ArticleGenome biology and evolution2018
Concordant Changes in Gene Expression and Nucleotides Underlie Independent Adaptation to Hydrogen-Sulfide-Rich Environments.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Comparative Embryology and Transcriptomics of Asellus infernus, an Isopod Crustacean From Sulfidic Groundwater.Evolution & development · 2025Article
- New Genome Assemblies for Poeciliidae: A Foundation for Adaptation Studies.Genome biology and evolution · 2025Article
- Selection Over Small and Large Spatial Scales in the Face of High Gene Flow.Molecular ecology · 2025Article
- Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.Genome biology and evolution · 2024Article
- Blind fish have cells that see light.Proceedings. Biological sciences · 2023Article
- Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide-rich springs.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish.BMC genomics · 2021Article
- Investigating population-scale allelic differential expression in wild populations ofEcology and evolution · 2020Article
- Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye (Ecology and evolution · 2020Article
- Expression analyses of cave mollies (Biology letters · 2019Article
- Local ancestry analysis reveals genomic convergence in extremophile fishes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary process. In this study, our objectives were 1) to better understand the qualitative concordance between conclusions drawn from analyses of differential expression and changes in genic sequence and 2) to quantitatively test whether differentially expressed genes were enriched for sites putatively under positive selection within gene regions. To achieve this, we compared populations of fish (Poecilia mexicana) that have independently adapted to hydrogen-sulfide-rich environments in southern Mexico to adjacent populations residing in nonsulfidic waters. Specifically, we used RNA-sequencing data to compare both gene expression and DNA sequence differences between populations. Analyzing these two different data types led to similar conclusions about which biochemical pathways (sulfide detoxification and cellular respiration) were involved in adaptation to sulfidic environments. Additionally, we found a greater overlap between genes putatively under selection and differentially expressed genes than expected by chance. We conclude that considering both differential expression and changes in DNA sequence led to a more comprehensive understanding of how these populations adapted to extreme environmental conditions. Our results imply that changes in both gene expression and DNA sequence-sometimes at the same loci-may be involved in adaptation.
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