关键词: 关键词: 系统发育, 基因树, 物种树, 基因流, 选择

Abstract

Background & Aims: Lineage sorting (LS) is defined as the process by which multiple populations are descended from a common species and developed into reproductively isolated lineages 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 are transmitted to progeny populations. We discussed the potential relationships between gene trees and species trees for neutral and selective genes, respectively. Secondly, we discussed 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 the methods of 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.

Key words: Key words: phylogeny, gene tree, species tree, gene flow, selection