Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.

IF 6.1 1区 生物学 Q1 EVOLUTIONARY BIOLOGY
Xiao-Xu Pang, Da-Yong Zhang
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引用次数: 0

Abstract

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.

利用拓扑结构和分支长度信息检测鬼怪进化
近年来,杂交和引种研究取得了重大进展,其中鬼魂引种--已灭绝或未取样种系的遗传物质向现存物种的转移--成为一个重要的研究领域。然而,准确识别幽灵引入是一项挑战。为了解决这个问题,我们重点研究了涉及已知系统发生树的三个物种的简单案例。通过数学分析和模拟,我们评估了流行的系统发生学方法(包括 HyDe 和 PhyloNet/MPL)和全似然法(贝叶斯系统发生学和系统地理学,Bayesian Phylogenetics and Phylogeography (BPP))在检测幽灵引入方面的性能。我们的研究结果表明,依靠位点模式计数或基因树拓扑结构的启发式方法难以区分幽灵引种和取样非姊妹物种之间的引种,经常导致供体和受体物种的错误鉴定。相比之下,直接使用多焦点序列比对的全似然方法 BPP,同时考虑了基因树拓扑和分支长度,能够检测出系统发生组数据集中的幽灵引入。我们分析了现实世界中 14 种茄科植物的系统发生组数据集,以展示全似然方法在准确推断引入方面的潜力。
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来源期刊
Systematic Biology
Systematic Biology 生物-进化生物学
CiteScore
13.00
自引率
7.70%
发文量
70
审稿时长
6-12 weeks
期刊介绍: Systematic Biology is the bimonthly journal of the Society of Systematic Biologists. Papers for the journal are original contributions to the theory, principles, and methods of systematics as well as phylogeny, evolution, morphology, biogeography, paleontology, genetics, and the classification of all living things. A Points of View section offers a forum for discussion, while book reviews and announcements of general interest are also featured.
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