Authors
Zitu Ma, He Gao, Chuanshuai Xie, Da Ji, Yongrui Lu, Haoyu Wang, Yili Cui, Francisco de Menezes Cavalcante Sassi, Dengyue Yuan, Haiping Liu, Luohao Xu
Published in
Molecular phylogenetics and evolution. Pages 108696. Jul 25, 2026. Epub Jul 25, 2026.
Abstract
Resolving species relationships in rapidly radiating lineages remains a major challenge in evolutionary biology, particularly when hybridization obscures phylogenetic signals. Here, we present a chromosome-level, haplotype-resolved genome assembly for Triplophysa pseudoscleroptera, a species residing at the Qinghai-Tibet Plateau, and integrate it with eight other Triplophysa genomes and resequencing data from 57 Triplophysa individuals to reconstruct a robust phylogeny of the genus. We uncovered extensive discordance between mitochondrial and nuclear phylogenies, driven by both ancient and recent introgression. Notably, the individual selected for genome assembly was found to have undergone a recent hybridization event, retaining ∼ 22% introgressed genomic segments. These introgressed segments are phylogenetically closer to T. dalaica, and their inclusion in concatenated whole-genome alignments was sufficient to mislead species tree inference. Empirical genomic resampling analyses demonstrate that as little as 14% introgression is sufficient to result in incorrect phylogenetic inference in our focal system. Our findings provide a cautionary example that reliance on a single individual genome can lead to erroneous phylogenetic conclusions, when a moderate proportion of introgressed segments is present. We therefore advocate chromosome-scale and window-based phylogenomic approaches as essential practices for reconstructing species relationships in systems shaped by reticulate evolution.
PMID:
42501809
Bibliographic data and abstract were imported from PubMed on 26 Jul 2026.
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