Paleogenomic time series reveal past population dynamics and their relevance for the conservation of the Alpine ibex
- 1Swiss Federal Research Institute WSL
Abstract
Endangered species often suffer from genetic threats such as inbreeding depression, the accumulation of mutation load and the general loss of genetic diversity, which may deprive them from future adaptation. Since the genetic make-up of a species is strongly affected by its evolutionary past, however, interspecific comparisons are difficult and absolute levels of genetic diversity may be a relatively poor predictor of extinction risk. To better interpret current levels of genetic diversity of actively managed species, the comparison of present-day genomic data to that of ancient material pre-dating recent anthropogenic population declines has been advocated, but remains rarely done at the evolutionary time scales necessary to understand past population dynamics. Here we demonstrate the usefulness of deep genomic time series through 40 high quality ancient genomes of the Alpine ibex, which faced near-extinction in the 19th century but has since been reintroduced across the Alps and recovered remarkably. The samples, which span the last 14,000 years, evidence strong and stable population structure at the continental scale, paired with frequent extinction and recolonization events at the local scale. These metapopulation dynamics resulted in small and largely isolated populations, with present-day, reintroduced populations only having 20% to 40% less neutral genetic diversity and 3% higher mutation load, likely due to efficient purging in the past. At the species level, however, the loss of genetic diversity was dramatic and reduced to the small fraction that segregated within the only surviving population in the Gran Paradiso area. Our analyses of ancient metapopulation dynamics in Alpine ibex underscore the importance of a healthy genetic pool for successful recolonization and long-term survival, as well as the real possibility of regional extinctions.
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BibTeX
@misc{wietlisbach2026paleogenomic,
title = {{Paleogenomic time series reveal past population dynamics and their relevance for the conservation of the Alpine ibex}},
author = {X. Wietlisbach and M. Robin and A. Füglistaler and G. Ferrari and P. Cloarec-Pioffet and A. Zechner and C. Griggo and M. Blant and W. Imhof and M. Trüssel and J.-M. Petillon and G. Gressman and L. Dalen and D. Wegmann and C. Grossen},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.28.755134},
url = {https://www.biorxiv.org/content/10.64898/2026.09.28.755134v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Paleogenomic time series reveal past population dynamics and their relevance for the conservation of the Alpine ibex
AU - X. Wietlisbach
AU - M. Robin
AU - A. Füglistaler
AU - G. Ferrari
AU - P. Cloarec-Pioffet
AU - A. Zechner
AU - C. Griggo
AU - M. Blant
AU - W. Imhof
AU - M. Trüssel
AU - J.-M. Petillon
AU - G. Gressman
AU - L. Dalen
AU - D. Wegmann
AU - C. Grossen
PY - 2026
DA - 2026/09/28
PB - bioRxiv
DO - 10.64898/2026.09.28.755134
UR - https://www.biorxiv.org/content/10.64898/2026.09.28.755134v1
AB - Endangered species often suffer from genetic threats such as inbreeding depression, the accumulation of mutation load and the general loss of genetic diversity, which may deprive them from future adaptation. Since the genetic make-up of a species is strongly affected by its evolutionary past, however, interspecific comparisons are difficult and absolute levels of genetic diversity may be a relatively poor predictor of extinction risk. To better interpret current levels of genetic diversity of actively managed species, the comparison of present-day genomic data to that of ancient material pre-dating recent anthropogenic population declines has been advocated, but remains rarely done at the evolutionary time scales necessary to understand past population dynamics. Here we demonstrate the usefulness of deep genomic time series through 40 high quality ancient genomes of the Alpine ibex, which faced near-extinction in the 19th century but has since been reintroduced across the Alps and recovered remarkably. The samples, which span the last 14,000 years, evidence strong and stable population structure at the continental scale, paired with frequent extinction and recolonization events at the local scale. These metapopulation dynamics resulted in small and largely isolated populations, with present-day, reintroduced populations only having 20% to 40% less neutral genetic diversity and 3% higher mutation load, likely due to efficient purging in the past. At the species level, however, the loss of genetic diversity was dramatic and reduced to the small fraction that segregated within the only surviving population in the Gran Paradiso area. Our analyses of ancient metapopulation dynamics in Alpine ibex underscore the importance of a healthy genetic pool for successful recolonization and long-term survival, as well as the real possibility of regional extinctions.
ER -