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CC BY-NC V4.0, Open Access
Journal article
Concordant Changes in Gene Expression and Nucleotides Underlie Independent Adaptation to Hydrogen-Sulfide-Rich Environments
Genome biology and evolution, Vol.10(11), pp.2867-2881
2018
Handle:
https://hdl.handle.net/2376/117471
PMCID: PMC6225894
PMID: 30215710
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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Details
- Title
- Concordant Changes in Gene Expression and Nucleotides Underlie Independent Adaptation to Hydrogen-Sulfide-Rich Environments
- Creators
- Anthony P Brown - School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164Lenin Arias-Rodriguez - División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, MéxicoMuh-Ching Yee - Stanford Functional Genomics Facility, CCSR 0120, Stanford, CA 94305Michael Tobler - Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506Joanna L Kelley - School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164
- Publication Details
- Genome biology and evolution, Vol.10(11), pp.2867-2881
- Academic Unit
- Kelley Lab; Biological Sciences, School of
- Publisher
- Oxford University Press
- Grant note
- W911NF-15-1-0175; W911NF-16-1-0225 / ; IOS-1121832; IOS-1463720; IOS-1557795; IOS-1557860 / ; ; DGOPA.09004.041111.3088; SGPA/DGVS/04315/11; PRMN/DGOPA-003/2014; PRMN/DGOPA-009/2015 / ;
- Identifiers
- 99900547844501842
- Language
- English
- Resource Type
- Journal article