دورية أكاديمية
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Comprehensive Species Sampling and Sophisticated Algorithmic Approaches Refute the Monophyly of Arachnida.

التفاصيل البيبلوغرافية
العنوان: Comprehensive Species Sampling and Sophisticated Algorithmic Approaches Refute the Monophyly of Arachnida.
المؤلفون: Ballesteros JA; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA., Santibáñez-López CE; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA.; Department of Biology, Western Connecticut State University, Danbury, CT, USA., Baker CM; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA.; Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA., Benavides LR; Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA., Cunha TJ; Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.; Smithsonian Tropical Research Institute, Panama City, Panama., Gainett G; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA., Ontano AZ; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA., Setton EVW; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA., Arango CP; Office for Research, Griffith University, Nathan, QLD, Australia., Gavish-Regev E; National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel., Harvey MS; Collections & Research, Western Australian Museum, Welshpool, WA, Australia.; School of Biological Sciences, University of Western Australia, Crawley, WA, Australia., Wheeler WC; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA., Hormiga G; Department of Biological Sciences, George Washington University, Washington, DC, USA., Giribet G; Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA., Sharma PP; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA.
المصدر: Molecular biology and evolution [Mol Biol Evol] 2022 Feb 03; Vol. 39 (2).
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE
أسماء مطبوعة: Publication: 2003- : New York, NY : Oxford University Press
Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983-
مواضيع طبية MeSH: Arachnida*/genetics, Animals ; Biological Evolution ; Fossils ; Genome ; Phylogeny
مستخلص: Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.
(© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
References: G3 (Bethesda). 2021 Dec 8;11(12):. (PMID: 34849767)
Mol Phylogenet Evol. 2007 Jun;43(3):936-51. (PMID: 17197202)
Mol Phylogenet Evol. 2006 Sep;40(3):772-94. (PMID: 16781168)
Bioinformatics. 2015 Oct 1;31(19):3210-2. (PMID: 26059717)
Mol Biol Evol. 2007 Sep;24(9):2139-50. (PMID: 17652333)
Mol Phylogenet Evol. 2018 Feb;119:105-117. (PMID: 29074461)
Sci Rep. 2020 Jan 9;10(1):101. (PMID: 31919367)
Proc Biol Sci. 2021 Aug 11;288(1956):20211168. (PMID: 34344178)
Curr Biol. 2017 Apr 3;27(7):958-967. (PMID: 28318975)
Curr Biol. 2015 Aug 3;25(15):1993-9. (PMID: 26212885)
Evol Bioinform Online. 2020 Feb 5;16:1176934320903735. (PMID: 32076367)
Syst Biol. 2017 Mar 01;66(2):232-255. (PMID: 27633354)
Curr Biol. 2019 Jun 17;29(12):R592-R602. (PMID: 31211983)
Mol Biol Evol. 2021 Aug 23;38(9):4025-4038. (PMID: 33983409)
Syst Biol. 2019 Nov 1;68(6):1003-1019. (PMID: 31140564)
Front Zool. 2018 Dec 19;15:52. (PMID: 30574172)
Proc Biol Sci. 2015 Apr 7;282(1804):20142953. (PMID: 25716788)
Curr Biol. 2016 Jan 25;26(2):224-229. (PMID: 26776737)
Cladistics. 2000 Jun;16(2):155-203. (PMID: 34902956)
Syst Biol. 2018 Sep 1;67(5):901-904. (PMID: 29718447)
Curr Biol. 2014 May 5;24(9):1017-23. (PMID: 24726154)
Arthropod Struct Dev. 2020 Nov;59:100997. (PMID: 33039753)
J Mol Evol. 2012 Feb;74(1-2):81-95. (PMID: 22362465)
Nat Commun. 2021 Mar 19;12(1):1783. (PMID: 33741994)
BMC Evol Biol. 2019 Jun 13;19(1):121. (PMID: 31195978)
Nat Ecol Evol. 2020 Dec;4(12):1703-1712. (PMID: 33262517)
Cladistics. 1990 Mar;6(1):1-38. (PMID: 34933471)
Curr Biol. 2019 Jan 21;29(2):312-318.e3. (PMID: 30639106)
Proc Biol Sci. 2019 Dec 18;286(1917):20192426. (PMID: 31847768)
BMC Evol Biol. 2010 Jul 13;10:210. (PMID: 20626897)
Mol Biol Evol. 2021 May 19;38(6):2446-2467. (PMID: 33565584)
Sci Adv. 2020 Dec 11;6(50):. (PMID: 33310849)
Arthropod Struct Dev. 2007 Jun;36(2):245-52. (PMID: 18089103)
Syst Biol. 2002 Jun;51(3):492-508. (PMID: 12079646)
Mol Phylogenet Evol. 2004 Apr;31(1):178-91. (PMID: 15019618)
Syst Biol. 2013 Jul;62(4):611-5. (PMID: 23564032)
BMC Evol Biol. 2010 Aug 02;10:235. (PMID: 20678229)
Arthropod Struct Dev. 2010 Mar-May;39(2-3):124-42. (PMID: 20093195)
Mol Phylogenet Evol. 2022 Mar;168:107378. (PMID: 34968680)
BMC Biol. 2017 Jul 31;15(1):62. (PMID: 28756775)
Sci Rep. 2019 Dec 6;9(1):18508. (PMID: 31811226)
Mol Biol Evol. 2016 Aug;33(8):2117-34. (PMID: 27189539)
Nature. 2019 Sep;573(7775):586-589. (PMID: 31511691)
Nat Ecol Evol. 2018 Apr;2(4):623-627. (PMID: 29403076)
Syst Biol. 2012 May;61(3):539-42. (PMID: 22357727)
Integr Comp Biol. 2003 Aug;43(4):522-30. (PMID: 21680460)
Proc Biol Sci. 2017 Mar 29;284(1851):. (PMID: 28330926)
Cladistics. 2002 Feb;18(1):5-70. (PMID: 14552352)
Syst Biol. 2021 Feb 10;70(2):360-375. (PMID: 32462193)
Syst Biol. 2021 Oct 13;70(6):1200-1212. (PMID: 33837789)
Syst Biol. 2021 Jan 1;70(1):14-20. (PMID: 32497195)
PeerJ. 2014 Nov 13;2:e641. (PMID: 25405073)
Mol Biol Evol. 2014 Nov;31(11):2963-84. (PMID: 25107551)
Mol Biol Evol. 2018 Feb 1;35(2):518-522. (PMID: 29077904)
Front Zool. 2013 Jul 11;10(1):40. (PMID: 23842208)
Mol Phylogenet Evol. 2009 Jan;50(1):117-28. (PMID: 18992830)
Sci Adv. 2021 Mar 19;7(12):. (PMID: 33741592)
Mol Biol Evol. 2015 Jan;32(1):268-74. (PMID: 25371430)
Evodevo. 2020 Aug 28;11:18. (PMID: 32874529)
Nature. 2016 Sep 8;537(7619):225-228. (PMID: 27533041)
Nat Commun. 2019 May 24;10(1):2295. (PMID: 31127117)
Syst Biol. 2021 Apr 15;70(3):421-439. (PMID: 32882040)
Dev Genes Evol. 2020 Mar;230(2):137-153. (PMID: 31927629)
Genome Biol Evol. 2016 Sep 02;8(8):2565-80. (PMID: 27492233)
Arthropod Struct Dev. 2021 Sep;64:101089. (PMID: 34399185)
Curr Biol. 2020 Nov 2;30(21):4316-4321.e2. (PMID: 32916114)
Cladistics. 1998 Jun;14(2):173-192. (PMID: 34902927)
Mol Biol Evol. 2021 Sep 27;38(10):4322-4333. (PMID: 34097041)
Cladistics. 2016 Jun;32(3):221-238. (PMID: 34727670)
Mol Biol Evol. 2020 Sep 1;37(9):2727-2733. (PMID: 32365179)
Syst Biol. 2020 Nov 1;69(6):1052-1067. (PMID: 32208492)
Nat Methods. 2017 Jun;14(6):587-589. (PMID: 28481363)
Syst Biol. 2019 Nov 1;68(6):896-917. (PMID: 30917194)
Integr Comp Biol. 2017 Sep 01;57(3):499-509. (PMID: 28957514)
Biol Rev Camb Philos Soc. 2004 May;79(2):253-300. (PMID: 15191225)
Mol Biol Evol. 2021 Mar 9;38(3):891-903. (PMID: 32986823)
Mol Biol Evol. 2018 Mar 1;35(3):543-548. (PMID: 29220515)
BMC Bioinformatics. 2018 May 8;19(Suppl 6):153. (PMID: 29745866)
Nat Ecol Evol. 2020 Dec;4(12):1694-1702. (PMID: 32747770)
BMC Bioinformatics. 2009 Dec 15;10:421. (PMID: 20003500)
Biol Lett. 2019 Jul 26;15(7):20190288. (PMID: 31311486)
Evol Bioinform Online. 2013 Oct 29;9:429-35. (PMID: 24250218)
Arthropod Struct Dev. 2019 Jul;51:23-31. (PMID: 31176004)
Mol Phylogenet Evol. 2016 Aug;101:75-90. (PMID: 27150348)
Nat Ecol Evol. 2017 Apr 10;1(5):126. (PMID: 28812701)
Nature. 2001 Sep 13;413(6852):157-61. (PMID: 11557979)
فهرسة مساهمة: Keywords: Chelicerata; orthologs; phylogenomics; supermatrix; total evidence
تواريخ الأحداث: Date Created: 20220209 Date Completed: 20220331 Latest Revision: 20220401
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC8845124
DOI: 10.1093/molbev/msac021
PMID: 35137183
قاعدة البيانات: MEDLINE
الوصف
تدمد:1537-1719
DOI:10.1093/molbev/msac021