Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species.

IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Ze-Tao Jin, Xiao-Hua Lin, Dai-Kun Ma, Si-Yu Xie, Jia-Xin Huang, Chen Ren, Liang Zhao, Lei Duan, Chao Xu, Richard G J Hodel, Jun Wu, Bin-Bin Liu
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Abstract

The traditional Tree of Life (ToL) model is increasingly challenged by the Web of Life (WoL) paradigm, which offers a more accurate depiction of organismal phylogeny, particularly in light of the incongruences often observed between gene and species trees. However, the absence of a standardised method for resolving evolutionary mechanisms - such as Incomplete Lineage Sorting (ILS), hybridisation, introgression, polyploidisation, and whole-genome duplication - remains a significant obstacle in defining the WoL. Characterised by extensive hybridisation events, the pear genus Pyrus provides an ideal model for exploring these complexities. In this study, we present a Step-by-Step Exclusion (SSE) approach for investigating the evolutionary pathways of Pyrus, based on Whole Genome Sequencing (WGS) and Deep Genome Skimming (DGS) data, and our results demonstrate that: (1) ILS, rather than polyploidisation, plays a dominant role in the origination of Pyrus; (2) the two subgenera of Pyrus followed independent evolutionary paths, influenced by geographical barriers formed through the uplift of the Tibetan Plateau and increased aridity in Central Asia; (3) both ILS and hybridisation have driven the diversification of subg. Pashia, while hybridisation alone has shaped the reticulate evolution of subg. Pyrus; (4) the establishment of the Silk Road during the Han Dynasty facilitated genetic exchange between subg. Pyrus and subg. Pashia. The SSE approach offers a versatile framework for studying the evolutionary mechanisms underlying the WoL paradigm.

揭开生命之网:不完全谱系分选和杂交是梨物种多倍体化进化动力学的主要机制。
传统的生命之树(ToL)模型正日益受到生命之网(WoL)范式的挑战,后者提供了更准确的生物系统发育描述,特别是考虑到基因树和物种树之间经常观察到的不一致。然而,缺乏一种标准化的方法来解决进化机制——如不完全谱系分类(ILS)、杂交、渗入、多倍体化和全基因组复制——仍然是定义WoL的一个重大障碍。梨属的特点是广泛的杂交事件,为探索这些复杂性提供了理想的模型。在这项研究中,我们基于全基因组测序(WGS)和深度基因组撇读(DGS)数据,提出了一种逐步排除(SSE)方法来研究梨的进化途径,我们的结果表明:(1)ILS而不是多倍化在梨的起源中起主导作用;(2)受青藏高原隆升和中亚地区干旱加剧所形成的地理屏障的影响,梨属的两个亚属具有独立的进化路径;(3) ILS和杂交都推动了subg的多样化。Pashia,而杂交单独塑造了subg的网状进化。Pyrus;(4)汉代丝绸之路的建立促进了各民族之间的基因交流。梨和子。Pashia。SSE方法为研究WoL范式下的进化机制提供了一个通用的框架。
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来源期刊
Molecular Ecology Resources
Molecular Ecology Resources 生物-进化生物学
CiteScore
15.60
自引率
5.20%
发文量
170
审稿时长
3 months
期刊介绍: Molecular Ecology Resources promotes the creation of comprehensive resources for the scientific community, encompassing computer programs, statistical and molecular advancements, and a diverse array of molecular tools. Serving as a conduit for disseminating these resources, the journal targets a broad audience of researchers in the fields of evolution, ecology, and conservation. Articles in Molecular Ecology Resources are crafted to support investigations tackling significant questions within these disciplines. In addition to original resource articles, Molecular Ecology Resources features Reviews, Opinions, and Comments relevant to the field. The journal also periodically releases Special Issues focusing on resource development within specific areas.
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