A statistical model for reference-free inference of archaic local ancestry

Area of Science:

• Genomics
• Population Genetics
• Paleoanthropology

Background:

• Genomic studies reveal interbreeding between archaic hominins (Neanderthals, Denisovans) and modern human ancestors.
• Accurate inference of archaic local ancestry typically requires reference genomes from ancestral archaic populations.
• The absence of archaic reference genomes hinders the characterization of certain archaic admixture events.

Purpose of the Study:

• To develop a statistical method for inferring archaic local ancestry without requiring archaic reference genomes.
• To provide a robust tool for studying archaic admixture events where reference genomes are unavailable.

Main Methods:

• A novel statistical method was developed that utilizes diverse population genetic summary statistics.
• The method infers archaic local ancestry by analyzing patterns within the genomes of present-day individuals.
• Accuracy and robustness were validated through extensive simulations.

Main Results:

• The method successfully infers archaic local ancestry in the absence of archaic reference genomes.
• Application to European genomes identified segments significantly enriched for Neanderthal ancestry.
• The findings demonstrate the method's capability even without direct Neanderthal genomic references.

Conclusions:

• The developed statistical method enables the inference of archaic local ancestry without archaic reference genomes.
• This approach expands the ability to study archaic admixture events across diverse human populations.
• The successful identification of Neanderthal ancestry segments highlights the method's practical utility in human evolutionary genomics.