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The lasting after-effects of an ancient polyploidy on the genomes of teleosts

Conant, Gavin C.·2020·PLOS ONE
DOI 10.1371/journal.pone.0231356PMC PMC7161988

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  • It remains unclear whether the teleost whole-genome duplication corresponds to an ancestral auto- or allotetraploidization event.

    “It remains unclear whether the teleost whole-genome duplication corresponds to an ancestral auto- or an allotetraploidization event, a significant gap in our understanding of the early vertebrate evolutionary processes that led to the diversification of teleosts (Martin and Holland 2014; Conant 2020).”

    From An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication (2022) · cites this paper as Conant 2020

  • Previous characterizations of double-conserved syntenic regions in teleosts were limited to regions of highly conserved gene order or small species sets; the largest multispecies data set comprised eight fish species and included about 29% of all genes in DCS regions.

    “Previous characterizations of DCS regions in teleosts were therefore limited to regions of highly conserved gene order or small species sets: the largest multispecies data set comprised eight fish species and included ∼29% of all genes in DCS regions (Conant 2020).”

    From An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication (2022) · cites this paper as Conant 2020

  • Previous observations on a limited subset of genes suggested that the ancestral teleost genome experienced biased gene retention after the TGD.

    “Previous observations on a limited subset of genes have suggested that the ancestral teleost genome has experienced biased gene retention after the TGD (Conant 2020).”

    From An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication (2022) · cites this paper as Conant 2020

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Research works printed but not linked: 127

  1. R Clausen, 1925, Interspecific hybridization in Nicotiana. II. A tetraploid glutinosa-tabacum hybrid, an experimental verification of Winge's hypothesis, Genetics, 10, 278, 10.1093/genetics/10.3.278 · DOI
  2. JS Taylor, 2004, Duplication and divergence: The evolution of new genes and old ideas, Annual Review of Genetics, 38, 615, 10.1146/annurev.genet.38.072902.092831 · DOI
  3. O Garsmeur, 2013, Two Evolutionarily Distinct Classes of Paleopolyploidy, Molecular Biology and Evolution, 31, 448, 10.1093/molbev/mst230 · DOI
  4. S. Ohno, 1970, Evolution by gene duplication, 10.1007/978-3-642-86659-3 · DOI · Paper page
  5. Y Van de Peer, 2017, The evolutionary significance of polyploidy, Nature Reviews Genetics, 18, 411, 10.1038/nrg.2017.26 · DOI
  6. DE Soltis, 2009, Polyploidy and angiosperm diversification, American Journal of Botany, 96, 336, 10.3732/ajb.0800079 · DOI
  7. KH Wolfe, 1997, Molecular evidence for an ancient duplication of the entire yeast genome, Nature, 387, 708, 10.1038/42711 · DOI · Paper page
  8. JM Aury, 2006, Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, 444, 171, 10.1038/nature05230 · DOI
  9. M Kasahara, 2007, The 2R hypothesis: an update, Current Opinion in Immunology, 19, 547, 10.1016/j.coi.2007.07.009 · DOI
  10. T Makino, 2010, Ohnologs in the human genome are dosage balanced and frequently associated with disease, Proceedings of the National Academy of Sciences, USA, 107, 9270, 10.1073/pnas.0914697107 · DOI
  11. R Blanc-Mathieu, 2017, Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes, PLoS Genetics, 13, e1006777, 10.1371/journal.pgen.1006777 · DOI
  12. EE Schwager, 2017, The house spider genome reveals an ancient whole-genome duplication during arachnid evolution, BMC Biology, 15, 62, 10.1186/s12915-017-0399-x · DOI
  13. I Braasch, 2012, Polyploidy and genome evolution, 341, 10.1007/978-3-642-31442-1_17 · DOI
  14. A Chenuil, 1999, A test of the hypothesis of an autopolyploid vs. allopolyploid origin for a tetraploid lineage: application to the genus Barbus (Cyprinidae), Heredity, 82, 373, 10.1038/sj.hdy.6884890 · DOI
  15. M Alves, 2001, Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review, Genetica, 111, 375, 10.1023/A:1013783029921 · DOI
  16. L Yang, 2015, Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes), Molecular Phylogenetics and Evolution, 85, 97, 10.1016/j.ympev.2015.01.014 · DOI
  17. K Vandepoele, 2004, Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates, Proceedings of the National Academy of Sciences, USA, 101, 1638, 10.1073/pnas.0307968100 · DOI
  18. A Christoffels, 2004, Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes, Molecular Biology and Evolution, 21, 1146, 10.1093/molbev/msh114 · DOI
  19. KD Crow, 2005, The “fish-specific” Hox cluster duplication is coincident with the origin of teleosts, Molecular Biology and Evolution, 23, 121, 10.1093/molbev/msj020 · DOI
  20. S Hoegg, 2004, Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish, Journal of Molecular Evolution, 59, 190, 10.1007/s00239-004-2613-z · DOI
  21. M Sémon, 2007, Rearrangement rate following the whole-genome duplication in teleosts, Molecular Biology and Evolution, 24, 860, 10.1093/molbev/msm003 · DOI
  22. JH Postlethwait, 1998, Vertebrate genome evolution and the zebrafish gene map, Nature Genetics, 18, 345, 10.1038/ng0498-345 · DOI
  23. A Meyer, 1999, Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions, Current Opinion in Cell Biology, 11, 699, 10.1016/S0955-0674(99)00039-3 · DOI
  24. Y. Van de Peer, 2004, Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids, Genome Biology, 5, 250, 10.1186/gb-2004-5-12-250 · DOI
  25. S Aparicio, 2002, Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes, Science, 297, 1301, 10.1126/science.1072104 · DOI · Paper page
  26. EM Kollitz, 2014, Functional diversification of vitamin D receptor paralogs in teleost fish after a whole genome duplication event, Endocrinology, 155, 4641, 10.1210/en.2014-1505 · DOI
  27. Y Moriyama, 2016, Evolution of the fish heart by sub/neofunctionalization of an elastin gene, Nature Communications, 7, 10397, 10.1038/ncomms10397 · DOI
  28. D Steinke, 2006, Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates, BMC Biology, 4, 16, 10.1186/1741-7007-4-16 · DOI
  29. KH Wolfe, 2000, Robustness: It’s not where you think it is, Nature Genetics, 25, 3, 10.1038/75560 · DOI
  30. A Force, 1999, Preservation of duplicate genes by complementary, degenerative mutations, Genetics, 151, 1531, 10.1093/genetics/151.4.1531 · DOI · Paper page
  31. B Guo, 2012, Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication, Molecular Biology and Evolution, 29, 3005, 10.1093/molbev/mss108 · DOI
  32. K Naruse, 2004, A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping, Genome Research, 14, 820, 10.1101/gr.2004004 · DOI
  33. M Semon, 2007, Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor, Trends in Genetics, 23, 108, 10.1016/j.tig.2007.01.003 · DOI
  34. DR Scannell, 2006, Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts, Nature, 440, 341, 10.1038/nature04562 · DOI
  35. CR Werth, 1991, A Model for Divergent, Allopatric Speciation of Polyploid Pteridophytes Resulting from Silencing of Duplicate-Gene Expression, American Naturalist, 137, 515, 10.1086/285180 · DOI
  36. JS Taylor, 2001, Comparative genomics provides evidence for an ancient genome duplication event in fish, Philosophical Transactions of the Royal Society B: Biological Sciences, 356, 1661, 10.1098/rstb.2001.0975 · DOI
  37. J Inoue, 2015, Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling, Proceedings of the National Academy of Sciences, USA, 112, 14918, 10.1073/pnas.1507669112 · DOI · Paper page
  38. CL McGrath, 2014, Differential retention and divergent resolution of duplicate genes following whole-genome duplication, Genome Research, 24, 1665, 10.1101/gr.173740.114 · DOI
  39. A Zwaenepoel, 2019, Finding evidence for whole genome duplications: a reappraisal, Molecular plant, 12, 133, 10.1016/j.molp.2018.12.019 · DOI
  40. Y Nakatani, 2019, Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects, Proceedings of the National Academy of Sciences, 116, 1816, 10.1073/pnas.1817937116 · DOI
  41. S Hoegg, 2007, Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni, BMC Genomics, 8, 317, 10.1186/1471-2164-8-317 · DOI
  42. M. Freeling, 2009, Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition, Annual Review of Plant Biology, 60, 433, 10.1146/annurev.arplant.043008.092122 · DOI
  43. M Freeling, 2006, Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity, Genome Research, 16, 805, 10.1101/gr.3681406 · DOI
  44. JA Birchler, 2007, The gene balance hypothesis: from classical genetics to modern genomics, Plant Cell, 19, 395, 10.1105/tpc.106.049338 · DOI
  45. PP Edger, 2009, Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes, Chromosome research: an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 17, 699, 10.1007/s10577-009-9055-9 · DOI
  46. GC Conant, 2014, Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time, Current opinion in plant biology, 19, 91, 10.1016/j.pbi.2014.05.008 · DOI
  47. RA Veitia, 2015, Gene dosage imbalances: action, reaction, and models, Trends in Biochemical Sciences, 40, 309, 10.1016/j.tibs.2015.03.011 · DOI
  48. B Papp, 2003, Dosage sensitivity and the evolution of gene families in yeast, Nature, 424, 194, 10.1038/nature01771 · DOI · Paper page
  49. JA Birchler, 2012, Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines, Proc Natl Acad Sci U S A, 109, 14746, 10.1073/pnas.1207726109 · DOI
  50. Jr GL Stebbins, 1947, Advances in genetics, 403
  51. BC Thomas, 2006, Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes, Genome Research, 16, 934, 10.1101/gr.4708406 · DOI
  52. H Tang, 2012, Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy, Genetics, 190, 1563, 10.1534/genetics.111.137349 · DOI
  53. JC Schnable, 2011, Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss, Proceedings of the National Academy of Sciences, USA, 108, 4069, 10.1073/pnas.1101368108 · DOI
  54. D Sankoff, 2010, The collapse of gene complement following whole genome duplication, BMC Genomics, 11, 313, 10.1186/1471-2164-11-313 · DOI
  55. M Emery, 2018, Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization, PLoS Genetics, 14, e1007267em, 10.1371/journal.pgen.1007267 · DOI
  56. JF Wendel, 2018, The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation, Current Opinion in Genetics & Development, 49, 1, 10.1016/j.gde.2018.01.004 · DOI · Paper page
  57. KA Bird, 2018, The causes and consequences of subgenome dominance in hybrids and recent polyploids, New Phytologist
  58. GC Conant, 2008, Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast, Genetics, 179, 1681, 10.1534/genetics.107.074450 · DOI
  59. A Schoonmaker, 2020, A single, shared triploidy in three species of parasitic nematodes, G3: Genes, Genomes, Genetics, 10, 225, 10.1534/g3.119.400650 · DOI
  60. KP Byrne, 2005, The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species, Genome Research, 15, 1456, 10.1101/gr.3672305 · DOI · Paper page
  61. J. Felsenstein, 1981, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, 17, 368, 10.1007/BF01734359 · DOI · Paper page
  62. JL Gordon, 2009, Additions, losses and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome, PLoS Genetics, 5, e1000485, 10.1371/journal.pgen.1000485 · DOI
  63. GC Conant, 2014, Comparative genomics as a time machine: How relative gene dosage and metabolic requirements shaped the time-dependent resolution of yeast polyploidy, Molecular Biology and Evolution, 31, 3184, 10.1093/molbev/msu250 · DOI
  64. LJ Jensen, 2008, eggNOG: automated construction and annotation of orthologous groups of genes, Nucleic Acids Research, 36, D250
  65. L Li, 2003, OrthoMCL: identification of ortholog groups for eukaryotic genomes, Genome Research, 13, 2178, 10.1101/gr.1224503 · DOI · Paper page
  66. M Marcet-Houben, 2015, Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage, PLoS biology, 13, e1002220, 10.1371/journal.pbio.1002220 · DOI
  67. JC Pires, 2016, Robust Yet Fragile: Expression Noise, Protein Misfolding and Gene Dosage in the Evolution of Genomes, Annual Review of Genetics, 50, 113, 10.1146/annurev-genet-120215-035400 · DOI
  68. JM Raser, 2005, Noise in gene expression: origins, consequences, and control, Science, 309, 2010, 10.1126/science.1105891 · DOI
  69. DG Howe, 2013, ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics, Nucleic Acids Research, 41, D854
  70. H Aanes, 2011, Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition, Genome Research, 21, 1328, 10.1101/gr.116012.110 · DOI · Paper page
  71. Y Benjamini, 1995, Controlling the false discovery rate: A practical and powerful approach to multiple testing, Journal of the Royal Statistical Society, Series B (Methodological), 57, 289, 10.1111/j.2517-6161.1995.tb02031.x · DOI · Paper page
  72. H Mi, 2017, PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements, Nucleic Acids Research, 45, D183, 10.1093/nar/gkw1138 · DOI
  73. J Roux, 2017, Selective constraints on coding sequences of nervous system genes are a major determinant of duplicate gene retention in vertebrates, Molecular biology and evolution, 34, 2773, 10.1093/molbev/msx199 · DOI
  74. A. Lyall, 1957, Cone arrangements in teleost retinae, Journal of Cell Science, 3, 189, 10.1242/jcs.s3-98.42.189 · DOI
  75. K. Engström, 1960, Cone types and cone arrangement in the retina of some cyprinids, Acta Zoologica, 41, 277, 10.1111/j.1463-6395.1960.tb00481.x · DOI
  76. DL Stenkamp, 2002, Cellular pattern formation in the retina: retinal regeneration as a model system, Molecular Vision, 8, 280
  77. JM Sukeena, 2016, Characterization and evolution of the spotted gar retina, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 326, 403, 10.1002/jez.b.22710 · DOI
  78. SE McGaugh, 2014, The cavefish genome reveals candidate genes for eye loss, Nature Communications, 5, 5307, 10.1038/ncomms6307 · DOI
  79. G Koscielny, 2013, The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data, Nucleic Acids Research, 42, D802, 10.1093/nar/gkt977 · DOI
  80. M. Bekaert, 2012, Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation, PLoS ONE, 7, e49903, 10.1371/journal.pone.0049903 · DOI
  81. DJ Watts, 1998, Collective dynamics of 'small-world' networks, Nature, 393, 440, 10.1038/30918 · DOI · Paper page
  82. MW Hahn, 2005, Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks, Molecular Biology and Evolution, 22, 803, 10.1093/molbev/msi072 · DOI · Paper page
  83. T Xie, 2016, Spatial colocalization of human ohnolog pairs acts to maintain dosage-balance, Molecular Biology and Evolution, 33, 2368, 10.1093/molbev/msw108 · DOI
  84. M Bekaert, 2011, Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative followed by absolute dosage constraints, The Plant Cell, 23, 1719, 10.1105/tpc.110.081281 · DOI
  85. KA Christensen, 2017, Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar), PloS one, 12, 10.1371/journal.pone.0173053 · DOI
  86. T Makino, 2012, Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant, Genome research, 22, 2427, 10.1101/gr.131953.111 · DOI
  87. J Roux, 2008, Developmental constraints on vertebrate genome evolution, PLoS Genet, 4, e1000311, 10.1371/journal.pgen.1000311 · DOI
  88. R De Smet, 2013, Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants, Proceedings of the National Academy of Sciences, USA, 110, 2898, 10.1073/pnas.1300127110 · DOI
  89. PWH Holland, 1994, Gene Duplications and the Origins of Vertebrate Development, Development, 125, 10.1242/dev.1994.Supplement.125 · DOI
  90. E Parey, 2020, Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications, BioRxiv
  91. PA Raymond, 2004, A moving wave patterns the cone photoreceptor mosaic array in the zebrafish retina, International Journal of Developmental Biology, 48, 935, 10.1387/ijdb.041873pr · DOI
  92. K Guschanski, 2017, The evolution of duplicate gene expression in mammalian organs, Genome research, 27, 1461, 10.1101/gr.215566.116 · DOI
  93. S Varadharajan, 2018, The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication, Genome Biol Evol, 10, 2785, 10.1093/gbe/evy201 · DOI
  94. M Satake, 2012, Evolution of vertebrate tissues driven by differential modes of gene duplication, DNA Res, 19, 305, 10.1093/dnares/dss012 · DOI
  95. PP Singh, 2012, On the expansion of “dangerous” gene repertoires by whole-genome duplications in early vertebrates, Cell reports, 2, 1387, 10.1016/j.celrep.2012.09.034 · DOI
  96. I Braasch, 2016, The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons, Nature Genetics, 48, 427, 10.1038/ng.3526 · DOI
  97. RV Rohlfs, 2015, Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution, Syst Biol, 64, 695, 10.1093/sysbio/syv042 · DOI
  98. S Woods, 2013, Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses, PLoS Genetics, 9, e1003330, 10.1371/journal.pgen.1003330 · DOI
  99. A Deluna, 2008, Exposing the fitness contribution of duplicated genes, Nature Genetics
  100. T Makino, 2009, The complex relationship of gene duplication and essentiality, Trends in Genetics, 25, 152, 10.1016/j.tig.2009.03.001 · DOI
  101. GC Conant, 2004, Duplicate genes and robustness to transient gene knockouts in Caenorhabditis elegans, Proceedings of the Royal Society, Biological Sciences, 271, 89, 10.1098/rspb.2003.2560 · DOI
  102. A Merico, 2007, Fermentative lifestyle in yeasts belonging to the Saccharomyces complex, FEBS Journal, 274, 976, 10.1111/j.1742-4658.2007.05645.x · DOI
  103. MJ van Hoek, 2009, Metabolic adaptation after whole genome duplication, Molecular Biology and Evolution, 26, 2441, 10.1093/molbev/msp160 · DOI
  104. GC Conant, 2007, Increased glycolytic flux as an outcome of whole-genome duplication in yeast, Molecular Systems Biology, 3, 129, 10.1038/msb4100170 · DOI · Paper page
  105. PP Edger, 2015, The butterfly plant arms-race escalated by gene and genome duplications, Proceedings of the National Academy of Sciences, USA, 112, 8362, 10.1073/pnas.1503926112 · DOI
  106. M Kasahara, 2007, The medaka draft genome and insights into vertebrate genome evolution, Nature, 447, 714, 10.1038/nature05846 · DOI · Paper page
  107. M Schartl, 2013, The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits, Nature Genetics, 45, 567, 10.1038/ng.2604 · DOI
  108. FC Jones, 2012, The genomic basis of adaptive evolution in threespine sticklebacks, Nature, 484, 55, 10.1038/nature10944 · DOI
  109. D Brawand, 2014, The genomic substrate for adaptive radiation in African cichlid fish, Nature, 513, 375, 10.1038/nature13726 · DOI
  110. GC Conant, 2002, GenomeHistory: A software tool and its application to fully sequenced genomes, Nucleic Acids Research, 30, 3378, 10.1093/nar/gkf449 · DOI
  111. SF Altschul, 1997, Gapped Blast and Psi-Blast: A new-generation of protein database search programs, Nucleic Acids Research, 25, 3389, 10.1093/nar/25.17.3389 · DOI · Paper page
  112. Y Nakatani, 2017, Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes, Bioinformatics, 33, i369, 10.1093/bioinformatics/btx259 · DOI · Paper page
  113. S Kirkpatrick, 1983, Optimization by simulated annealing, Science, 220, 671, 10.1126/science.220.4598.671 · DOI · Paper page
  114. GC Conant, 2006, Functional partitioning of yeast co-expression networks after genome duplication, PLoS biology, 4, e109, 10.1371/journal.pbio.0040109 · DOI
  115. D Sankoff, 1998, Multiple genome rearrangement and breakpoint phylogeny, Journal of Computational Biology, 5, 555, 10.1089/cmb.1998.5.555 · DOI
  116. C Notredame, 2000, T-Coffee: A novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, 302, 205, 10.1006/jmbi.2000.4042 · DOI
  117. S Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Systematic Biology, 52, 696, 10.1080/10635150390235520 · DOI
  118. J. Felsenstein, 1978, Cases in which parsimony or compatibility methods will be positively misleading, Systematic Zoology, 27, 401, 10.2307/2412923 · DOI · Paper page
  119. K Scienski, 2015, Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex, Genome Biology and Evolution, 7, 3249, 10.1093/gbe/evv216 · DOI
  120. AM Evangelisti, 2010, Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling, Genome Biology and Evolution, 2, 826, 10.1093/gbe/evq067 · DOI
  121. K Chen, 2000, NOTUNG: a program for dating gene duplications and optimizing gene family trees, Journal of Computational Biology, 7, 429, 10.1089/106652700750050871 · DOI
  122. RR Sokal, 1995, Biometry
  123. TJ Near, 2012, Resolution of ray-finned fish phylogeny and timing of diversification, Proceedings of the National Academy of Sciences, USA, 109, 13698, 10.1073/pnas.1206625109 · DOI · Paper page
  124. PP Singh, 2020, OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates, Nucleic acids research, 48, D724
  125. H Mi, 2013, Large-scale gene function analysis with the PANTHER classification system, Nature Protocols, 8, 1551, 10.1038/nprot.2013.092 · DOI
  126. M Bekaert, 2011, Copy number alterations among mammalian enyzmes cluster in the metabolic network, Molecular Biology and Evolution, 28, 1111, 10.1093/molbev/msq296 · DOI
  127. Y Hao, 2020, Baby genomics: tracing the evolutionary changes that gave rise to placentation, Genome Biol Evol

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Metadata

Authors
Conant, G. C.
ORCID
Conant, Gavin C.
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2020-04-16
Volume
15
Issue
4
Pages
e0231356
ISSN
1932-6203
DOI
10.1371/journal.pone.0231356
PMC
PMC7161988
Cited by
42
References
8
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Division of Integrative Organismal Systems (NSF-IOS-1339156)
  • Division of Computing and Communication Foundations (NSF-CCF-1421765)

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