-by": "crossref",
      "first-page": "e1000281",
      "DOI": "10.1371/journal.pbio.1000281",
      "article-title": "The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins",
      "volume": "8",
      "author": "Santarella-Mellwig",
      "year": "2010",
      "journal-title": "PLoS Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib76",
      "doi-asserted-by": "crossref",
      "first-page": "686",
      "DOI": "10.1128/MMBR.68.4.686-691.2004",
      "article-title": "Status of the microbial census",
      "volume": "68",
      "author": "Schloss",
      "year": "2004",
      "journal-title": "Microbiol Mol Biol Rev."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib77",
      "doi-asserted-by": "crossref",
      "first-page": "793",
      "DOI": "10.1007/s00239-005-0239-4",
      "article-title": "Positive selection on nucleotide substitutions and indels in accessory gland proteins of the Drosophila pseudoobscura subgroup",
      "volume": "62",
      "author": "Schully",
      "year": "2006",
      "journal-title": "J Mol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib78",
      "doi-asserted-by": "crossref",
      "first-page": "1033",
      "DOI": "10.1093/genetics/142.3.1033",
      "article-title": "Synonymous nucleotide divergence: what is \u201csaturation\u201d?",
      "volume": "142",
      "author": "Smith",
      "year": "1996",
      "journal-title": "Genetics"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib79",
      "doi-asserted-by": "crossref",
      "first-page": "1449",
      "DOI": "10.1126/science.1147112",
      "article-title": "Genome-wide experimental determination of barriers to horizontal gene transfer",
      "volume": "318",
      "author": "Sorek",
      "year": "2007",
      "journal-title": "Science"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib80",
      "doi-asserted-by": "crossref",
      "first-page": "735",
      "DOI": "10.1038/307735a0",
      "article-title": "Molecular genetic evidence for early evolutionary origin of budding peptidoglycan-less eubacteria",
      "volume": "307",
      "author": "Stackebrandt",
      "year": "1984",
      "journal-title": "Nature"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib81",
      "doi-asserted-by": "crossref",
      "first-page": "2688",
      "DOI": "10.1093/bioinformatics/btl446",
      "article-title": "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models",
      "volume": "22",
      "author": "Stamatakis",
      "year": "2006",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib82",
      "doi-asserted-by": "crossref",
      "first-page": "555",
      "DOI": "10.1101/gr.1977804",
      "article-title": "Occurrence and consequences of coding sequence insertions and deletions in mammalian genomes",
      "volume": "14",
      "author": "Taylor",
      "year": "2004",
      "journal-title": "Genome Res."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib83",
      "doi-asserted-by": "crossref",
      "first-page": "32",
      "DOI": "10.1016/S0723-2020(11)80028-7",
      "article-title": "About the order of divergence of the major bacterial taxa during evolution",
      "volume": "17",
      "author": "Van de Peer",
      "year": "1994",
      "journal-title": "Syst Appl Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib84",
      "doi-asserted-by": "crossref",
      "first-page": "939",
      "DOI": "10.1038/nsb1197-939",
      "article-title": "Loop length, intramolecular diffusion and protein folding",
      "volume": "4",
      "author": "Viguera",
      "year": "1997",
      "journal-title": "Nat Struct Mol Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib85",
      "doi-asserted-by": "crossref",
      "first-page": "241",
      "DOI": "10.1016/j.copbio.2006.05.005",
      "article-title": "The planctomycetes, verrucomicrobia, chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance",
      "volume": "17",
      "author": "Wagner",
      "year": "2006",
      "journal-title": "Curr Opin Biotechnol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib86",
      "doi-asserted-by": "crossref",
      "first-page": "23",
      "DOI": "10.1186/1471-2148-9-23",
      "article-title": "Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance",
      "volume": "9",
      "author": "Wang",
      "year": "2009",
      "journal-title": "BMC Evol Biol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib87",
      "doi-asserted-by": "crossref",
      "first-page": "1965",
      "DOI": "10.1099/00207713-50-6-1965",
      "article-title": "Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny",
      "volume": "50",
      "author": "Ward",
      "year": "2000",
      "journal-title": "Int J Syst Evol Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib88",
      "first-page": "757",
      "article-title": "The order Planctomycetales, including the genera Planctomyces, Pirellula, Gemmata and Isosphaera and the Candidatus genera Brocadia, Kuenenia and Scalindua",
      "volume-title": "The Prokaryotes: a Handbook on the Biology of Bacteria. New York: Springer",
      "author": "Ward",
      "year": "2006"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib89",
      "doi-asserted-by": "crossref",
      "first-page": "691",
      "DOI": "10.1093/oxfordjournals.molbev.a003851",
      "article-title": "A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach",
      "volume": "18",
      "author": "Whelan",
      "year": "2001",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib90",
      "first-page": "1396",
      "article-title": "Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites",
      "volume": "10",
      "author": "Yang",
      "year": "1993",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib91",
      "doi-asserted-by": "crossref",
      "DOI": "10.1093/acprof:oso/9780198567028.001.0001",
      "volume-title": "Computational molecular evolution",
      "author": "Yang",
      "year": "2006"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib96",
      "doi-asserted-by": "crossref",
      "first-page": "1586",
      "DOI": "10.1093/molbev/msm088",
      "article-title": "PAML 4: Phylogenetic Analysis by Maximum Likelihood",
      "volume": "24",
      "author": "Yang",
      "year": "2007",
      "journal-title": "Mol Biol Evol"
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib92",
      "doi-asserted-by": "crossref",
      "first-page": "908",
      "DOI": "10.1093/oxfordjournals.molbev.a004148",
      "article-title": "Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages",
      "volume": "19",
      "author": "Yang",
      "year": "2002",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib93",
      "doi-asserted-by": "crossref",
      "first-page": "2472",
      "DOI": "10.1093/molbev/msi237",
      "article-title": "Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level",
      "volume": "22",
      "author": "Zhang",
      "year": "2005",
      "journal-title": "Mol Biol Evol."
    },
    {
      "key": "key\n\t\t\t\t20180618192339_bib94",
      "doi-asserted-by": "crossref",
      "first-page": "17090",
      "DOI": "10.1073/pnas.0406475101",
      "article-title": "The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli",
      "volume": "101",
      "author": "Zheng",
      "year": "2004",
      "journal-title": "Proc Natl Acad Sci U S A."
    },
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      "first-page": "1912",
      "DOI": "10.1093/molbev/msq077",
      "article-title": "Detecting positive and purifying selection at synonymous sites in yeast and worm",
      "volume": "27",
      "author": "Zhou",
      "year": "2010",
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