Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

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dc.authoridDrew, Bryan T./0000-0001-7248-2799
dc.authoridDiNicola, Alexa/0000-0001-7763-4376
dc.authoridLemmon, Alan/0000-0003-4577-5064
dc.authoridKriebel, Ricardo/0000-0002-1138-7533
dc.contributor.authorRose, Jeffrey P.
dc.contributor.authorKriebel, Ricardo
dc.contributor.authorKahan, Larissa
dc.contributor.authorDiNicola, Alexa
dc.contributor.authorGonzalez-Gallegos, Jesus G.
dc.contributor.authorCelep, Ferhat
dc.contributor.authorLemmon, Emily M.
dc.date.accessioned2025-01-21T16:44:18Z
dc.date.available2025-01-21T16:44:18Z
dc.date.issued2021
dc.departmentKırıkkale Üniversitesi
dc.description.abstractNext-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 similar to 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.
dc.identifier.doi10.3389/fpls.2021.767478
dc.identifier.issn1664-462X
dc.identifier.pmid34899789
dc.identifier.scopus2-s2.0-85120886187
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.3389/fpls.2021.767478
dc.identifier.urihttps://hdl.handle.net/20.500.12587/25420
dc.identifier.volume12
dc.identifier.wosWOS:000738352800001
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherFrontiers Media Sa
dc.relation.ispartofFrontiers In Plant Science
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241229
dc.subjectanchored hybrid enrichment; cyto-nuclear discordance; distance metrics; incongruence; Lamiaceae; Robinson-Foulds distance; Salvia
dc.titleSage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes
dc.typeArticle

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