Computational Genomics and Its Applications to Anthropological Questions DOI Creative Commons
Kelsey E. Witt, Fernando A. Villanea

American Journal of Physical Anthropology, Journal Year: 2024, Volume and Issue: 186(S78)

Published: Dec. 1, 2024

ABSTRACT The advent of affordable genome sequencing and the development new computational tools have established a era genomic knowledge. Sequenced human genomes number in tens thousands, including thousands ancient genomes. abundance data has been met with analysis that can be used to understand populations' demographic evolutionary histories. Thus, variety methods now exist leveraged answer anthropological questions. This includes novel likelihood Bayesian methods, machine learning techniques, vast array population simulators. These provide powerful insights gained from datasets, although they are generally inaccessible those less experience. Here, we outline theoretical workings behind genomics limitations other considerations when applying these examples how already applied We hope this review will empower anthropologists utilize their own research.

Language: Английский

Potential Adaptive Introgression From Dogs in Iberian Grey Wolves (Canis lupus) DOI Creative Commons
Carlos Sarabia, Isabel Salado, Alberto Fernández‐Gil

et al.

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

ABSTRACT Invading species along with increased anthropogenization may lead to hybridization events between wild and closely related domesticates. As a consequence, carry introgressed alleles from domestic species, which is generally assumed yield adverse effects in populations. The opposite evolutionary adaptive introgression, where genes are positively selected the possible but has rarely been documented. Grey wolves ( Canis lupus ) widely distributed across Holarctic frequently coexist their close relative, dog C. familiaris ). Despite ample opportunity, occurs most Here we studied geographically isolated grey of Iberian Peninsula, who have coexisted large population loosely controlled dogs for thousands years human‐modified landscape. We assessed extent impact introgression on current wolf by analysing 150 whole genomes other Eurasian as well originating Europe western Siberia. identified almost no recent small (< 5%) overall ancient ancestry. Using combination single scan statistics ancestry enrichment estimates, positive selection six DAPP1 , NSMCE4A MPPED2 PCDH9 MBTPS1 CDH13 dogs. include functions immune response brain functions, explain some unique behavioural phenotypes such reduced dispersal compared

Language: Английский

Citations

0
Opportunities and challenges of local ancestry in genetic association analyses DOI
Quan Sun, Andréa R. V. R. Horimoto, Brian Chen

et al.

The American Journal of Human Genetics, Journal Year: 2025, Volume and Issue: 112(4), P. 727 - 740

Published: April 1, 2025

Language: Английский

Citations

0
Diffusion-based artificial genomes and their usefulness for local ancestry inference DOI Creative Commons
Antoine Szatkownik,

Léo Planche,

Maïwen Demeulle

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 31, 2024

Abstract The creation of synthetic data through generative modeling has emerged as a significant area research in genomics, offering versatile applications from tailoring functional sequences with specific attributes to generating high-quality, privacy-preserving silico genomes. Notwithstanding these advancements, key challenge remains: while some methods exist evaluate artificially generated genomic data, comprehensive tools assess its usefulness are still limited. To tackle this issue and present promising use case, we test artificial genomes within the framework population genetics local ancestry inference (LAI). Building on previous work deep for introduce novel, frugal diffusion model show that it produces high-quality data. We then performance downstream machine learning LAI trained composite datasets comprising both real and/or Our findings reveal achieves comparable when exclusively versus Moreover, highlight how augmentation using significantly benefits model, particularly is Finally, compare conventional single dataset robust ensemble approach, wherein multiple models diverse datasets, their predictions aggregated. study highlights potential diffusion-based integration genomics. This approach could improve fair representation across populations by overcoming accessibility challenges, ensuring reliability analyses conducted

Language: Английский

Citations

0
Computational Genomics and Its Applications to Anthropological Questions DOI Creative Commons
Kelsey E. Witt, Fernando A. Villanea

American Journal of Physical Anthropology, Journal Year: 2024, Volume and Issue: 186(S78)

Published: Dec. 1, 2024

ABSTRACT The advent of affordable genome sequencing and the development new computational tools have established a era genomic knowledge. Sequenced human genomes number in tens thousands, including thousands ancient genomes. abundance data has been met with analysis that can be used to understand populations' demographic evolutionary histories. Thus, variety methods now exist leveraged answer anthropological questions. This includes novel likelihood Bayesian methods, machine learning techniques, vast array population simulators. These provide powerful insights gained from datasets, although they are generally inaccessible those less experience. Here, we outline theoretical workings behind genomics limitations other considerations when applying these examples how already applied We hope this review will empower anthropologists utilize their own research.

Language: Английский

Citations

0