Biomedical subjects

Flora Jay

Publications and source records attributed to Flora Jay.

3 recordsLinked to original sources

PubMed2026

An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes.

Admixture between populations is a common feature of human history. Admixture events introduce new genetic variation that can fuel evolution. Characterizing the significance of admixture events on the evolution of populations across various species is of great interest to evolutionary geneticists. Local Ancestry Inference (LAI) methods infer genetic ancestry of an individual at a particular chromosomal location. Certain methods specialize in detecting archaic introgression, which consists of interbreeding between modern and archaic humans like Neanderthals and Denisovans. Most current LAI methods allow the detection of a single archaic ancestry, and post-processing may distinguish between multiple waves of introgression. These methods vary in how they choose archaic or modern reference genomes for the inference. Here, we present a new HMM-based method (DAIseg), which has the advantage of simultaneously distinguishing between multiple waves of ancient and recent admixture, using only modern human reference genomes. Simulations demonstrate that DAIseg achieves higher overall performance than state-of-the-art methods. We also apply DAIseg to Papuan populations to jointly detect Denisovan and Neanderthal introgressed segments, and identify a higher number of archaic segments than previous methods. Analysis of inferred introgressed segments, shows that we can identify evidence for two Denisovan introgression events in Papuans. Overall, on top of being able to deal with both Archaic and recent admixture, DAIseg provides a more principled approach for detecting and classifying Denisovan and Neanderthal segments which will improve downstream analysis of introgressed segments to infer the impact of archaic introgression in humans.

Denisovan↗

PubMed2026

Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters.

Inferring coalescent trees from genomic data has become a major subject in population genetics, particularly with the recent advances in tree sequence reconstruction methods. However, it remains unclear how well these methods perform for imbalanced genealogies. Such imbalances can arise from processes such as cultural transmission of reproductive success (CTRS) or positive selection. Using simulated genomic data, we benchmarked three major software packages, SINGER, Relate, and tsinfer, by comparing the imbalance of reconstructed trees by these methods with that of the true simulated trees, for three indices that quantify this imbalance. The three methods performed well under scenarios yielding balanced trees. However, their accuracy declined as imbalance increased. Performances also varied with mutation rate, recombination rate, and sample size. This study opens possibilities for applying these methods to infer CTRS or positive selection in large-scale genomic datasets, using simulation-based inference such as approximate Bayesian computation.

Models, Genetic↗

PubMed2026

Archaic ancestry inference in imputed ancient human genomes.

When modern humans expanded from Africa into Eurasia, they interbred with archaic hominins such as Neanderthals and Denisovans. This introgression shaped human evolution, yet most insights have been gained from present-day genomes, leaving little known about how archaic variants evolved after interbreeding. Ancient genomes offer a direct view of this process, but low coverage and poor quality have limited their use. Recent advances in genotype imputation offer a way to overcome these challenges by reconstructing missing information from reference panels and recovering evolutionary signals from low-coverage data. Here, we show that imputation enables accurate detection and quantification of archaic introgression in ancient genomes, improves local archaic ancestry inference, and that regions of archaic ancestry are imputed with especially high accuracy. We further demonstrate that imputed genomes can reconstruct the trajectories of introgressed haplotypes, distinguish populations across time and geography, and identify both known and additional candidates for adaptive introgression.

Humans↗