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

First author: Diego F. Morales〣riones; Affiliations: University of Idaho (美国爱达荷大学): Moscow, USA

Corresponding author: Diego F. Morales〣riones

Hybridization, incomplete lineage sorting (不完全谱系分拣), and phylogenetic error produce similar incongruence (不一致的) 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 (新热带区) 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 (近缘属). 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 (网状).

杂交、不完全谱系分拣以及系统演化上的误差会产生不一致的模式，进而不利于系统发育的重建。本文利用测序数据以及多个物种树和物种网络的方法解决了新热带区Lachemilla属的演化框架，并区分了各种不一致的来源。作者利用来自于27个物种的396个核位点以及近乎全部的质体序列鉴定了Lachemilla属的四个主要类群，并且剖析了导致基因树和物种树之间不一致的多个来源。所有的系统发育方法均显示Lachemilla属含有4个主要类群，这与先前的报道一致，但采用物种树的方法得到了不一样的拓扑结构。物种网络分析显示一个主要类群Orbiculate可能是古老的杂交来源，代表了不同物种树之间不一致的主要来源。另外，作者发现Lachemilla属与其近缘属共享了一次潜在的全基因组复制事件。Lachemilla属类群在演化早期和晚期均发生过杂交事件。同时，作者发现在研究具有网络演化模式的类群时，采用系统发育网络的方法可以同时解决不完全谱系分拣和基因流的问题。

P.S. 基因树与物种谱系树或种群树不一致，这一现象称作不完全谱系分拣（incomplete lineage sorting，ILS）。

doi: https://doi.org/10.1111/nph.15099

Journal: New Phytologist

First Published date: 31 March, 2018

（P.S. 欢迎关注微信公众号：微信号Plant_Frontiers）