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That being said, it seems trivial, but the increasing discovery of highly divergent populations or divergent clusters among populations reveals the presence of possible cryptic species, somehow by serendipity, that the sole use of traditional taxonomic characters may have not highlighted. Indeed, the populations among which we want to assess the exchanges of alleles must be composed of individuals that belong to a unique and same species, in order to estimate genetic distances among comparable entities. Studying population genetic connectivity is first a matter of knowing what we work on, that is, accurately delimiting the evolutionary units. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.
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The issue is now to understand which hierarchical level ( SSH, cluster, or even below) corresponds to the species one. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels ( PSH > SSH > cluster), each level hiding highly differentiated genetic groups. From a large sampling (2,507 colonies) achieved in three marine provinces, genetic structuring analysis conducted with two clustering analyses ( structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. Here, we examined the genetic variability in the coral genus Pocillopora, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods and which was found to split into three secondary species hypotheses ( SSH09a, SSH09b, and SSH09c) according to assignment tests using multi‐locus genotypes (13 microsatellites).