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Molecular studies have shown that Neotropical fishes of the order Characiformes have undergone two independent events of cave colonization. Among these fishes are the Mexican blind cavefish ( Astyanax mexicanus ), a well-studied model system for cave adaptation, and the lesser-known Brazilian blind characid ( Stygichthys typhlops ). Although various genomic and transcriptomic approaches have been used to identify genes responsible for cave adaptation in A. mexicanus , these genetic factors have not been explored in an evolutionary comparative framework in cave-adapted characiforms. To address this gap, we assembled a de novo transcriptome for the Brazilian blind characid, identifying 27,845 assembled unigenes, of which 22,580 were assigned as putative one-to-one orthologs to the Mexican cavefish. We then used the package RELAX to analyze 789 genes in cavefishes, identifying 311 genes under intensified or relaxed selection. Our analysis revealed 26 genes with signatures of convergent, relaxed selection linked to vision, circadian cycles, pigmentation, and hematopoiesis processes. Additionally, we conducted differential gene expression analyzes between the snout region and a control tissue sample (muscle), identifying 96 differentially expressed genes associated with cell-surface-bound and calcium-binding proteins. Our study offers insights into the genetic mechanisms underlying cave adaptation in characiform fishes, particularly the Brazilian blind characid. Moreover, our transcriptome dataset and list of genes under convergent, relaxed, and intensified selection serve as a valuable resource for future functional studies of genes involved in cave adaptation. Our work highlights the importance of examining genetic adaptations in multiple independent lineages to better understand the evolutionary processes underlying cave adaptation.
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This content will become publicly available on July 1, 2026
Ancient climate changes and relaxed selection shape cave colonization in North American cavefishes
Extreme environments serve as natural laboratories for studying evolutionary processes, with caves offering replicated instances of independent colonizations. The timing, mode and genetic underpinnings underlying cave-obligate organismal evolution remain enigmatic. We integrate phylogenomics, fossils, palaeoclimatic modelling and newly sequenced genomes to elucidate the evolutionary history and adaptive processes of cave colonization in the study group, the North American Amblyopsidae fishes. Amblyopsid fishes present a unique system for investigating cave evolution, encompassing surface, facultative cave-dwelling and cave-obligate (troglomorphic) species. Using 1105 exon markers and total-evidence dating, we reconstructed a robust phylogeny that supports the nested position of eyed, facultative cave-dwelling species within blind cavefishes. We identified three independent cave colonizations, dated to the Early Miocene (18.5 Ma), Late Miocene (10.0 Ma) and Pliocene (3.0 Ma). Evolutionary model testing supported a climate-relict hypothesis, suggesting that global cooling trends since the Early–Middle Eocene may have influenced cave colonization. Comparative genomic analyses of 487 candidate genes revealed both relaxed and intensified selection on troglomorphy-related loci. We found more loci under relaxed selection, supporting neutral mutation as a significant mechanism in cave-obligate evolution. Our findings provide empirical support for climate-driven cave colonization and offer insights into the complex interplay of selective pressures in extreme environments.
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- Award ID(s):
- 2047939
- PAR ID:
- 10632136
- Publisher / Repository:
- The Royal Society Publishing
- Date Published:
- Journal Name:
- Proceedings of the Royal Society B: Biological Sciences
- Volume:
- 292
- Issue:
- 2051
- ISSN:
- 1471-2954
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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