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Cited by 160Subterranean biodiversity and taxonomyEvolution and Genetic DynamicsEvolution and Paleontology Studies

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

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Partha, Raghavendran, Chauhan, Bharesh K, Ferreira, Zelia, Robinson, Joseph D, Lathrop, Kira, Nischal, Ken K, Chikina, Maria, Clark, Nathan L·2017·eLife
DOI 10.7554/elife.25884PMC PMC5643096
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Abstract

The underground environment imposes unique demands on life that have led subterranean species to evolve specialized traits, many of which evolved convergently. We studied convergence in evolutionary rate in subterranean mammals in order to associate phenotypic evolution with specific genetic regions. We identified a strong excess of vision- and skin-related genes that changed at accelerated rates in the subterranean environment due to relaxed constraint and adaptive evolution. We also demonstrate that ocular-specific transcriptional enhancers were convergently accelerated, whereas enhancers active outside the eye were not. Furthermore, several uncharacterized genes and regulatory sequences demonstrated convergence and thus constitute novel candidate sequences for congenital ocular disorders. The strong evidence of convergence in these species indicates that evolution in this environment is recurrent and predictable and can be used to gain insights into phenotype–genotype relationships.

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  • Convergence at the molecular level can arise because of identical substitutions.

    “Convergence at the molecular level can arise because of identical substitutions, and convergent rate changes can arise via consistent shifts in substitution rate in genomic regions influencing particular phenotypic targets of natural selection”

    From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Partha et al. 2017

  • Convergent rate changes can arise via consistent shifts in substitution rate in genomic regions influencing particular phenotypic targets of natural selection.

    “Convergence at the molecular level can arise because of identical substitutions, and convergent rate changes can arise via consistent shifts in substitution rate in genomic regions influencing particular phenotypic targets of natural selection”

    From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Partha et al. 2017

  • Chikina et al. quantified the difference of relative substitution rates between terrestrial and marine branches using a nonparametric test (Wilcoxon rank sum test); the same approach has been extended to noncoding regions.

    “Chikina et al. (2016), studying protein-coding genes with convergent substitution rate shifts in marine mammals, quantified the difference of relative substitution rates between “terrestrial” and “marine” branches using a nonparametric test (Wilcoxon rank sum test); the same approach has subsequently been extended to noncoding regions (Partha et al. 2017).”

    From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Partha et al. 2017

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Cited by

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Authors
Partha, R., Chauhan, B. K., Ferreira, Z., Robinson, J. D., Lathrop, K., Nischal, K. K., Chikina, M., & Clark, N. L.
Affiliations
  • University of Pittsburgh (US)
  • Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
  • University of California, Berkeley (US)
Corresponding author
  • Chikina, Maria
  • Clark, Nathan L
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2017-10-16
Volume
6
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.25884
PMC
PMC5643096
OpenAlex
W2766475821
Cited by
160
References
5
Citations by year
2026: 12 · 2025: 20 · 2024: 19 · 2023: 23 · 2022: 15 · 2021: 14 · 2020: 21 · 2019: 21 · 2018: 14 · 2017: 1
FWCI
10.63
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Eye Institute (Core Grant P30 EY008098)
  • Research to Prevent Blindness
  • Eye and Ear Foundation of Pittsburgh
  • Jack Buncher Foundation
  • National Institutes of Health (Core Grant P30 EY008098, U54HG008540, R03MH109009, R01HG009299)
  • National Science Foundation and Department of Defense (Research Experience for Undergraduates NSF-DBI 1263020)
  • Pittsburgh Foundation (Charles E. Kaufman New Investigator Award)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Subterranean biodiversity and taxonomy
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Keywords
subterranean mammals, convergent evolution, enhancers, constraint relaxation, vision loss, genotype-phenotype correlation, regulatory evolution
MeSH terms
Adaptation, Biological, Animals, Biological Evolution, Eye, Mammals, Ocular Physiological Phenomena, Ecosystem

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