A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia.

Publisher: Academic Press Country of Publication: United States NLM ID: 9304400 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9513 (Electronic) Linking ISSN: 10557903 NLM ISO Abbreviation: Mol Phylogenet Evol Subsets: MEDLINE

Publication: San Diego, CA ; Orlando, FL : Academic Press
Original Publication: San Diego : Academic Press, c1992-

Phylogeny* ; Camellia*/genetics ; Camellia*/classification; Cell Nucleus/genetics ; Sequence Analysis, DNA ; Bayes Theorem ; DNA, Plant/genetics ; Evolution, Molecular ; Genetic Speciation ; Models, Genetic

Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 Elsevier Inc. All rights reserved.)

Keywords: Herbarium specimen; Incomplete lineage sorting (ILS); Locus filtering; Phylogenetic discordance; Phylogenomics; Target enrichment

Date Created: 20240428 Date Completed: 20240517 Latest Revision: 20240517

20240518

10.1016/j.ympev.2024.108089

38679302