دورية أكاديمية
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae).
| العنوان: | Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae). |
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| المؤلفون: | Chan KO; Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore., Hutter CR; Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA., Wood PL Jr; Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA., Grismer LL; Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA 92505, USA., Brown RM; Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA. |
| المصدر: | Proceedings. Biological sciences [Proc Biol Sci] 2020 Dec 09; Vol. 287 (1940), pp. 20202102. Date of Electronic Publication: 2020 Dec 09. |
| نوع المنشور: | Journal Article; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: Royal Society of London Country of Publication: England NLM ID: 101245157 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1471-2954 (Electronic) Linking ISSN: 09628452 NLM ISO Abbreviation: Proc Biol Sci Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : Royal Society of London, c1990- |
| مواضيع طبية MeSH: | Phylogeny*, Anura/*physiology, Animals ; Genomics |
| مستخلص: | Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)-a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets. |
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| فهرسة مساهمة: | Keywords: anomaly zone; bootstrap; branch support; concordance factor; incomplete lineage sorting; parsimony informative sites |
| سلسلة جزيئية: | Dryad 10.5061/dryad.8cz8w9gn7 figshare 10.6084/m9.figshare.c.5218608 |
| تواريخ الأحداث: | Date Created: 20201208 Date Completed: 20210113 Latest Revision: 20231110 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC7739936 |
| DOI: | 10.1098/rspb.2020.2102 |
| PMID: | 33290680 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1471-2954 |
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| DOI: | 10.1098/rspb.2020.2102 |