Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling
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...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2017-10-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/25884 |
| _version_ | 1811199316866367488 |
|---|---|
| author | Raghavendran Partha Bharesh K Chauhan Zelia Ferreira Joseph D Robinson Kira Lathrop Ken K Nischal Maria Chikina Nathan L Clark |
| author_facet | Raghavendran Partha Bharesh K Chauhan Zelia Ferreira Joseph D Robinson Kira Lathrop Ken K Nischal Maria Chikina Nathan L Clark |
| author_sort | Raghavendran Partha |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T01:47:10Z |
| format | Article |
| id | doaj.art-3fee9cd90e3946e7a883fc4e029ebc93 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T01:47:10Z |
| publishDate | 2017-10-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-3fee9cd90e3946e7a883fc4e029ebc932022-12-22T03:53:03ZengeLife Sciences Publications LtdeLife2050-084X2017-10-01610.7554/eLife.25884Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunnelingRaghavendran Partha0https://orcid.org/0000-0002-7900-4375Bharesh K Chauhan1https://orcid.org/0000-0002-6429-9190Zelia Ferreira2https://orcid.org/0000-0002-7619-7466Joseph D Robinson3Kira Lathrop4Ken K Nischal5Maria Chikina6Nathan L Clark7https://orcid.org/0000-0003-0006-8374Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United StatesUPMC Eye Center, Children’s Hospital of Pittsburgh, Pittsburgh, United States; Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United StatesDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United StatesDepartment of Molecular and Cell Biology, University of California, Berkeley, United StatesUPMC Eye Center, Children’s Hospital of Pittsburgh, Pittsburgh, United States; Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United StatesUPMC Eye Center, Children’s Hospital of Pittsburgh, Pittsburgh, United States; Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United StatesDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United StatesDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United StatesThe 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.https://elifesciences.org/articles/25884convergent evolutionregressive evolutionsubterranean lifegenetics of visionrelaxation of constraintfunctional constraint |
| spellingShingle | Raghavendran Partha Bharesh K Chauhan Zelia Ferreira Joseph D Robinson Kira Lathrop Ken K Nischal Maria Chikina Nathan L Clark Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling eLife convergent evolution regressive evolution subterranean life genetics of vision relaxation of constraint functional constraint |
| title | Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling |
| title_full | Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling |
| title_fullStr | Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling |
| title_full_unstemmed | Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling |
| title_short | Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling |
| title_sort | subterranean mammals show convergent regression in ocular genes and enhancers along with adaptation to tunneling |
| topic | convergent evolution regressive evolution subterranean life genetics of vision relaxation of constraint functional constraint |
| url | https://elifesciences.org/articles/25884 |
| work_keys_str_mv | AT raghavendranpartha subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling AT bhareshkchauhan subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling AT zeliaferreira subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling AT josephdrobinson subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling AT kiralathrop subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling AT kenknischal subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling AT mariachikina subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling AT nathanlclark subterraneanmammalsshowconvergentregressioninoculargenesandenhancersalongwithadaptationtotunneling |