Data and scripts for the colour analysis from: Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high
environmental heterogeneity across space and time. Indeed, different soft
barriers structure the marine environment, which offers an appealing
opportunity to study various evolutionary processes such as population
differentiation and speciation. Here, we focus on Amphiprion clarkii
(Actinopterygii; Perciformes), the most widespread of clownfishes that
exhibits the highest colour polymorphism. Clownfishes can only disperse
during a short pelagic larval phase before their sedentary adult
lifestyle, which might limit connectivity among populations, thus
facilitating speciation events. Consequently, the taxonomic status of A.
clarkii has been under debate. We used whole-genome resequencing
data of 67 A. clarkii specimens spread across the Indian and Pacific
Oceans to characterise the species' population structure, demographic
history, and colour polymorphism. We found that A. clarkii spread
from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a
stepping-stone dispersal and that gene flow was pervasive throughout its
demographic history. Interestingly, colour patterns differed noticeably
among the Indonesian populations and the two populations at the extreme of
the sampling distribution (i.e. Maldives and New Caledonia), which
exhibited more comparable colour patterns despite their geographic and
genetic distances. Our study emphasises how whole-genome studies can
uncover the intricate evolutionary past of wide-ranging species with
diverse phenotypes, shedding light on the complex nature of the species
concept paradigm.