Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae).
UCEs
anura
exon capture
gene tree estimation error
target capture
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
05 05 2023
05 05 2023
Historique:
accepted:
09
03
2023
medline:
12
5
2023
pubmed:
2
5
2023
entrez:
2
5
2023
Statut:
ppublish
Résumé
An emerging challenge in interpreting phylogenomic data sets is that concatenation and multi-species coalescent summary species tree approaches may produce conflicting results. Concatenation is problematic because it can strongly support an incorrect topology when incomplete lineage sorting (ILS) results in elevated gene-tree discordance. Conversely, summary species tree methods account for ILS to recover the correct topology, but these methods do not account for erroneous gene trees ("EGTs") resulting from gene tree estimation error (GTEE). Third, site-based and full-likelihood methods promise to alleviate GTEE as these methods use the sequence data from alignments. To understand the impact of GTEE on species tree estimation in Hylidae tree frogs, we use an expansive data set of ∼9,000 exons, introns, and ultra-conserved elements and initially found conflict between all three types of analytical methods. We filtered EGTs using alignment metrics that could lead to GTEE (length, parsimony-informative sites, and missing data) and found that removing shorter, less informative alignments reconciled the conflict between concatenation and summary species tree methods with increased gene concordance, with the filtered topologies matching expected results from past studies. Contrarily, site-based and full-likelihood methods were mixed where one method was consistent with past studies and the other varied markedly. Critical to other studies, these results suggest a widespread conflation of ILS and GTEE, where EGTs rather than ILS are driving discordance. Finally, we apply these recommendations to an R package named PhyloConfigR, which facilitates phylogenetic software setup, summarizes alignments, and provides tools for filtering alignments and gene trees.
Identifiants
pubmed: 37129064
pii: 7147705
doi: 10.1093/gbe/evad070
pmc: PMC10171231
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
Références
Zootaxa. 2016 Apr 19;4104(1):1-109
pubmed: 27394762
Syst Biol. 2018 Mar 01;67(2):285-303
pubmed: 29029338
Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):14942-7
pubmed: 22930817
BMC Evol Biol. 2015 Apr 11;15:62
pubmed: 25880916
Mol Biol Evol. 2013 May;30(5):1188-95
pubmed: 23418397
Bioinformatics. 2014 Dec 1;30(23):3317-24
pubmed: 25104814
Mol Phylogenet Evol. 2011 Nov;61(2):300-7
pubmed: 21742044
BMC Genomics. 2013;14 Suppl 1:S7
pubmed: 23368723
Syst Biol. 2017 Sep 01;66(5):857-879
pubmed: 28369655
Nature. 2003 Oct 23;425(6960):798-804
pubmed: 14574403
PeerJ. 2019 Oct 11;7:e7724
pubmed: 31616583
Syst Biol. 2012 Oct;61(5):835-49
pubmed: 22389443
Bioinformatics. 2010 Jun 15;26(12):1569-71
pubmed: 20421198
Bioessays. 2016 Feb;38(2):140-9
pubmed: 26709836
Mol Biol Evol. 2016 Apr;33(4):1110-25
pubmed: 26715628
Syst Biol. 2007 Apr;56(2):222-31
pubmed: 17464879
PLoS One. 2017 Oct 26;12(10):e0185056
pubmed: 29073143
Syst Biol. 2021 Jun 16;70(4):803-821
pubmed: 33367855
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17519-24
pubmed: 23045684
Syst Biol. 2009 Oct;58(5):463-7
pubmed: 20525600
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Mol Phylogenet Evol. 2015 Nov;92:63-71
pubmed: 26115844
Evolution. 2009 Jan;63(1):1-19
pubmed: 19146594
Am J Bot. 2018 Mar;105(3):376-384
pubmed: 29710372
Mol Phylogenet Evol. 2015 Nov;92:140-6
pubmed: 26079130
Mol Phylogenet Evol. 2009 Oct;53(1):320-8
pubmed: 19501178
PeerJ. 2019 Oct 11;7:e7755
pubmed: 31616586
PLoS One. 2015 Jun 18;10(6):e0129183
pubmed: 26086579
Syst Biol. 2020 May 1;69(3):502-520
pubmed: 31550008
Mol Biol Evol. 2020 Mar 1;37(3):904-922
pubmed: 31710677
Syst Biol. 2018 Sep 1;67(5):847-860
pubmed: 29471536
Mol Phylogenet Evol. 2013 Feb;66(2):526-38
pubmed: 22197804
Mol Phylogenet Evol. 2015 Jan;82 Pt A:146-55
pubmed: 25315885
Evolution. 2005 Jan;59(1):24-37
pubmed: 15792224
Syst Biol. 2007 Feb;56(1):17-24
pubmed: 17366134
BMC Evol Biol. 2010 Oct 11;10:302
pubmed: 20937096
PLoS One. 2013 Jun 18;8(6):e65923
pubmed: 23824177
Genome Biol Evol. 2017 Aug 1;9(8):1998-2012
pubmed: 28830116
Science. 2014 Dec 12;346(6215):1311-20
pubmed: 25504712
J Comput Biol. 2015 Jun;22(6):528-45
pubmed: 25734602
J Theor Biol. 2017 May 7;420:174-179
pubmed: 28263815
Syst Biol. 2019 Nov 1;68(6):937-955
pubmed: 31135914
Mol Biol Evol. 2008 May;25(5):821-30
pubmed: 18296416
Mol Biol Evol. 2023 May 2;40(5):
pubmed: 37140129
Mol Biol Evol. 2016 Jan;33(1):281-94
pubmed: 26474846
BMC Evol Biol. 2018 Feb 05;18(1):15
pubmed: 29402211
Mol Phylogenet Evol. 2019 May;134:164-171
pubmed: 30790674
Syst Biol. 2009 Oct;58(5):468-77
pubmed: 20525601
Syst Biol. 2015 Sep;64(5):727-40
pubmed: 25979143
Nature. 2015 Oct 22;526(7574):569-73
pubmed: 26444237
Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5936-41
pubmed: 17392434
Syst Biol. 2019 Jan 1;68(1):145-156
pubmed: 29939341
Genetics. 1983 Oct;105(2):437-60
pubmed: 6628982
Syst Biol. 2011 May;60(3):358-65
pubmed: 21303824
Evolution. 1983 Jan;37(1):203-217
pubmed: 28568026
Mol Phylogenet Evol. 2010 Jun;55(3):871-82
pubmed: 20304077
Appl Plant Sci. 2015 Aug 14;3(8):
pubmed: 26312196
Mol Phylogenet Evol. 2018 Sep;126:116-128
pubmed: 29626666
Proc Biol Sci. 2020 Dec 9;287(1940):20202102
pubmed: 33290680
Science. 2014 Dec 12;346(6215):1320-31
pubmed: 25504713
Mol Ecol Resour. 2022 Apr;22(3):1100-1119
pubmed: 34569723
Mol Phylogenet Evol. 2014 Nov;80:231-66
pubmed: 25152276
J Theor Biol. 2009 Jan 21;256(2):247-52
pubmed: 18955066
Syst Biol. 2016 May;65(3):465-77
pubmed: 26738927
Genome Res. 2011 Mar;21(3):349-56
pubmed: 21270173
Trends Ecol Evol. 2013 Dec;28(12):719-28
pubmed: 24094331
Biol Lett. 2012 Oct 23;8(5):783-6
pubmed: 22593086
Mol Biol Evol. 2000 Jun;17(6):839-50
pubmed: 10833190
Mol Biol Evol. 2016 Jul;33(7):1654-68
pubmed: 27189547
Mol Phylogenet Evol. 2014 Dec;81:221-31
pubmed: 25193610
Evolution. 2016 Jan;70(1):7-17
pubmed: 26639662
Mol Phylogenet Evol. 2011 Nov;61(2):543-83
pubmed: 21723399
Mol Phylogenet Evol. 2015 Oct;91:98-122
pubmed: 26002829
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):E1257-62
pubmed: 25733869
Mol Phylogenet Evol. 2013 May;67(2):367-78
pubmed: 23415987
Syst Biol. 2015 Sep;64(5):824-37
pubmed: 26099258
Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18644-9
pubmed: 19846765
PLoS Genet. 2006 Oct 27;2(10):e173
pubmed: 17132051
Syst Biol. 2017 May 01;66(3):352-366
pubmed: 28039387
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Genetics. 2016 Dec;204(4):1353-1368
pubmed: 27927902
Mol Phylogenet Evol. 2016 Jan;94(Pt A):1-33
pubmed: 26238460
Syst Biol. 2012 Oct;61(5):717-26
pubmed: 22232343
Cancer Res. 2017 Nov 1;77(21):e39-e42
pubmed: 29092936
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Syst Biol. 2019 Mar 1;68(2):298-316
pubmed: 30239963
Syst Biol. 2005 Oct;54(5):778-807
pubmed: 16243760
Syst Biol. 2021 Apr 15;70(3):491-507
pubmed: 33169797
Am J Bot. 2017 Jan;104(1):102-115
pubmed: 28104589
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
BMC Evol Biol. 2015 May 14;15:86
pubmed: 25968460
Mol Phylogenet Evol. 2018 Feb;119:128-143
pubmed: 29111477
Mol Biol Evol. 2018 Oct 1;35(10):2585-2593
pubmed: 30053098
Syst Biol. 2010 Oct;59(5):573-83
pubmed: 20833951
Mol Phylogenet Evol. 2020 Oct;151:106899
pubmed: 32590046
Evolution. 2017 Apr;71(4):913-922
pubmed: 28186341
Mol Biol Evol. 2020 Sep 1;37(9):2727-2733
pubmed: 32365179
Mol Phylogenet Evol. 2016 Jan;94(Pt A):447-62
pubmed: 26518740
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
PLoS Genet. 2006 May;2(5):e68
pubmed: 16733550
Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5864-E5870
pubmed: 28673970
BMC Bioinformatics. 2018 May 8;19(Suppl 6):153
pubmed: 29745866
Syst Biol. 2015 Jul;64(4):663-76
pubmed: 25813358
Syst Biol. 2014 Jan 1;63(1):83-95
pubmed: 24021724
J Exp Zool B Mol Dev Evol. 2005 Jan 15;304(1):64-74
pubmed: 15593277