Genome-Wide Evolution of Lineage-Specific Chromatin Accessibility Links Regulatory Changes to Cichlid Phenotypic Diversity.
6 affiliations
- 1Department of Biochemistry, Cell and Systems Biology, University of Liverpool, Liverpool L69 7BE, UK.
- 2Earlham Institute, Norwich NR4 7UZ, UK.
- 3Evolutionary and Ecological Genomics Group, School of Environmental and Life Sciences, University of Hull, Kingston Upon Hull HU6 7RX, UK.
- 4Department of Environmental Sciences, Zoological Institute, University of Basel, 4056 Basel, Switzerland.
- 5Department of Medical Genetics, University of British Columbia, Vancouver V6H 3N1, Canada.
- 6School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
Abstract
East African cichlids from Lakes Victoria, Malawi, and Tanganyika have undergone explosive adaptive radiation, generating extensive morphological, ecological, and behavioral diversity within a few million years. Understanding how genome-wide regulatory evolution contributes to this diversification requires comparative analyses of chromatin accessibility, transcription factor (TF) binding, and gene regulatory networks across species and tissues. Here, we combine high-coverage ATAC-seq with matched RNA-seq in forebrain, retina, liver, and testis from five East African cichlid species spanning radiating and nonradiating lineages to characterize the evolution of regulatory landscapes in this radiation. Thousands of promoter-associated accessible sites are conserved across species and tissues, yet more than half of these shared promoters show signatures of accelerated nucleotide evolution, particularly in genes linked to development and sensory function. In contrast, smaller sets of lineage- and tissue-specific accessible promoters, especially in retina, exhibit strong regulatory divergence and functional enrichment for visual system processes. Integrating TF footprinting and expression data uncovers pervasive TF binding site (TFBS) turnover at active promoters and extensive, tissue-dependent rewiring of motif-supported gene regulatory networks, with 86% to 97% of high-confidence edges being species-specific. Extending promoter TFBS variants into broader Malawi and tilapia phylogenies shows that functional variants in promoters of visual genes, such as actr1, segregate by clade and ecological niche. Together, these results demonstrate how accelerated regulatory sequence evolution, chromatin accessibility divergence, and TFBS turnover jointly reshape regulatory architecture genome-wide in an iconic vertebrate radiation, providing insights into how noncoding regulatory evolution can drive rapid phenotypic diversification.
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BibTeX
@article{mehta2026genomewide,
title = {{Genome-Wide Evolution of Lineage-Specific Chromatin Accessibility Links Regulatory Changes to Cichlid Phenotypic Diversity.}},
author = {Tarang K Mehta and Angela L Man and Graham Etherington and Alan M Smith and Adrian Indermaur and Walter Salzburger and Domino Joyce and Federica Di-Palma and Wilfried Haerty},
journal = {Genome biology and evolution},
year = {2026},
month = oct,
doi = {10.1093/gbe/evag247},
url = {https://europepmc.org/article/MED/42848741},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genome-Wide Evolution of Lineage-Specific Chromatin Accessibility Links Regulatory Changes to Cichlid Phenotypic Diversity.
AU - Tarang K Mehta
AU - Angela L Man
AU - Graham Etherington
AU - Alan M Smith
AU - Adrian Indermaur
AU - Walter Salzburger
AU - Domino Joyce
AU - Federica Di-Palma
AU - Wilfried Haerty
PY - 2026
DA - 2026/10/01
JO - Genome biology and evolution
DO - 10.1093/gbe/evag247
UR - https://europepmc.org/article/MED/42848741
AB - East African cichlids from Lakes Victoria, Malawi, and Tanganyika have undergone explosive adaptive radiation, generating extensive morphological, ecological, and behavioral diversity within a few million years. Understanding how genome-wide regulatory evolution contributes to this diversification requires comparative analyses of chromatin accessibility, transcription factor (TF) binding, and gene regulatory networks across species and tissues. Here, we combine high-coverage ATAC-seq with matched RNA-seq in forebrain, retina, liver, and testis from five East African cichlid species spanning radiating and nonradiating lineages to characterize the evolution of regulatory landscapes in this radiation. Thousands of promoter-associated accessible sites are conserved across species and tissues, yet more than half of these shared promoters show signatures of accelerated nucleotide evolution, particularly in genes linked to development and sensory function. In contrast, smaller sets of lineage- and tissue-specific accessible promoters, especially in retina, exhibit strong regulatory divergence and functional enrichment for visual system processes. Integrating TF footprinting and expression data uncovers pervasive TF binding site (TFBS) turnover at active promoters and extensive, tissue-dependent rewiring of motif-supported gene regulatory networks, with 86% to 97% of high-confidence edges being species-specific. Extending promoter TFBS variants into broader Malawi and tilapia phylogenies shows that functional variants in promoters of visual genes, such as actr1, segregate by clade and ecological niche. Together, these results demonstrate how accelerated regulatory sequence evolution, chromatin accessibility divergence, and TFBS turnover jointly reshape regulatory architecture genome-wide in an iconic vertebrate radiation, providing insights into how noncoding regulatory evolution can drive rapid phenotypic diversification.
SN - 1759-6653
ER -