Molecular phylogeny and ancestral biogeographic reconstruction of Platanthera subgenus Limnorchis (Orchidaceae) using target capture methods

• Published in: Molecular phylogenetics and evolution 2021-04, Vol.157, p.107070-107070, Article 107070
• Main Authors: Wettewa, Eranga, Wallace, Lisa E.
• Format: Article
• Language: English
• Subjects: Biogeography; Cell Nucleus - genetics; DNA, Mitochondrial - genetics; Genetic Loci; Limnorchis; Orchidaceae; Orchidaceae - classification; Orchidaceae - genetics; Phylogenomics; Phylogeny; Phylogeography; Platanthera; Sequence Analysis, DNA - methods; Species Specificity; Target-capture
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2021.107070

[Display omitted] •A novel phylogenomic toolkit was developed for Platanthera consisting of genomic information from 617 low-copy nuclear loci.•Subgenus Limnorchis is a monophyletic clade with 100% bootstrap support.•Subgenus Limnorchis originated in western North America from an ancestor that was widespread in North America and Asia, following isolation from Asian conspecifics due to vicariance from closure of the Bering Land Bridge.•Species of subgenus Limnorchis diversified across western North America beginning ca. 3 Mya, and some species dispersed to eastern North America more recently. Platanthera is one of the largest genera of temperate orchids in the Holarctic and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are North America and eastern Asia. Despite its diversity, a thorough phylogenetic hypothesis for the genus is lacking because no studies have yet sampled taxa exhaustively or developed a robust molecular toolkit. While there is strong evidence that suggests monophyly of subgenus Limnorchis, most taxa in this group have not been included in a phylogenetic analysis. In this study, we developed a new toolkit for Platanthera consisting of genomic information from 617 low-copy nuclear loci. Using a targeted enrichment approach, we collected high-throughput sequence data in 23 accessions of nine of the 12 diploid species of subgenus Limnorchis and outgroup species across Platanthera. A maximum likelihood analysis resolved a strongly supported monophyletic clade for subgenus Limnorchis. Ancestral biogeographic reconstruction indicated that subgenus Limnorchis originated in western North America ca. 3–4.5 Mya from an ancestor that was widespread in western North America and eastern Asia and subsequently diversified in western North America, followed by dispersal of some species to eastern North America. Our results indicate complex biogeographic connections between Asia and North America, and therefore it suggests that Platanthera is a suitable system to test biogeographic hypotheses over time and space in the Holarctic. Our results are also expected to facilitate further study of diversification and biogeographic spread across Platanthera and lay the groundwork for understanding independent origins, biogeography, and morphological diversification of polyploid species within subgenus Limnorchis.