Abstract
Abstract
Defining what a species is remains one of the biggest questions in biology and directly challenges species delimitation in species complexes. The wide-spread Clark’s anemonefish
Amphiprion clarkii
has the widest range of all anemonefishes, from the Indian Ocean to the Central Pacific. However, the taxonomy of this species has been confused since its initial description due to its great variation in morphology and pigmentation even within the same locality. Here, we combined whole genome re-sequencing data from 166 individuals spanning most of the distribution of
A. clarkii,
including remote islands such as Ogasawara and Guam in the northwestern Pacific, and also including three individuals of the closely related
A. tricinctus
from the Marshall Islands. Our population genomic analyses reveal an unexpected level of divergence, with five deeply separated lineages corresponding to the Indian Ocean, Central Indo-Pacific, Melanesia, and the isolated population of Ogasawara. The fifth lineage comprises
A. clarkii
from Guam and
A. tricinctus
, revealing that
A. tricinctus
is phylogenetically nested within
A. clarkii
, challenging its current taxonomic status. The most divergent lineage, Melanesia, is genetically more distant from other
A. clarkii
lineages than several recognised species pairs within the
Amphiprion
genus, yet demographic modelling shows ongoing gene flow between all lineages. Together, our results highlight a hidden diversity and stress the necessity of an integrative taxonomic revision of the
A. clarkii
species complex.