Limits of long-term selection against Neandertal introgression

Area of Science:

• Paleogenetics
• Human Evolution
• Population Genetics

Background:

• Previous studies suggested negative selection reduced Neandertal DNA in modern humans.
• An observed decline in Neandertal ancestry over 45,000 years in Europe supported this hypothesis.

Purpose of the Study:

• To re-evaluate the evidence for negative selection acting on Neandertal DNA in modern humans.
• To investigate the demographic factors influencing estimates of Neandertal ancestry over time.

Main Methods:

• Utilized a novel statistic accounting for modern human gene flow to estimate Neandertal ancestry.
• Employed whole-genome simulations to model selection and introgression dynamics.
• Analyzed two high-coverage Neandertal genomes.

Main Results:

• The apparent decline in Neandertal ancestry in Europe is an artifact of population gene flow, not negative selection.
• No evidence of changing Neandertal ancestry in Europe over the past 45,000 years was found.
• Selection against Neandertal alleles is concentrated in conserved noncoding and regulatory regions, and protein-coding sequences.

Conclusions:

• The long-term decline of Neandertal ancestry is not driven by widespread negative selection.
• Specific Neandertal genetic elements, particularly in functional regions, show evidence of selection.
• Understanding Neandertal introgression requires accounting for complex human population movements.