An ancient recombination desert is a speciation supergene in placental mammals
Article metadata
Article Date = 2025-11-12
Article URL = https://www.nature.com/articles/s41586-025-09740-2
Article Title = An ancient recombination desert is a speciation supergene in placental mammals
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Summary
The paper identifies a deeply conserved genomic region — a long-standing “recombination desert” — that behaves like a supergene influencing speciation across placental mammals. The region shows strongly reduced recombination, structural stability across lineages and signatures consistent with limiting gene flow between species. The authors combine comparative genomics, recombination-aware phylogenomics and analyses of structural variation to argue that this ancient region contributes disproportionately to reproductive isolation and the genomic architecture of speciation in mammals.
Key Points
- Researchers characterise an ancient genomic region with persistently low recombination across many placental mammal lineages.
- The region functions like a speciation supergene: linked variants and structural features reduce recombination and hinder introgression.
- Evidence comes from broad phylogenomic sampling and recombination-aware analyses that reveal consistent patterns across species.
- The locus is associated with genes and features that can influence reproduction and hybrid incompatibility, helping explain X-linked and autosomal contributions to isolation.
- Findings clarify why some genomic regions resist gene flow and cause discordant phylogenetic signals among loci.
- Implications span speciation theory, sex-chromosome evolution and practical interpretation of genome-wide introgression studies.
Content summary
The authors document a conserved block with markedly suppressed crossover activity — a recombination desert — present across diverse placental mammals. Using whole-genome comparisons, linkage- and recombination-aware phylogenomic methods, and structural-variation characterisation, they show this block maintains tight linkage among multiple functional elements. That linkage preserves allele combinations that are likely to affect reproductive traits and reduces the likelihood that beneficial alleles move freely between species via hybridisation.
The study situates this supergene as a recurring barrier to gene flow, explaining patterns of deep divergence and localised genomic resistance to introgression. It also highlights how long-term recombination suppression can shape gene content and contribute to hybrid sterility or reduced hybrid fitness in multiple clades.
Context and relevance
This work is important because it links long-term recombination landscape features with macroevolutionary outcomes. By showing that an ancient recombination-suppressed block can act as a speciation supergene across placental mammals, the paper helps explain why some genomic regions repeatedly contribute to species boundaries. It also informs interpretation of phylogenomic conflicts, and is relevant for researchers studying hybridisation, conservation genetics and sex-chromosome evolution.
Why should I read this?
Quick heads up — if you care about how species form (or why genomes tell conflicting evolutionary stories), this paper is a tidy package. It explains a neat mechanism — a persistent low-recombination chunk acting like a supergene — that helps account for repeated barriers to gene flow across mammals. Read it if you want the shortcut that connects recombination maps to real-world speciation results.
Author style
Punchy: this is a paper that reframes parts of speciation genetics. If you work on phylogenomics, hybridisation or sex-chromosome evolution, the details matter — the methods and comparative breadth here could change how you interpret introgression and genomic islands of divergence.