德州农工大学William J. Murphy课题组宣布他们研制了一个古老的重组沙漠是胎盘哺乳动物的物种形成超级基因。相关论文发表在2025年11月12日出版的《自然》杂志上。

本研究采用深度学习方法对22种胎盘哺乳动物进行基因组比对，以推断重组景观的演变。课题组研究人员发现了一个大的和进化上保守的X连锁重组沙漠，占染色体的30%。对94个物种的系统基因组分析表明，X连锁的重组沙漠是一个古老的、反复出现的基因流动障碍，当基因渗入主导全基因组祖先时，它保留了物种历史。这个超基因的功能基础是多方面的，富含影响性染色体沉默和生殖性状的基因。由于该位点支持有序谱系的生殖隔离，因此它可能是解决哺乳动物系统发育中具有挑战性关系的可靠标记。

据了解，生物物种之间的基因流动是贯穿生命之树的一种常见的适应性进化现象。考虑到基因交换的普遍性，一个令人生畏的挑战是如何从基因组中排列的复杂历史集合中最好地推断出物种之间的正确关系。在物种形成的早期阶段，减数分裂重组的局部速率影响着基因流动的特征分布和障碍。尽管如此，由于缺乏重组图谱，对这种关系的更广泛的理解及其在准确识别系统发育方面的应用仍然缺乏。

附：英文原文

Title: An ancient recombination desert is a speciation supergene in placental mammals

Author: Foley, Nicole M., Rasulis, Richard G., Wani, Zoya, Mendoza Cerna, Mayra N., Figueir, Henrique V., Koepfli, Klaus Peter, Raudsepp, Terje, Murphy, William J.

Issue&Volume: 2025-11-12

Abstract: Gene flow between biological species is a common and often adaptive evolutionary phenomenon throughout the tree of life1,2,3,4. Given the pervasive nature of genetic exchange, a daunting challenge is how best to infer the correct relationships between species from the complex collection of histories arrayed across genomes5. The local rate of meiotic recombination influences the distribution of signatures of, and barriers to, gene flow during the early stages of speciation6. Still, a broader understanding of this relationship and its application to accurately discerning phylogeny is lacking due to a scarcity of recombination maps. Here we applied deep learning methods to genome alignments from 22 divergent placental mammal species to infer the evolution of the recombination landscape. We identified a large and evolutionarily conserved X-linked recombination desert constituting 30% of the chromosome. Recombination-aware phylogenomic analyses from 94 species revealed that the X-linked recombination desert is an ancient and recurrent barrier to gene flow and retains the species history when introgression dominates genome-wide ancestry. The functional basis for this supergene is manifold, enriched with genes that influence sex chromosome silencing and reproduction traits. Because the locus underpins reproductive isolation across ordinal lineages, it may represent a reliable marker for resolving challenging relationships across the mammalian phylogeny.

DOI: 10.1038/s41586-025-09740-2

Source: https://www.nature.com/articles/s41586-025-09740-2