Homo denisova, Correspondence Spectral Analysis, Finite Sites Reticulate Hierarchical Coalescent Models and the Ron Jeremy Hypothesis

TL;DR

This paper develops advanced spectral analysis models to fit genetic data from modern and archaic humans, revealing insights into interbreeding events and gene flow patterns among ancient human lineages.

Contribution

It introduces reticulate finite and infinite sites spectral models for demographic inference from human genome data, improving fit over previous models.

Findings

Evidence of male-biased gene flow from Denisova to Papuans

Possible additional archaic gene flow events

Uncertainty about multiple Neanderthal interbreeding episodes

Abstract

This article shows how to fit reticulate finite and infinite sites sequence spectra to aligned data from five modern human genomes (San, Yoruba, French, Han and Papuan) plus two archaic humans (Denisovan and Neanderthal), to better infer demographic parameters. These include interbreeding between distinct lineages. Major improvements in the fit of the sequence spectrum are made with successively more complicated models. Findings include some evidence of a male biased gene flow from the Denisova lineage to Papuan ancestors and possibly even more archaic gene flow. It is unclear if there is evidence for more than one Neanderthal interbreeding, as the evidence suggesting this largely disappears when a finite sites model is fitted.