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Dryad

Phylogenomics of Boraginaceae using lineage-specific and angiosperms353 loci

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Mar 20, 2025 version files 23.62 MB

Abstract

During the past 20 years, the phylogenetics of Boraginaceae has taken shape using plastid DNA regions and the nuclear ribosomal internal transcribed spacer (ITS), but these regions only represent a limited understanding of the evolutionary history of the family. Using hybridization-enrichment sequencing, 531 nuclear regions from lineage-specific and Angiosperms353 loci were sequenced and aligned for 49 species from across Boraginaceae. Additionally, the Angiosperms353 loci were incorporated with a broader dataset of the same loci from 115 accessions of Boraginales and relatives. Based on multiple phylogenetic approaches and datasets, the resolved phylogenies of Boraginaceae were quite similar to our current understanding, yet multiple taxa were recognized in different positions. These included: 1) Echiochiloideae as sister to Cynoglossoideae instead of to the rest of the entire family, 2) Moritzinae as nested within Boragininae, and 3) Lasiocaryeae and Trichodesmeae not resolved as sisters. These different positions recovered, via different methods, using hundreds of nuclear loci suggest that incomplete lineage sorting, hybridization, and heterotachy may have occurred during the early origin of the family. In analyses of Boraginales, Namaceae was resolved as non-monophyletic, providing evidence that a broader Hydrophyllaceae may again be appropriate, and Lennoaceae was nested in Ehretiaceae. While both sets of loci allowed for a well-resolved and well-supported phylogeny to be reconstructed, the lineage-specific loci recovered some of the more intriguing phylogenetic relationships in part because these loci appear to be less conserved than those from Angiosperms353. The two sets of loci provide an interesting complement for understanding patterns of evolution within the family and order.