谱系分选理论与检测方法的研究进展  

Advances in lineage sorting theories and their detection methods

作　　者：吕燕文 王子韵 肖钰 何梓晗 吴超 胡新生 Yanwen Lv;Ziyun Wang;Yu Xiao;Zihan He;Chao Wu;Xinsheng Hu(College of Forestry and Landscape Architecture,South China Agricultural University,Guangzhou 510642;Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm,Guangzhou 510642)

机构地区：[1]华南农业大学林学与风景园林学院,广州510642 [2]广东省森林植物种质资源与利用重点实验室,广州510642

出　　处：《生物多样性》2024年第4期117-134,共18页Biodiversity Science

基　　金：广东省自然科学基金(2023A515012137);国家自然科学基金(32171819);华南农业大学人才引进启动项目(4400-K16013)。

摘　　要：谱系分选为理解物种形成机制提供了一个途径,常被划分为复系、并系及单系3个阶段,对应着不同的基因树与物种树关系。本文首先系统地探讨了不同进化属性(中性和选择性)的基因组位点在祖先群体中如何传递到子代群体中的相关理论,分析了可能的基因树与物种树关系。其次探讨了基于中性序列谱系分选分析方法,包括在不完全谱系分选下物种树构建和系统发育网络分析。进一步探讨了选择对谱系分选的影响,基于基因树和物种树途径检测选择的方法,包括定向选择和平衡选择检测。最后,探讨了植物交配系统对谱系分选的影响,不完全谱系分选检测存在的问题以及在花粉流和种子流及不完全谱系分选的综合条件下系统发育网络分析方法,澄清这些问题有助于深度理解植物种的谱系分选过程。Background&Aims:Lineage sorting(LS)refers to the process in which multiple populations are descended from a common ancestral population or species and are now reproductively isolated from one another.It provides an approach to gain insights into speciation,and is often classified into the phases of polyphyly,paraphyly,and monophyly.The first two phases are in the state of incomplete lineage sorting(ILS)where gene trees do not correctly reflect species trees.The third phase is in the state of complete LS where gene trees are concordant with species trees.Here,we reviewed relevant theories and summarized recent progresses in method for LS detection.Progress:We first systematically discussed the coalescent theories of how genome sites with distinct evolutionary properties(neutral or selective)in an ancestral population were transmitted to progeny populations.We discussed the potential relationships between gene trees and species trees for neutral and selective genes,respectively.Secondly,we delved into LS analyses based on the neutral DNA sequences,including construction of phylogeny under ILS and the network-based phylogenetic analysis.We then discussed the impacts of selection on LS analysis and methods for detecting both directional and balancing selection based on gene trees and species trees.Finally,we discussed a few open questions about the effects of mating system on LS,the detection of ILS,and the effects of pollen and seed flow on LS.Prospect:New theories are needed to explore how mating system shapes the LS process for both selective and neutral genes.To appropriately assess ILS for individual genes based on species trees,it is crucial to improve the method estimating species trees and to fully utilize the potential of genome sequence data in future study.Given a high frequency of natural hybridization in plant species,a phylogenetic network method is needed to simultaneously examine pollen and seed flow together with ILS.Answers to these questions could help us to understand in-depth the LS process in pl

关 键 词：系统发育 基因树 物种树 基因流 选择 

分 类 号：Q-0[生物学]