Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans

Area of Science:

• Human evolutionary genetics
• Population genomics
• Paleoanthropology

Background:

• Contemporary human genomes contain DNA from archaic hominins, with some segments rising to high frequencies due to positive selection.
• Previous research has not specifically analyzed the population dynamics following archaic introgression events.

Purpose of the Study:

• To define and identify cases of immediate adaptive introgression (iAI) in humans.
• To differentiate iAI from selection on standing introgressed variation (SI).
• To investigate the post-introgression evolutionary dynamics of archaic haplotypes.

Main Methods:

• Defining iAI as archaic haplotypes reaching high frequencies shortly after introgression due to a selective sweep.
• Defining SI as introgressed haplotypes initially segregating neutrally before positive selection.
• Analyzing a geographically diverse human genome dataset to identify and categorize instances of selection on introgressed variation.

Main Results:

• Novel cases of selection on introgressed variation in living human populations were identified.
• Several cases were shortlisted as potentially representing iAI rather than SI.
• Three inferred iAI haplotypes with potential biological relevance, including immune-related genes, were found in West Siberians, South Asians, and West Eurasians.

Conclusions:

• Immediate adaptive introgression (iAI) is a distinct evolutionary mechanism shaping human genomes.
• The identified iAI cases, particularly those involving immune genes, highlight the functional impact of archaic introgression.
• Further research is needed to fully understand the contribution of both iAI and selection on standing introgressed variation (SI) in the archaic introgression landscape.