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

作者：Jeffrey P. Rose, Ricardo Kriebel, Larissa Kahan, Alexa DiNicola, Jesús Guadalupe González‐Gallegos, Ferhat Celep, Emily Moriarty Lemmon, Alan R. Lemmon, Kenneth J. Sytsma, Bryan T. Drew · 发表于：Frontiers in Plant Science · 年份：2021 · DOI：10.3389/fpls.2021.767478 · 被引用次数：38 · 研究领域：Plant and Fungal Species Descriptions、Genomics and Phylogenetic Studies、Plant Diversity and Evolution

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. Mor...