Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals

With the advent of genomics, sequencing thousands of loci from hundreds of
individuals now appears feasible at reasonable costs, allowing complex
phylogenies to be resolved. This is particularly relevant for cnidarians,
for which insufficient data due to the small number of currently available
markers, coupled with difficulties in inferring gene trees and
morphological incongruences, encrypts species boundaries, thereby blurring
the study and conservation of these organisms. Yet, can genomics alone be
used to delimit species in an integrative taxonomic context? Here,
focusing on the coral genus Pocillopora, which plays key roles in
Indo-Pacific reef ecosystems but has challenged taxonomists for decades,
we explored and discussed the usefulness of multiple criteria (genetics,
morphology, biogeography and symbiosis ecology) to delimit species of this
genus. Phylogenetic inferences, clustering approaches and species
delimitation methods based on genome-wide single-nucleotide polymorphisms
(SNPs) were first used to resolve Pocillopora phylogeny and propose
genomic species hypotheses from 356 colonies sampled across the
Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and
south-east Polynesia). These species hypotheses were then compared to
previous genetic evidences, as well as to evidences based on morphology,
biogeography and symbiosis. Genomics allowed to delimit 21 species
hypotheses where only seven are currently recognised based on current
taxonomy. Moreover, 13 species were strongly supported by all approaches,
either confirming their currently recognised species status, or supporting
the presence of new species that need to be formally described. Some of
the other genomic species hypotheses were supported by biogeographic or
symbiosis evidences, but additional investigations are needed to state on
their species status. Altogether, our results support (1) the obsolescence
of macromorphology (i.e., overall colony and branches shape) but the
relevance of micromorphology (i.e., corallite structures) to refine
Pocillopora species limits, (2) the need to identify molecularly species
prior to their study, as morphology can blur species identification on the
field, (3) the relevance of the mtORF (coupled with other markers in some
cases) as a diagnostic marker of most species, and (4) the need for a
taxonomical revision in the Pocillopora genus. These results give new
insights into the usefulness of multiple criteria for resolving
Pocillopora species limits and will ultimately provide helpful insights
for the conservation of the species from this scleractinian genus.