Evolution of transcriptional regulation as motor of morphological diversification in cichlid fishes
Evolutionary Cell and Developmental Biology (Zoology)
Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Final Report Abstract
Cichlid fishes are a striking example for repeated ‘explosive’ evolution, forming some of the largest species radiations among vertebrates. In less than ten million years over 1,200 species evolved alone in the species flocks of the three large East African Lakes Victoria, Tanganyika, and Malawi. This astonishing biodiversity with a wide variety of color patterns makes them an ideal vertebrate system to investigate the molecular changes underlying phenotypic diversification. Objective of this grant was to address (1) how phenotypic diversity in the adaptive radiations of cichlids are brought about genetically, especially addressing whether the underlying molecular basis is coding (differences in amino acid sequences) or regulatory (differences in gene expression). Moreover, we wanted to address (2) what the genomic basis of cisregulatory variation is and is for example driven by transposon insertions, SNPs or deletions in DNA sequences and lastly (3) if we can find “master genes” or “master regulatory elements” that are necessary and sufficient to induce species-specific traits? While we initially planned to use a combination of Chromatin ImmunoPrecipitation DNA-Sequencing (ChIP-seq) and RNA sequencing (RNA-seq) we identified a more straightforward approach to address our objectives. Using an available hybrid cross between the two African cichlid species Haplochromis sauvagei and Pundamilia nyererei we were able to comprehensively analyze the molecular and gene-regulatory basis of an adaptive color pattern phenotype: horizontal stripe patterns. Using a combination of this and two additional crosses as well as population mapping data we could identify that a small partially transposon-derived cis-regulatory interval of 1.1kbp is responsible for an approximately 10- fold expression difference of the gene agouti related peptide 2, agrp2. This expression difference (the gene has higher expression in the non-striped species) seems to explain the absence/presence of stripe patterns. In fact, using CRISPR-Cas9 in the Lake Victoria cichlid Pundamilia nyererei, we show that the knockout of agrp2 is sufficient to generate stripe patterns in this naturally non-striped species. Therefore, through genome engineering, we provide functional proof for the role of agrp2 as a repressor of horizontal stripe patterns. Moreover, we were able to show that agrp2 also constitutes the genetic basis of the convergently evolved stripe patterns across several lineages in the East African species flocks of the Lakes Victoria, Malawi and Tanganyika. Hence, we discovered and described how repeated cis-regulatory evolutionary changes are responsible for triggering the remarkable convergence of color patterns. More generally, this study provides evidence that regulatory regions, even of single “master-regulator” loci with large effects, could more generally serve as genomic hotspots of divergence that underlie the repeated origin of conspicuous convergent phenotypes during adaptive radiations. These results provide exciting and novel implications that, beyond cichlids, advance the understanding of the evolution of color patterns and the gene regulatory mechanisms underlying phenotypic diversification and convergence more generally.
Publications
- "Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus)—towards understanding gene function and regulatory evolution in an ecological model system for rapid phenotypic diversification." BMC developmental biology 17.1 (2017): 15
Kratochwil, Claudius F., et al.
(See online at https://doi.org/10.1186/s12861-017-0157-x) - "Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations." Science 362.6413 (2018): 457-460
Kratochwil, Claudius F., et al.
(See online at https://doi.org/10.1126/science.aao6809) - "Evolutionary dynamics of structural variation at a key locus for color pattern diversification in cichlid fishes." Genome Biology and Evolution 11.12 (2019): 3452-3465
Kratochwil, Claudius F., et al.
(See online at https://doi.org/10.1093/gbe/evz261) - "Fragile DNA contributes to repeated evolution." Genome biology 20.1 (2019): 39
Kratochwil, Claudius F., and Axel Meyer
(See online at https://doi.org/10.1186/s13059-019-1655-x) - "Genome of the Malawi golden cichlid fish (Melanochromis auratus) reveals exon loss of oca2 in an amelanistic morph." Pigment cell & melanoma research 32.5 (2019): 719-723
Kratochwil, Claudius F., Sabine Urban, and Axel Meyer
(See online at https://doi.org/10.1111/pcmr.12799) - "Molecular mechanisms of convergent color pattern evolution." Zoology 134 (2019): 66-68
Kratochwil, Claudius F.
(See online at https://doi.org/10.1016/j.zool.2019.04.004)
