Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Evolution of regulatory networks associated with traits under selection in cichlids

View ORCID ProfileTarang K. Mehta, Christopher Koch, Will Nash, Sara A. Knaack, Padhmanand Sudhakar, Marton Olbei, Sarah Bastkowski, Luca Penso-Dolfin, Tamas Korcsmaros, Wilfried Haerty, Sushmita Roy, Federica Di-Palma
doi: https://doi.org/10.1101/496034
Tarang K. Mehta
1Earlham Institute (EI), Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tarang K. Mehta
Christopher Koch
2Dept. of Biostatistics and Medical Informatics, UW Madison, Madison, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Will Nash
1Earlham Institute (EI), Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sara A. Knaack
3Wisconsin Institute for Discovery (WID), Madison, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Padhmanand Sudhakar
1Earlham Institute (EI), Norwich, UK
4Quadram Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marton Olbei
1Earlham Institute (EI), Norwich, UK
4Quadram Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sarah Bastkowski
1Earlham Institute (EI), Norwich, UK
4Quadram Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luca Penso-Dolfin
1Earlham Institute (EI), Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tamas Korcsmaros
1Earlham Institute (EI), Norwich, UK
4Quadram Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wilfried Haerty
1Earlham Institute (EI), Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sushmita Roy
2Dept. of Biostatistics and Medical Informatics, UW Madison, Madison, USA
3Wisconsin Institute for Discovery (WID), Madison, USA
5Dept. of Computer Sciences, UW Madison, Madison, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: federica.di-palma@earlham.ac.uk
Federica Di-Palma
1Earlham Institute (EI), Norwich, UK
6Norwich Medical School, University of East Anglia, Norwich, UK
7School of Biological Sciences, University of East Anglia, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: federica.di-palma@earlham.ac.uk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is still known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically-diverse species. Using a novel approach to reconstruct GRNs in vertebrate species, we aimed to study GRN evolution in representative species of the most striking example of an adaptive radiation, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids is attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. To investigate these mechanisms across species at a genome-wide scale, our novel network-based approach identifies ancestral and extant gene co-expression modules along a phylogeny, and by integrating associated regulators, predicts candidate regulatory regions implicated in traits under selection in cichlids. As a case study, we present data from a well-studied adaptive trait - the visual system - for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate the plausibility of their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species, and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Our approach revealed numerous novel potential candidate regulatory regions across cichlid genomes with no prior association, as well as those with previously reported associations to known adaptive evolutionary traits, thus providing proof of concept.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Several updates to results and discussion, including the addition of a figure; supplementary material also updated.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted April 17, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Evolution of regulatory networks associated with traits under selection in cichlids
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Evolution of regulatory networks associated with traits under selection in cichlids
Tarang K. Mehta, Christopher Koch, Will Nash, Sara A. Knaack, Padhmanand Sudhakar, Marton Olbei, Sarah Bastkowski, Luca Penso-Dolfin, Tamas Korcsmaros, Wilfried Haerty, Sushmita Roy, Federica Di-Palma
bioRxiv 496034; doi: https://doi.org/10.1101/496034
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Evolution of regulatory networks associated with traits under selection in cichlids
Tarang K. Mehta, Christopher Koch, Will Nash, Sara A. Knaack, Padhmanand Sudhakar, Marton Olbei, Sarah Bastkowski, Luca Penso-Dolfin, Tamas Korcsmaros, Wilfried Haerty, Sushmita Roy, Federica Di-Palma
bioRxiv 496034; doi: https://doi.org/10.1101/496034

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2530)
  • Biochemistry (4972)
  • Bioengineering (3482)
  • Bioinformatics (15212)
  • Biophysics (6897)
  • Cancer Biology (5390)
  • Cell Biology (7738)
  • Clinical Trials (138)
  • Developmental Biology (4530)
  • Ecology (7147)
  • Epidemiology (2059)
  • Evolutionary Biology (10227)
  • Genetics (7512)
  • Genomics (9786)
  • Immunology (4844)
  • Microbiology (13215)
  • Molecular Biology (5138)
  • Neuroscience (29435)
  • Paleontology (203)
  • Pathology (837)
  • Pharmacology and Toxicology (1463)
  • Physiology (2138)
  • Plant Biology (4748)
  • Scientific Communication and Education (1013)
  • Synthetic Biology (1338)
  • Systems Biology (4012)
  • Zoology (768)