Leveraging shared ancestral variation to detect local introgression.

"plos publication stage vor-update-to-uncorrected-proof publication update 2024-01-19 data availability all data analyzed is publicly available 1000 genomes data from [ 28 ]: all autosomes pindel 20130502 complexindex low_coverage genotypes vcf gz neanderthal introgressed tracts from [ 7 ]: https://reich hms harvard edu/datasets/landscape-neandertal-ancestry-present-day-humans heliconius data from [ 29 ]: https://datadryad org/stash/downloads/file_stream/63229 and https://datadryad org/stash/downloads/file_stream/63228 altai neanderthal data from [ 27 ]: http://cdna eva mpg de/neandertal/altai/altaineandertal/vcf scripts are available in https://github com/leslylopezfang/dplus .; data availability all data analyzed is publicly available 1000 genomes data from [ 28 ]: all autosomes pindel 20130502 complexindex low_coverage genotypes vcf gz neanderthal introgressed tracts from [ 7 ]: https://reich hms harvard edu/datasets/landscape-neandertal-ancestry-present-day-humans heliconius data from [ 29 ]: https://datadryad org/stash/downloads/file_stream/63229 and https://datadryad org/stash/downloads/file_stream/63228 altai neanderthal data from [ 27 ]: http://cdna eva mpg de/neandertal/altai/altaineandertal/vcf scripts are available in https://github com/leslylopezfang/dplus . file s1 table (xlsx"

"plos publication stage vor-update-to-uncorrected-proof publication update 2024-01-19 data availability all data analyzed is publicly available 1000 genomes data from [ 28 ]: all autosomes pindel 20130502 complexindex low_coverage genotypes vcf gz neanderthal introgressed tracts from [ 7 ]: https://reich hms harvard edu/datasets/landscape-neandertal-ancestry-present-day-humans heliconius data from [ 29 ]: https://datadryad org/stash/downloads/file_stream/63229 and https://datadryad org/stash/downloads/file_stream/63228 altai neanderthal data from [ 27 ]: http://cdna eva mpg de/neandertal/altai/altaineandertal/vcf scripts are available in https://github com/leslylopezfang/dplus .; data availability all data analyzed is publicly available 1000 genomes data from [ 28 ]: all autosomes pindel 20130502 complexindex low_coverage genotypes vcf gz neanderthal introgressed tracts from [ 7 ]: https://reich hms harvard edu/datasets/landscape-neandertal-ancestry-present-day-humans heliconius data from [ 29 ]: https://datadryad org/stash/downloads/file_stream/63229 and https://datadryad org/stash/downloads/file_stream/63228 altai neanderthal data from [ 27 ]: http://cdna eva mpg de/neandertal/altai/altaineandertal/vcf scripts are available in https://github com/leslylopezfang/dplus ."

"No competing interests."

"This work was supported by the National Science Foundation (NSF - www.nsf.gov) grant 1557151 to L.L.F., E.J.M., and E.H.S., the National Science Foundation Research Traineeship grant DGE-1633722 to L.L.F., the Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica - Universidad Nacional Autónoma de México (grant IA200620), the University of California Institute for Mexico and the United States CONACYT grant CN-19-29 to D.O.D.V and the NIH grant R01HG012605, the National Science Foundation grant 1759846 to E.J.M., the National Institutes of Health (NIH -www.nih.gov/) grant R35GM128946-01 to E.H.S, and the Alfred P. Sloan Foundation Fellowship to E.H.S. DP is supported by the Biological Data Science training grant (NIH T32 GM128596) and NIH grant no. R35GM128946 (to E.H.S).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."