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- 저자 : Garcia-Jacas, Nú (검색결과 1 건)
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Herrando-Moraira, Sonia,Calleja, Juan Antonio,Carnicero, Pau,Fujikawa, Kazumi,Galbany-Casals, Mercè,Garcia-Jacas, Nú,ria,Im, Hyoung-Tak,Kim, Seung-Chul,Liu, Jian-Quan,Ló,pez-Alvarado Elsevier 2018 Molecular phylogenetics and evolution Vol.128 No.-
<P><B>Abstract</B></P> <P>Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: <I>Arctium</I>, <I>Cousinia</I>, <I>Saussurea</I>, and <I>Jurinea</I>. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, <I>Arctium</I>-<I>Cousinia</I> and <I>Saussurea</I>-<I>Jurinea</I>, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of <I>Arctium</I>, <I>Cousinia</I>, and <I>Saussurea</I> are also well defined. Conversely, conflicting species relationships remain for <I>Jurinea</I>. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that: (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Target enrichment resolved relationships among the four genera of the Cardueae. </LI> <LI> Bioinformatic choices can largely affect the phylogenetic reconstructions. </LI> <LI> Filtering strategies improve support values only under concatenation analyses. </LI> <LI> The coalescence approach yields higher topological robustness than concatenation. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
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