The paper uses sequence-to-function models to predict the functional impact of archaic hominin introgression in Papuan individuals, identifying genes associated with introgressed haplotypes.

bioRxiv · Sep 1, 2026 · PreprintGenomics

A global map for introgressed structural variation and selection in humans

PingHsun Hsieh, Natthapon Soisangwan, David Gordon, Athef Javidh, William T. Harvey, David Porubskỳ, Kendra Hoekzema, Carl A. Baker, Katherine M. Munson, Christopher Kinipi, Matthew Leavesley, Nicolas Brucato, Murray P. Cox, François‐Xavier Ricaut, Irene Gallego Romero, Evan E. Eichler

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Science · Jun 11, 2026Peer-reviewedEvolutionary Biology✦ In-depth digest

Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans

Maddy Comerford, Davide Maria Vespasiani, Navya Shukla, Laura E. Cook, Danat Yermakovich, Michael Dannemann, Matthew Leavesley, Christopher Kinipi, François‐Xavier Ricaut, Nicolas Brucato, Murray P. Cox, Irene Gallego Romero

The paper investigates the regulatory effects of Neanderthal and Denisovan introgression in Papuan populations using a massively parallel reporter assay, finding differential activity in immune-related genes.

PLoS Genetics · Mar 24, 2026Peer-reviewedEvolutionary Biology

Denisovan introgression has shaped the immune system of present-day Papuans

Davide Maria Vespasiani, Guy S. Jacobs, Laura E. Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, François‐Xavier Ricaut, Murray P. Cox, Irene Gallego Romero

The paper identifies Denisovan introgression in Papuan genomes that influences immune-related processes and regulatory elements, with experimental validation of functional impacts.

bioRxiv · Jul 9, 2020 · PreprintEvolutionary Biology