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...

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Autores principales:	Jeffrey P. Rose, Ricardo Kriebel, Larissa Kahan, Alexa DiNicola, Jesús G. González-Gallegos, Ferhat Celep, Emily M. Lemmon, Alan R. Lemmon, Kenneth J. Sytsma, Bryan T. Drew
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	anchored hybrid enrichment cyto-nuclear discordance distance metrics incongruence Lamiaceae Robinson–Foulds distance Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/0a0c55871d0c45e08b0be2f80c35dcac
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spelling	oai:doaj.org-article:0a0c55871d0c45e08b0be2f80c35dcac2021-11-30T19:07:43ZSage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes1664-462X10.3389/fpls.2021.767478https://doaj.org/article/0a0c55871d0c45e08b0be2f80c35dcac2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.767478/fullhttps://doaj.org/toc/1664-462XNext-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.Jeffrey P. RoseJeffrey P. RoseRicardo KriebelLarissa KahanAlexa DiNicolaJesús G. González-GallegosFerhat CelepEmily M. LemmonAlan R. LemmonKenneth J. SytsmaBryan T. DrewFrontiers Media S.A.articleanchored hybrid enrichmentcyto-nuclear discordancedistance metricsincongruenceLamiaceaeRobinson–Foulds distancePlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	anchored hybrid enrichment cyto-nuclear discordance distance metrics incongruence Lamiaceae Robinson–Foulds distance Plant culture SB1-1110
spellingShingle	anchored hybrid enrichment cyto-nuclear discordance distance metrics incongruence Lamiaceae Robinson–Foulds distance Plant culture SB1-1110 Jeffrey P. Rose Jeffrey P. Rose Ricardo Kriebel Larissa Kahan Alexa DiNicola Jesús G. González-Gallegos Ferhat Celep Emily M. Lemmon Alan R. Lemmon Kenneth J. Sytsma Bryan T. Drew Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes
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	article
author	Jeffrey P. Rose Jeffrey P. Rose Ricardo Kriebel Larissa Kahan Alexa DiNicola Jesús G. González-Gallegos Ferhat Celep Emily M. Lemmon Alan R. Lemmon Kenneth J. Sytsma Bryan T. Drew
author_facet	Jeffrey P. Rose Jeffrey P. Rose Ricardo Kriebel Larissa Kahan Alexa DiNicola Jesús G. González-Gallegos Ferhat Celep Emily M. Lemmon Alan R. Lemmon Kenneth J. Sytsma Bryan T. Drew
author_sort	Jeffrey P. Rose
title	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_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_sort	sage insights into the phylogeny of salvia: dealing with sources of discordance within and across genomes
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/0a0c55871d0c45e08b0be2f80c35dcac
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Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

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