Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.
Bibliographical noteFunding Information:
We thank K. Romoleroux for access to DNA samples and illustrations of Lachemilla, K. Wieteimer for assistance with the sequence capture protocol, M. Johnson for assistance with HYBPIPER, and Ya Yang and three anonymous reviewers for comments on earlier versions of the manuscript. This work was funded in part by a Secretaría de Educación Superior, Ciencia, Tecnología e Innovación del Ecuador (SENESCYT) doctoral scholarship to D.F.M-B., Graduate Student Research Grants from the Botanical Society of America, American Society of Plant Taxonomists, International Association of Plant Taxonomists, and the University of Idaho Stillinger Herbarium Expedition Funds to D.F.M-B., and a National Science Foundation Doctoral Dissertation Improvement Grant to D.C.T. for D.F.M-B. (DEB-1502049). Access to genomic and computational resources was granted through the University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST) supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health (P30 GM103324).
- Lachemilla (Rosaceae)
- cytonuclear discordance
- gene flow
- phylogenetic networks
- species trees