Phylotranscriptomic analyses reveal a deep gene tree discordance of Camellia (Theaceae) and the possible ancestral origin of cultivated C. oleifera

An increasing use of genomic data has forced molecular phylogeneticists to confront gene tree discordance. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss, and the influence of incomplete sampling through assembly errors and filtering criteria. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history including interspecific gene flow. Here, we used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests for hard vs. soft conflict. In order to assess the impact of selective pressure on phylogenetic topology reconstruction, we also performed a selective pressure analysis. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene discordance. Furthermore, we confirmed that none of the currently proposed sections from Camellia was monophyletic and discuss the possible ancestral origin of cultivated C. oleifera. Combing all orthologous genes could provide an improved phylogenetic resolution and minimize the incongruence between gene trees and species tree of Camellia.随着基因组数据的应用愈发广泛，分子系统发育学家不得不直面基因树冲突（gene tree discordance）问题。多种因素均可导致基因间的系统发育不一致，例如渐渗（introgression）、不完全谱系分选（incomplete lineage sorting, ILS）、基因重复或丢失，以及组装错误与筛选标准引发的抽样不完整所带来的影响。山茶属（Camellia）是山茶科（Theaceae）最大的属，其分类学与系统学研究长期存在争议，部分原因在于其演化历史复杂，包含种间基因流。本研究利用覆盖山茶属15个组、共计55个物种的60份转录组数据，对其系统发育关系及基因树冲突的潜在成因展开探究。本研究基于1617个直系同源低拷贝核基因（orthologous low-copy nuclear genes）开展基因树冲突分析，主要采用溯祖物种树（coalescent species trees）方法与多歧支检验（polytomy tests）来区分硬冲突与软冲突（hard vs. soft conflict）。为评估选择压力（selective pressure）对系统发育拓扑结构重建的影响，本研究同时开展了选择压力分析。研究结果显示，山茶属系统发育主干存在不同程度的基因树冲突，并证实快速分化是导致基因冲突的潜在成因之一。此外，本研究证实当前划分的山茶属所有组均非单系群（monophyletic），并对栽培油茶（C. oleifera）的潜在祖先起源展开了讨论。整合所有直系同源基因可提升山茶属的系统发育分辨率，并最大程度降低基因树与物种树之间的冲突。