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Archaic adaptive introgression in modern human reproductive genes.
Christopher Kendall1,2, Amin Nooranikhojasteh3, Esteban J Parra4
1Neurosciences and Mental Health Department, The Hospital for Sick Children, Toronto, ON, Canada. chris.kendall@sickkids.ca.
Communications Biology
|September 27, 2025
Summary
Modern humans carry genes from archaic hominins like Neanderthals, influencing reproduction and adaptation. This study reveals adaptive introgression of 118 reproductive genes, impacting human development and disease resistance.
Area of Science:
- Human evolutionary genetics
- Reproductive biology
- Paleogenomics
Background:
- Modern humans admixed with archaic hominins (Neanderthals, Denisovans) outside Africa.
- Archaic introgression facilitated adaptation to new environments.
- The impact of archaic introgression on reproductive genes remains understudied.
Purpose of the Study:
- Investigate adaptive introgression of genes related to reproduction in modern humans.
- Identify archaic alleles and haplotypes influencing reproductive traits.
- Explore the functional consequences of archaic introgression in reproductive tissues and pathways.
Main Methods:
- Genome-wide association studies (GWAS) for archaic alleles.
- Identification of archaic core haplotypes and positively selected regions.
- Expression quantitative trait loci (eQTL) analysis to identify regulatory variants.
- Enrichment analysis for developmental, cancer, and reproductive pathways.
Main Results:
- Identified 118 adaptively introgressed genes associated with reproduction.
- Discovered 327 genome-wide significant archaic alleles, including 11 core haplotypes (3 positively selected).
- Found over 300 archaic variants acting as eQTLs, regulating 176 genes, with 81% in reproductive tissue expression regions.
- Linked introgressed genes to embryo development, endometriosis, preeclampsia, and prostate cancer protection.
Conclusions:
- Archaic introgression has significantly impacted reproductive gene regulation in modern humans.
- Selected archaic alleles influence key developmental and reproductive processes throughout the lifespan.
- Archaic variants offer protection against certain cancers, such as prostate cancer.
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