DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf
The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is...
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ftfrontimediafig:oai:figshare.com:article/11822958 2023-05-15T14:55:51+02:00 DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf Rebecca L. Stubbs Ryan A. Folk Chun-Lei Xiang Shichao Chen Douglas E. Soltis Nico Cellinese 2020-02-07T13:26:15Z https://doi.org/10.3389/fpls.2019.01773.s003 https://figshare.com/articles/DataSheet_3_A_Phylogenomic_Perspective_on_Evolution_and_Discordance_in_the_Alpine-Arctic_Plant_Clade_Micranthes_Saxifragaceae_pdf/11822958 unknown doi:10.3389/fpls.2019.01773.s003 https://figshare.com/articles/DataSheet_3_A_Phylogenomic_Perspective_on_Evolution_and_Discordance_in_the_Alpine-Arctic_Plant_Clade_Micranthes_Saxifragaceae_pdf/11822958 CC BY 4.0 CC-BY Botany Plant Biology Plant Systematics and Taxonomy Plant Cell and Molecular Biology Plant Developmental and Reproductive Biology Plant Pathology Plant Physiology Plant Biology not elsewhere classified arctic alpine diversification coalescent gene tree conflict phylogenomics incongruence Saxifragaceae Dataset 2020 ftfrontimediafig https://doi.org/10.3389/fpls.2019.01773.s003 2020-02-12T23:52:17Z The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is a need for methods to investigate discordance, and in turn, use this conflict to inform and aid in downstream analyses. Therefore, we drew upon multiple analytical tools to investigate the evolution of Micranthes (Saxifragaceae), a clade of primarily arctic-alpine herbs impacted by reticulate and rapid radiations. To elucidate the evolution of Micranthes we sought near-complete taxon sampling with multiple accessions per species and assembled extensive nuclear (518 putatively single copy loci) and plastid (95 loci) datasets. In addition to a robust phylogeny for Micranthes, this research shows that genetic discordance presents a valuable opportunity to develop hypotheses about its underlying causes, such as hybridization, polyploidization, and range shifts. Specifically, we present a multi-step approach that incorporates multiple checks points for paralogy, including reciprocally blasting targeted genes against transcriptomes, running paralogy checks during the assembly step, and grouping genes into gene families to look for duplications. We demonstrate that a thorough assessment of discordance can be a source of evidence for evolutionary processes that were not adequately captured by a bifurcating tree model, and helped to clarify processes that have structured the evolution of Micranthes. Dataset Arctic Frontiers: Figshare Arctic |
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Open Polar |
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Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Botany Plant Biology Plant Systematics and Taxonomy Plant Cell and Molecular Biology Plant Developmental and Reproductive Biology Plant Pathology Plant Physiology Plant Biology not elsewhere classified arctic alpine diversification coalescent gene tree conflict phylogenomics incongruence Saxifragaceae |
spellingShingle |
Botany Plant Biology Plant Systematics and Taxonomy Plant Cell and Molecular Biology Plant Developmental and Reproductive Biology Plant Pathology Plant Physiology Plant Biology not elsewhere classified arctic alpine diversification coalescent gene tree conflict phylogenomics incongruence Saxifragaceae Rebecca L. Stubbs Ryan A. Folk Chun-Lei Xiang Shichao Chen Douglas E. Soltis Nico Cellinese DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf |
topic_facet |
Botany Plant Biology Plant Systematics and Taxonomy Plant Cell and Molecular Biology Plant Developmental and Reproductive Biology Plant Pathology Plant Physiology Plant Biology not elsewhere classified arctic alpine diversification coalescent gene tree conflict phylogenomics incongruence Saxifragaceae |
description |
The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is a need for methods to investigate discordance, and in turn, use this conflict to inform and aid in downstream analyses. Therefore, we drew upon multiple analytical tools to investigate the evolution of Micranthes (Saxifragaceae), a clade of primarily arctic-alpine herbs impacted by reticulate and rapid radiations. To elucidate the evolution of Micranthes we sought near-complete taxon sampling with multiple accessions per species and assembled extensive nuclear (518 putatively single copy loci) and plastid (95 loci) datasets. In addition to a robust phylogeny for Micranthes, this research shows that genetic discordance presents a valuable opportunity to develop hypotheses about its underlying causes, such as hybridization, polyploidization, and range shifts. Specifically, we present a multi-step approach that incorporates multiple checks points for paralogy, including reciprocally blasting targeted genes against transcriptomes, running paralogy checks during the assembly step, and grouping genes into gene families to look for duplications. We demonstrate that a thorough assessment of discordance can be a source of evidence for evolutionary processes that were not adequately captured by a bifurcating tree model, and helped to clarify processes that have structured the evolution of Micranthes. |
format |
Dataset |
author |
Rebecca L. Stubbs Ryan A. Folk Chun-Lei Xiang Shichao Chen Douglas E. Soltis Nico Cellinese |
author_facet |
Rebecca L. Stubbs Ryan A. Folk Chun-Lei Xiang Shichao Chen Douglas E. Soltis Nico Cellinese |
author_sort |
Rebecca L. Stubbs |
title |
DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf |
title_short |
DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf |
title_full |
DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf |
title_fullStr |
DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf |
title_full_unstemmed |
DataSheet_3_A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).pdf |
title_sort |
datasheet_3_a phylogenomic perspective on evolution and discordance in the alpine-arctic plant clade micranthes (saxifragaceae).pdf |
publishDate |
2020 |
url |
https://doi.org/10.3389/fpls.2019.01773.s003 https://figshare.com/articles/DataSheet_3_A_Phylogenomic_Perspective_on_Evolution_and_Discordance_in_the_Alpine-Arctic_Plant_Clade_Micranthes_Saxifragaceae_pdf/11822958 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
doi:10.3389/fpls.2019.01773.s003 https://figshare.com/articles/DataSheet_3_A_Phylogenomic_Perspective_on_Evolution_and_Discordance_in_the_Alpine-Arctic_Plant_Clade_Micranthes_Saxifragaceae_pdf/11822958 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fpls.2019.01773.s003 |
_version_ |
1766327866498220032 |