Cargando…
Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes
Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., w...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8652245/ https://www.ncbi.nlm.nih.gov/pubmed/34899789 http://dx.doi.org/10.3389/fpls.2021.767478 |
_version_ | 1784611554749054976 |
---|---|
author | Rose, Jeffrey P. Kriebel, Ricardo Kahan, Larissa DiNicola, Alexa González-Gallegos, Jesús G. Celep, Ferhat Lemmon, Emily M. Lemmon, Alan R. Sytsma, Kenneth J. Drew, Bryan T. |
author_facet | Rose, Jeffrey P. Kriebel, Ricardo Kahan, Larissa DiNicola, Alexa González-Gallegos, Jesús G. Celep, Ferhat Lemmon, Emily M. Lemmon, Alan R. Sytsma, Kenneth J. Drew, Bryan T. |
author_sort | Rose, Jeffrey P. |
collection | PubMed |
description | Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation. |
format | Online Article Text |
id | pubmed-8652245 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-86522452021-12-09 Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes Rose, Jeffrey P. Kriebel, Ricardo Kahan, Larissa DiNicola, Alexa González-Gallegos, Jesús G. Celep, Ferhat Lemmon, Emily M. Lemmon, Alan R. Sytsma, Kenneth J. Drew, Bryan T. Front Plant Sci Plant Science Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation. Frontiers Media S.A. 2021-11-24 /pmc/articles/PMC8652245/ /pubmed/34899789 http://dx.doi.org/10.3389/fpls.2021.767478 Text en Copyright © 2021 Rose, Kriebel, Kahan, DiNicola, González-Gallegos, Celep, Lemmon, Lemmon, Sytsma and Drew. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Rose, Jeffrey P. Kriebel, Ricardo Kahan, Larissa DiNicola, Alexa González-Gallegos, Jesús G. Celep, Ferhat Lemmon, Emily M. Lemmon, Alan R. Sytsma, Kenneth J. Drew, Bryan T. Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes |
title | Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes |
title_full | Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes |
title_fullStr | Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes |
title_full_unstemmed | Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes |
title_short | Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes |
title_sort | sage insights into the phylogeny of salvia: dealing with sources of discordance within and across genomes |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8652245/ https://www.ncbi.nlm.nih.gov/pubmed/34899789 http://dx.doi.org/10.3389/fpls.2021.767478 |
work_keys_str_mv | AT rosejeffreyp sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT kriebelricardo sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT kahanlarissa sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT dinicolaalexa sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT gonzalezgallegosjesusg sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT celepferhat sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT lemmonemilym sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT lemmonalanr sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT sytsmakennethj sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes AT drewbryant sageinsightsintothephylogenyofsalviadealingwithsourcesofdiscordancewithinandacrossgenomes |