María C. Ávila‐Arcos

DAIseg is a new HMM-based method that detects both Neanderthal and Denisovan introgression in modern human genomes without archaic references, outperforming existing methods in Papuan populations.

TRACTINATOR infers continental and archaic ancestry in admixed genomes using deep learning, revealing archaic introgression patterns in Latin American populations.

This paper investigates using imputation to improve archaic ancestry inference in ancient human genomes, showing that imputed genomes can reliably detect and quantify introgression and identify introgressed segments.

This study recovers an 18th-century rhinovirus genome from ancient RNA isolated from human lung specimens, revealing insights into viral evolution.

This paper evaluates neural network-based methods for local ancestry inference in challenging admixture scenarios and finds they perform best with specialized preprocessing.

This study identifies ancient S. enterica Paratyphi C DNA in 19th-century Mexico, linking it to European strains and showing its persistence in urban settings.

This study introduces a frugal diffusion model for generating artificial genomes and evaluates its utility for local ancestry inference using synthetic and real data.

This study benchmarks haplotype inference methods on ancient DNA by simulating aDNA data and shows that accurate phasing is possible even for very ancient individuals with sufficient contamination control and read depth.

The paper analyzes pre-Hispanic genetic data from Mexico to show population continuity despite climate change and identifies an ancient unsampled ghost population's contribution.

The paper sequences 24 ancient Brazilian genomes, including 22 Botocudos, revealing Indigenous American ancestry without external gene flow and low heterozygosity, and identifies ancient pathogen lineages.

This study reconstructs ancient viral genomes from Colonial-era remains in Mexico, linking their origin to Africa via the transatlantic slave trade.

This study analyzes 76 exomes from five Mexican indigenous populations to infer population history and identify genes under positive selection.

The paper uses ancient DNA analysis of 20 individuals from St Helena to determine the genetic origins of liberated Africans, finding they came from West Central Africa and were culturally diverse.

This study applies Y-chromosome capture-enrichment to ancient DNA libraries, showing increased recovery of Y-DNA sequences and enabling haplogroup assignment.

This paper analyzes ancient genomes from North Africa to show prehistoric migrations brought genetic influences from both the Levant and Europe to the Maghreb.