The genomic timeline of cichlid fish diversification across continents

Michael Matschiner,Fabrizia Ronco,Astrid Böhne,Walter Salzburger

doi:10.1038/s41467-020-17827-9

Abstract

Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; however, a central aspect of their evolution — the timeline of their diversification — remains contentious. Here, we generate draft genome assemblies of 14 species representing the global cichlid diversity and integrate these into a new phylogenomic hypothesis of cichlid and teleost evolution that we time-calibrate with 58 re-evaluated fossil constraints and a new Bayesian model accounting for fossil-assignment uncertainty. Our results support cichlid diversification long after the breakup of the supercontinent Gondwana and lay the foundation for precise temporal reconstructions of the exceptional continental cichlid adaptive radiations.

Highlights

Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; a central aspect of their evolution — the timeline of their diversification — remains contentious
The different age estimates imply contrasting scenarios for the spread of cichlids across continents: the oldest estimates are compatible with an ancestral cichlid lineage that lived in freshwaters of the former supercontinent Gondwana and diverged by vicariance with its tectonic breakup between 150 and 85 Ma3, all younger timelines require either long-distance oceanic dispersal events or multiple independent transitions to freshwater from an unknown common marine ancestor (Fig. 1)
In this study, we generated draft genome assemblies of 14 representative cichlid species and developed a new Bayesian model to account for fossil-assignment uncertainty to estimate clade ages in a set of 90 teleosts with a particular focus on cichlid diversification times, using 58 re-evaluated fossil constraints

Summary

Introduction

Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; a central aspect of their evolution — the timeline of their diversification — remains contentious. The contrasting estimates regarding the timeline of cichlid evolution are due—at least in part—to the use of small phylogenetic datasets dominated by mitochondrial sequences[7,8,9] and to the application of strategies for time calibration that rely exclusively on the cichlid fossil record, without taking into consideration the larger context of teleost evolution, into which the cichlid timeline must be placed[5,10,11] Even if these two issues are addressed, age estimates are still heavily influenced by the often ambiguous assignment of calibration fossils to taxonomic clades, as highlighted in recent studies[12,13,14]. The resulting timeline based on 91 fish genomes and the fossil record supports the diversification of cichlid fishes long after the breakup of the Gondwanan supercontinent

Methods

Results

Conclusion