Ecotype-associated structural variants across multiple locally adapted Poeciliid fishes.
6 affiliations
- 1Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
- 2División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, México.
- 3Department of Biology, University of Missouri-St. Louis, St. Louis, MO, 63121, USA.
- 4Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO, 63121, USA.
- 5WildCare Institute, Saint Louis Zoo, St. Louis, MO, 63110, USA.
- 6Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA. [email protected].
Abstract
Background
Extreme environments provide powerful natural laboratories for studying evolutionary convergence across taxa. While convergent phenotypes frequently evolve in response to similar selective pressures, consistent molecular signatures at the nucleotide level are often elusive, potentially due to overlooked genetic variants such as structural variants. Here, we leverage recent advances in long-read sequencing and pangenome approaches to investigate the role of structural variants in repeated adaptation to toxic springs rich in hydrogen sulfide (H₂S) across multiple independently evolved populations within the Poecilia mexicana species complex.Results
We identified more than 99,000 structural variants over 50 base pairs in length, including insertions, deletions, duplications and inversions, using complementary graph- and read-based methods. We then integrated these with population genomic data and RNA-sequencing data to detect variants in highly differentiated regions between ecotypes and assess their functional impacts. Structural variants in both coding and regulatory regions were enriched in genes involved in sulfide metabolism and ion transport, including ethe1, slc13a1, and sqor. We found ecotype-specific structural variants in promoter and intronic regions of key detoxification genes that exhibited elevated expression in H₂S-adapted populations.Conclusions
Our findings suggest that structural variation may contribute to adaptive phenotypes and should be considered in studies of genomic convergence.
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BibTeX
@article{ryan2026ecotypeassociated,
title = {{Ecotype-associated structural variants across multiple locally adapted Poeciliid fishes.}},
author = {Kara Ryan and Rishi De-Kayne and Lenin Arias-Rodriguez and Michael Tobler and Joanna L Kelley},
journal = {BMC genomics},
year = {2026},
month = aug,
doi = {10.1186/s12864-026-13205-9},
url = {https://europepmc.org/article/MED/42958033},
note = {CC BY},
}
RIS
TY - JOUR
TI - Ecotype-associated structural variants across multiple locally adapted Poeciliid fishes.
AU - Kara Ryan
AU - Rishi De-Kayne
AU - Lenin Arias-Rodriguez
AU - Michael Tobler
AU - Joanna L Kelley
PY - 2026
DA - 2026/08/01
JO - BMC genomics
DO - 10.1186/s12864-026-13205-9
UR - https://europepmc.org/article/MED/42958033
AB - Background Extreme environments provide powerful natural laboratories for studying evolutionary convergence across taxa. While convergent phenotypes frequently evolve in response to similar selective pressures, consistent molecular signatures at the nucleotide level are often elusive, potentially due to overlooked genetic variants such as structural variants. Here, we leverage recent advances in long-read sequencing and pangenome approaches to investigate the role of structural variants in repeated adaptation to toxic springs rich in hydrogen sulfide (H₂S) across multiple independently evolved populations within the Poecilia mexicana species complex.Results We identified more than 99,000 structural variants over 50 base pairs in length, including insertions, deletions, duplications and inversions, using complementary graph- and read-based methods. We then integrated these with population genomic data and RNA-sequencing data to detect variants in highly differentiated regions between ecotypes and assess their functional impacts. Structural variants in both coding and regulatory regions were enriched in genes involved in sulfide metabolism and ion transport, including ethe1, slc13a1, and sqor. We found ecotype-specific structural variants in promoter and intronic regions of key detoxification genes that exhibited elevated expression in H₂S-adapted populations.Conclusions Our findings suggest that structural variation may contribute to adaptive phenotypes and should be considered in studies of genomic convergence.
SN - 1471-2164
ER -