Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals

Molluscs have a wide variety of sexual systems and have undergone many transitions from separate sexes to hermaphroditism or vice versa, which is of interest for studying the evolution of sex determination and differentiation. Following the serendipitous observation that sex was the primary driver of genetic structure in the hydrothermal vent gastropod Alviniconcha boucheti , we investigated sexual systems and sex determination in this species and two others of the same genus. We combined genome-wide multi-locus genotypes obtained from RAD sequencing with anatomical observations of the gonads of the three Alviniconcha species occurring in the southwest Pacific Ocean: A. boucheti ( n =199), A. strummeri ( n =41 ind.) and A. kojimai ( n =246). In two of the species ( A. boucheti and A. strummeri ), the sexes are separate and genetically determined by a male-heterogametic (XY) system. External observation of the gonads in the third species ( A. kojimai ) also suggested that the sexes were separate, but histological analyses revealed that 76% of the individuals classified as females from external observation of the gonads presented a mosaic of male and female reproductive tissue. Empirical analyses and simulations showed nonetheless that 14 RAD loci were sex-linked with an XY signature in A. kojimai (as compared with 64 in A. strummeri and 373 in A. boucheti ). Comparison across species and mapping of RAD loci to a non-contiguous reference genome assembly of the related species A. marisindica showed that all sex-linked loci identified in A. kojimai are located on five scaffolds that also contain 15 and 67 sex-linked RAD loci in the other two species, respectively. These results suggest that all three Alviniconcha species share the same XY sex determination system, but that the gonad of XX A. kojimai individuals are invaded by a variable proportion of male reproductive tissue. It remains to be seen whether the male tissue in these intersex individuals is functional or not. The identification of Y-specific RAD loci (found only in A. boucheti ) and the phylogenetic analysis of three sex-linked loci shared by all species suggested that X-Y recombination has evolved differently within each species. This situation of three species showing variation in gonadal development around a probably common sex determination system provides new insights into the reproductive mode of poorly known deep-sea species and questions the evolution of gametogenetic polymorphism in these species.