Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Abstract

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.

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

“…This suggests that the rapidity of the speciation events separating the lineages Gentianidae + (Cornales + Ericales) created an opportunity for extensive ILS. If the branches separating the speciation events were longer, little or no conflict should be observed in the simulated organellar trees (Folk et al., ; Morales‐Briones et al., ). Similarly, conflict among the simulated organellar trees is also appreciable along the backbone of Lamiidae (Fig.…”

“…To distinguish between chloroplast capture and ILS, following several studies (Folk et al., ; García et al., ; Morales‐Briones et al., ), we simulated 1000 organellar trees under the coalescent using the program DendroPy (Sukumaran and Holder, ), with the inferred species tree acting as the guide tree. The guide tree (which was inferred from the nuclear data set) was scaled by a factor of four to approximate the branch lengths expected from organellar inheritance; this was done because the effective population size of the plastome is generally expected to be one‐fourth that of the nuclear genome given the assumptions of equal sex ratios, haploidy (homoplasmic), and uniparental inheritance (McCauley, ).…”

“…In plants, hybridization in particular—often accompanied by polyploidy, or whole‐genome duplication (WGD)—has been emphasized as an important evolutionary process (e.g., Stebbins, ; Soltis and Soltis, ) and a major source of observed cytonuclear discordance due to chloroplast capture (e.g., Rieseberg and Soltis, ; Soltis and Kuzoff, ; Linder and Rieseberg, ). While such instances of discordance are typically observed at shallow phylogenetic levels (e.g., Huang et al., ), recent studies have shown that ancient hybridization events can produce lasting signatures of cytonuclear discordance (Folk et al., ; García et al., ; Morales‐Briones et al., ), even among major lineages of angiosperms (e.g., members of the rosid COM clade; Sun et al., ). We might expect ILS, as well, to result in persistent cytonuclear discordance in some cases, but this possibility has been poorly explored across the phylogeny of green plants.…”

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)

“…These results add to the growing number of studies that have formally evaluated the role of introgression in generating phylogenetic incongruence between plant nuclear and organellar genomes (e.g. Winkler et al ., ; Folk et al ., ; García et al ., ; Morales‐Briones et al ., ; Gernandt et al ., ). What has emerged is the robust detection of cytoplasmic introgression in diverse taxa representing both angiosperms and gymnosperms.…”

“…What has emerged is the robust detection of cytoplasmic introgression in diverse taxa representing both angiosperms and gymnosperms. Both ancient and recent hybridization seem to contribute to cytonuclear discordance in many systems (Folk et al ., ; Morales‐Briones et al ., ), with the sunflowers demonstrating the potential for cytoplasmic introgression to be ongoing in species that are broadly sympatric with many opportunities to hybridize. Why organellar genomes frequently disregard species’ boundaries, whether they do so more than other genes (e.g.…”