Phylogeographical patterns and a cryptic species provide new insights into Western Indian Ocean giant clams phylogenetic relationships and colonization history

Aim The unique biodiversity in the Red Sea is the result of complex ecological and evolutionary processes driven by Pleistocene climatic change. Here we investigate the species diversity, phylogenetic relationships and phylogeographical patterns of giant clams in the Western Indian Ocean (WIO) and the Red Sea to explore scenarios of marine speciation in this under‐studied region. Location Mozambique Channel, Madagascar, and the Mascarene Islands (WIO); the Farasan Islands (Red Sea). Taxon Giant clams of the genus Tridacna (Cardiidae: Tridacninae). Methods Giant clams were sampled as complete organisms or through underwater biopsies. Nuclear ( 28S ) and mitochondrial ( 16S and COI ) DNA sequences were subjected to Bayesian and maximum likelihood analyses to generate a phylogenetic hypothesis for all known species within the genus Tridacna . Bayesian inference with molecular and fossil calibration was used to infer their colonization history. Results From the 10 genetically distinct clades recovered from the analyses of 253 sequenced specimens, five distinct Tridacna lineages were sampled, three of which were endemics of the WIO and the Red Sea. Each lineage corresponded to a distinct species, except one grouping the two formerly known WIO endemics, T. lorenzi and T. rosewateri . This lineage clustered with two other well‐supported lineages: the Red Sea endemic T. squamosina , and a previously unrecognized lineage, restricted to the WIO, for which we resurrect the long‐forgotten name T. elongatissima Bianconi, 1856. For the two other species sampled ( T. maxima and T. squamosa ), contrasting phylogeographical patterns were observed. Main conclusions Our data confirm the validity of the species T. rosewateri , a WIO endemic genetically indistinguishable from T. lorenzi , which should be considered a junior synonym. The phylogenetic placement of the newly resurrected T. elongatissima provides insights into the probable origin of T. squamosina , which split from its sister species no later than 2 Ma, likely during Middle Pleistocene glacial periods. Two scenarios are discussed. Our results also suggest that T. maxima invaded the Red Sea more recently and that contemporary gene flow between Red Sea and WIO T. maxima is highly restricted. The deep Red Sea partition observed in T. squamosa suggests a much older divergence and raises the question of a possible cryptic lineage.