Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification

Abstract

Premise To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target‐enriched nuclear data to improve our understanding of phylogenetic relationships in the family. Methods We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral‐state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia. Results Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. Conclusions Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene‐tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character‐state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

“…Incomplete lineage sorting is common in rapid Andean radiations (Morales-Briones et al 2018, Murillo-A. et al 2022).…”

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

“…Brunelliaceae (rosids: Oxalidales; Figure 8) is a small family containing one genus and 70 species (Murillo et al, 2022). An analysis using 317 genes (part of the Angio-sperm353 probe set) from 53 species recognized two large clades and 13 subclades with well resolved relationships among them (Murillo et al, 2022). In another family of Oxalidales, Oxalidaceae, the phylogeny of the genus Oxalis was analyzed using nuclear genes (Schmickl et al, 2016).…”

“…In addition to fruit types, the evolution processes of some other fruit traits were investigated in some angiosperm groups. For example, fruit colors of Maleae (Rosaceae) (Zhang et al, 2023b), fruit shapes and fruit segmentation of Brassicaceae (Huang et al, 2016b), and carpel number of Brunelliaceae (Murillo et al, 2022).…”

“…The histories of flower merosity (the number of organs in the same whorl of floral organs) and the shape of the floral disk of Vitaceae were reconstructed using nuclear phylogenomic trees, and the ancestor of the family was shown to have 5-merous flower with a cupular shape of the floral disk (Ma et al, 2021). Also, the evolutionary pattern of calyx merosity and ratio of calyx/carpel merosity in Brunelliaceae were analyzed, and the results showed that these two traits changed multiple times within the family (Murillo et al, 2022). The analysis in Brassicaceae showed that the ancestors of the family had an entire stigma and the stigma changed to lobed in multiple lineages in parallel (Huang et al, 2016b).…”

Phylogenetic and geographic diversification/differentiation as an evolutionary avenue in the genus Cephalocereus (Cactaceae) Evolutionary Avenue in Cephalocereus

“…The ecological isolation and the isolation by distance are also examples of divergentist models, where spatial or ecological isolation and differentiation are expected to occur simultaneously. On the other hand, processes as hybridization and incomplete lineage sorting (ILS) reveal discrepancies in observed characters, either morphological, genetical or both (Soltis & Soltis, 2009;Murillo et al, 2022).…”