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Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils
Weevils (Curculionoidea) comprise one of the most diverse groups of organisms on earth. There is hardly a vascular plant or plant part without its own species of weevil feeding on it and weevil species diversity is greater than the number of fishes, birds, reptiles, amphibians and mammals combined....
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699822/ https://www.ncbi.nlm.nih.gov/pubmed/29166661 http://dx.doi.org/10.1371/journal.pone.0188044 |
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author | Van Dam, Matthew H. Lam, Athena W. Sagata, Katayo Gewa, Bradley Laufa, Raymond Balke, Michael Faircloth, Brant C. Riedel, Alexander |
author_facet | Van Dam, Matthew H. Lam, Athena W. Sagata, Katayo Gewa, Bradley Laufa, Raymond Balke, Michael Faircloth, Brant C. Riedel, Alexander |
author_sort | Van Dam, Matthew H. |
collection | PubMed |
description | Weevils (Curculionoidea) comprise one of the most diverse groups of organisms on earth. There is hardly a vascular plant or plant part without its own species of weevil feeding on it and weevil species diversity is greater than the number of fishes, birds, reptiles, amphibians and mammals combined. Here, we employ ultraconserved elements (UCEs) designed for beetles and a novel partitioning strategy of loci to help resolve phylogenetic relationships within the radiation of Australasian smurf-weevils (Eupholini). Despite being emblematic of the New Guinea fauna, no previous phylogenetic studies have been conducted on the Eupholini. In addition to a comprehensive collection of fresh specimens, we supplement our taxon sampling with museum specimens, and this study is the first target enrichment phylogenomic dataset incorporating beetle specimens from museum collections. We use both concatenated and species tree analyses to examine the relationships and taxonomy of this group. For species tree analyses we present a novel partitioning strategy to better model the molecular evolutionary process in UCEs. We found that the current taxonomy is problematic, largely grouping species on the basis of similar color patterns. Finally, our results show that most loci required multiple partitions for nucleotide rate substitution, suggesting that single partitions may not be the optimal partitioning strategy to accommodate rate heterogeneity for UCE loci. |
format | Online Article Text |
id | pubmed-5699822 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-56998222017-12-08 Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils Van Dam, Matthew H. Lam, Athena W. Sagata, Katayo Gewa, Bradley Laufa, Raymond Balke, Michael Faircloth, Brant C. Riedel, Alexander PLoS One Research Article Weevils (Curculionoidea) comprise one of the most diverse groups of organisms on earth. There is hardly a vascular plant or plant part without its own species of weevil feeding on it and weevil species diversity is greater than the number of fishes, birds, reptiles, amphibians and mammals combined. Here, we employ ultraconserved elements (UCEs) designed for beetles and a novel partitioning strategy of loci to help resolve phylogenetic relationships within the radiation of Australasian smurf-weevils (Eupholini). Despite being emblematic of the New Guinea fauna, no previous phylogenetic studies have been conducted on the Eupholini. In addition to a comprehensive collection of fresh specimens, we supplement our taxon sampling with museum specimens, and this study is the first target enrichment phylogenomic dataset incorporating beetle specimens from museum collections. We use both concatenated and species tree analyses to examine the relationships and taxonomy of this group. For species tree analyses we present a novel partitioning strategy to better model the molecular evolutionary process in UCEs. We found that the current taxonomy is problematic, largely grouping species on the basis of similar color patterns. Finally, our results show that most loci required multiple partitions for nucleotide rate substitution, suggesting that single partitions may not be the optimal partitioning strategy to accommodate rate heterogeneity for UCE loci. Public Library of Science 2017-11-22 /pmc/articles/PMC5699822/ /pubmed/29166661 http://dx.doi.org/10.1371/journal.pone.0188044 Text en © 2017 Van Dam et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Van Dam, Matthew H. Lam, Athena W. Sagata, Katayo Gewa, Bradley Laufa, Raymond Balke, Michael Faircloth, Brant C. Riedel, Alexander Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils |
title | Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils |
title_full | Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils |
title_fullStr | Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils |
title_full_unstemmed | Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils |
title_short | Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils |
title_sort | ultraconserved elements (uces) resolve the phylogeny of australasian smurf-weevils |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699822/ https://www.ncbi.nlm.nih.gov/pubmed/29166661 http://dx.doi.org/10.1371/journal.pone.0188044 |
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