Ancient DNA, Modern Impact: How archaic introgression influences human growth, reproduction, and disease

 By: Ma. Shereena S. Tabur | Chromoplexy

Thousands of years ago, human ancestors interbred with Neanderthals and Denisovans after leaving Africa. This phenomenon is called archaic introgression or simply the incorporation of DNA from extinct hominins into the genomes of modern humans. This archaic DNA from these hominins is said to have remained in modern human DNA because it helped in survival and reproduction in new environments. A paper by Kendall et al. (2025) utilized archaic introgression to identify genetic elements that continue to shape human development and reproduction. The authors showed that these archaic variants were likely maintained by positive selection due to benefits such as improved developmental processes. 

Figure 1. Modern human ancestors leaving Africa and interbreeding with Neanderthals and Denisovans

Around 1,700 genes were found to be associated with reproductive functions and 47 of those were uncovered to be archaic DNA segments. Kendall et al. (2025) narrowed these down into 11 main haplotypes, maintained by natural selection. These haplotypes are distributed in regions across the world and were present in low frequencies through the years. However, the AHRR haplotype in Finnish genomes and FLT1 in Peruvians increased 10,000 years ago. This simply suggests that evolution did not stop thousands of years ago, but rather we are continuing to adapt locally through ancient DNA in our genomes.

Moreover, around fifteen ancient alleles on a segment of chromosome 2 showed a connection to reduced prostate cancer risks as seen in major genome-wide association study (GWAS) datasets. Downstream analyses tied these introgressed genes to developmental pathways such as Notch signaling, carbon metabolism, and cardiovascular formation. The authors propose that these variants helped support growth and development under specific environmental pressures. This was said to have indirectly boosted reproductive fitness, which could compromise or increase modern human’s vulnerability to modern diseases. Think of ancient genes as heavy tight boots that people wore to walk on rocky roads. It helped in travelling through that path. But now that the roads are smooth, those boots have no effect anymore and make your feet hurt. This just highlights evolutionary trade-offs.

The authors acknowledge that this study had several limitations. The overlap between the GWAS findings does not prove causation which is why the functional validation to test how these archaic alleles change gene function still needs to be conducted. Overall, they demonstrated that these introgressed alleles continue to influence human development, reproduction, and health. This study helped us gain a better view as to how history shaped who we are today.