Data from: Rapid radiation in a highly diverse marine environment

Rapid diversification is often observed when founding species invade
isolated or newly formed habitats that provide ecological opportunity for
adaptive radiation. However, most of the Earth’s diversity arose in
diverse environments where ecological opportunities appear to be more
constrained. Here, we present a striking example of a rapid radiation in a
highly diverse marine habitat. The hamlets, a group of reef fishes from
the wider Caribbean, have radiated into a stunning diversity of color
patterns but show low divergence across other ecological axes. Although
the hamlet lineage is approximately 26 million years old, the radiation
appears to have occurred within the last 10,000 generations in a burst of
diversification that ranks among the fastest in fishes. As such, the
hamlets provide a compelling backdrop to uncover the genomic elements
associated with phenotypic diversification and an excellent opportunity to
build a broader comparative framework for understanding the drivers of
adaptive radiation. The analysis of 170 genomes suggests that color
pattern diversity is generated by different combinations of alleles at a
few large-effect loci. Such a modular genomic architecture of
diversification has been documented before in Heliconius butterflies,
capuchino finches and munia finches, three other tropical radiations that
took place in highly diverse and complex environments. The hamlet
radiation also occurred in a context of high effective population size,
which is typical of marine populations. This allows for the accumulation
of new variants through mutation and the retention of ancestral genetic
variation, both of which appear to be important in this radiation.