title: Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales.
abstract: Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.
authors.affiliation: Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.; University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wu
authors.affiliation: Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
authors.forename: Hai-Fei
authors.initials: HF
authors.lastname: Yan
authors.affiliation: Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
authors.forename: Xue-Jun
authors.initials: XJ
authors.lastname: Ge
keywords: Ericales; coalescence methods; concatenation methods; evolving rates; phylogenomics
references.citation: Syst Biol. 2008 Oct;57(5):758-71
references.pmid: 18853362
references.citation: Am J Bot. 2003 Dec;90(12):1758-76
references.pmid: 21653353
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Genome Biol. 2007;8(9):R199
references.pmid: 17883877
references.citation: BMC Evol Biol. 2009 Jul 08;9:157
references.pmid: 19586527
references.citation: PLoS One. 2014 Oct 01;9(10):e107709
references.pmid: 25272037
references.citation: Mol Phylogenet Evol. 2014 Aug;77:25-33
references.pmid: 24732681
references.citation: Nat Commun. 2013;4:2640
references.pmid: 24136039
references.citation: Syst Biol. 2005 Oct;54(5):697-709
references.pmid: 16195214
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17519-24
references.pmid: 23045684
references.citation: BMC Bioinformatics. 2013 Nov 19;14:330
references.pmid: 24252138
references.citation: Am J Bot. 2004 Feb;91(2):262-73
references.pmid: 21653382
references.citation: Ann Bot. 2014 Jan;113(1):119-33
references.pmid: 24280362
references.citation: Am J Bot. 2002 Jan;89(1):132-44
references.pmid: 21669721
references.citation: Proc Biol Sci. 2015 Feb 22;282(1801):20142332
references.pmid: 25589608
references.citation: PLoS Genet. 2011 Dec;7(12):e1002411
references.pmid: 22194700
references.citation: Curr Biol. 2013 Oct 21;23(20):2058-62
references.pmid: 24094856
references.citation: BMC Genomics. 2014 Feb 08;15:112
references.pmid: 24507483
references.citation: Trends Ecol Evol. 1996 Apr;11(4):152-8
references.pmid: 21237790
references.citation: PLoS Biol. 2006 Nov;4(11):e352
references.pmid: 17105342
references.citation: Nucleic Acids Res. 2008 Jun;36(10):3420-35
references.pmid: 18445632
references.citation: Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):14942-7
references.pmid: 22930817
references.citation: J Hered. 2011 Jan-Feb;102(1):130-8
references.pmid: 20696667
references.citation: Syst Biol. 2008 Feb;57(1):38-57
references.pmid: 18275001
references.citation: Mol Biol Evol. 2011 Aug;28(8):2197-210
references.pmid: 21393604
references.citation: DNA Res. 2011 Aug;18(4):253-61
references.pmid: 21676972
references.citation: Syst Biol. 2007 Feb;56(1):17-24
references.pmid: 17366134
references.citation: BMC Evol Biol. 2010 Oct 11;10:302
references.pmid: 20937096
references.citation: Genome Biol Evol. 2011;3:1340-8
references.pmid: 22016337
references.citation: Syst Biol. 2011 Mar;60(2):126-37
references.pmid: 21088009
references.citation: Genetica. 2015 Apr;143(2):195-205
references.pmid: 25681232
references.citation: Ann N Y Acad Sci. 2015 Dec;1360:36-53
references.pmid: 25873435
references.citation: Mol Biol Evol. 2014 Jun;31(6):1500-13
references.pmid: 24674821
references.citation: BMC Genomics. 2014 Jan 17;15:32
references.pmid: 24438217
references.citation: Genome Biol. 2008;9(3):R49
references.pmid: 18315873
references.citation: PLoS One. 2013 Sep 17;8(9):e74394
references.pmid: 24069307
references.citation: Science. 2014 Nov 7;346(6210):763-7
references.pmid: 25378627
references.citation: Mol Phylogenet Evol. 2015 Feb;83:278-92
references.pmid: 25482362
references.citation: BMC Genomics. 2011 Oct 30;12:533
references.pmid: 22035094
references.citation: Am J Bot. 2000 Sep;87(9):1325-41
references.pmid: 10991903
references.citation: Ann Bot. 2014 Apr;113(5):753-61
references.pmid: 24380843
references.citation: Mol Phylogenet Evol. 2004 May;31(2):711-29
references.pmid: 15062805
references.citation: Cladistics. 2013 Feb;29(1):65-87
references.pmid: 34814372
references.citation: Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5936-41
references.pmid: 17392434
references.citation: BMC Plant Biol. 2012 Apr 02;12:46
references.pmid: 22471859
references.citation: Mol Biol Evol. 2015 Jun;32(6):1611-27
references.pmid: 25660373
references.citation: Trends Plant Sci. 2013 Sep;18(9):492-5
references.pmid: 23707196
references.citation: Genome Res. 2007 May;17(5):594-601
references.pmid: 17420184
references.citation: BMC Biol. 2012 Jul 27;10:65
references.pmid: 22839781
references.citation: Mol Biol Evol. 2013 Sep;30(9):2134-44
references.pmid: 23813978
references.citation: Annu Rev Genomics Hum Genet. 2008;9:217-31
references.pmid: 18767964
references.citation: PLoS One. 2013 Nov 21;8(11):e80870
references.pmid: 24278335
references.citation: Mol Phylogenet Evol. 2014 Nov;80:231-66
references.pmid: 25152276
references.citation: Syst Biol. 2013 Sep;62(5):763-85
references.pmid: 23749787
references.citation: Syst Biol. 2008 Feb;57(1):131-40
references.pmid: 18300026
references.citation: Syst Biol. 2007 Jun;56(3):504-14
references.pmid: 17562474
references.citation: Syst Biol. 2004 Feb;53(1):47-67
references.pmid: 14965900
references.citation: Proc Biol Sci. 2014 Jul 7;281(1786):
references.pmid: 24850925
references.citation: Syst Biol. 2004 Dec;53(6):978-89
references.pmid: 15764565
references.citation: BMC Evol Biol. 2014 Mar 20;14(1):52
references.pmid: 24646345
references.citation: Mol Biol Evol. 2015 Aug;32(8):2001-14
references.pmid: 25837578
references.citation: Mol Biol Evol. 2015 Jan;32(1):193-210
references.pmid: 25349287
references.citation: Mol Biol Evol. 2013 Dec;30(12):2725-9
references.pmid: 24132122
references.citation: Evolution. 1985 May;39(3):609-622
references.pmid: 28561973
references.citation: BMC Genomics. 2012 Jun 08;13:227
references.pmid: 22681756
references.citation: Evolution. 1999 Jun;53(3):932-937
references.pmid: 28565639
references.citation: Syst Biol. 2008 Jun;57(3):503-7
references.pmid: 18570042
references.citation: PLoS One. 2013 Nov 21;8(11):e79348
references.pmid: 24278129
references.citation: Nucleic Acids Res. 2013 Jul;41(Web Server issue):W238-41
references.pmid: 23661681
references.citation: Proc Natl Acad Sci U S A. 2010 May 18;107(20):9264-9
references.pmid: 20439743
references.citation: Mol Biol Evol. 2014 Jun;31(6):1391-401
references.pmid: 24567512
references.citation: Am J Bot. 2002 Apr;89(4):677-87
references.pmid: 21665668
references.citation: Am J Bot. 2011 Apr;98(4):704-30
references.pmid: 21613169
references.citation: Mol Phylogenet Evol. 2015 Apr;85:221-9
references.pmid: 25721539
references.citation: Proc Biol Sci. 2014 Aug 7;281(1788):20140970
references.pmid: 24966318
references.citation: BMC Genomics. 2013 May 14;14:329
references.pmid: 23672467
references.citation: Nat Commun. 2014 Sep 24;5:4956
references.pmid: 25249442
references.citation: Genetics. 2003 Aug;164(4):1645-56
references.pmid: 12930768
references.citation: Cladistics. 2007 Jun;23(3):229-294
references.pmid: 34905864
references.citation: Proc Biol Sci. 2014 Nov 7;281(1794):20141739
references.pmid: 25232139
references.citation: Mol Biol Evol. 2013 Dec;30(12):2709-13
references.pmid: 24030555
references.citation: Genome Res. 1999 Sep;9(9):868-77
references.pmid: 10508846
references.citation: Curr Biol. 2014 Aug 18;24(16):1874-9
references.pmid: 25065752
references.citation: J Evol Biol. 2003 Jul;16(4):558-76
references.pmid: 14632220
references.citation: Syst Biol. 2014 Nov;63(6):919-32
references.pmid: 25077515
references.citation: Nature. 2011 Jul 10;475(7355):189-95
references.pmid: 21743474
references.citation: Mol Biol Evol. 2012 Jun;29(6):1695-701
references.pmid: 22319168
references.citation: Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68
references.pmid: 25355905
references.citation: Mol Biol Evol. 2014 Jan;31(1):239-49
references.pmid: 24140757
references.citation: Genome Biol Evol. 2013;5(6):1233-45
references.pmid: 23737327
references.citation: Mol Phylogenet Evol. 2002 Aug;24(2):274-301
references.pmid: 12144762
references.citation: Am J Bot. 2001 Feb;88(2):348-61
references.pmid: 11222255
references.citation: Syst Biol. 2008 Dec;57(6):920-38
references.pmid: 19085333