Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean population has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during the post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2,232 SNPs to assess how the species evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. ABC analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species.

Understanding the evolution of sexual vs asexual reproduction and their consequences in population genetics is a central tenet of evolutionary biology. Nevertheless, until now, it has proved unachievable to assess partially clonal reproduction when the rate of clonality is less than 95%, especially without the use of genome-wide data or temporal samples. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. The results of these investigations have been interpreted by comparison with the sexually reproducing congeneric species Laminaria digitata. Genome-wide variation was assessed by dd-RAD sequencing using 4077 SNPs in L. rodriguezii and 7364 SNPs in L. digitata. As predicted for partially clonal populations, the distribution of FIS within populations of L. rodriguezii was centered in negative values, with heterozygote excess at most loci along the genomes. This finding is the opposite of what we reported within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, two distinct distribution patterns of FIS were reported among populations of L. rodriguezii, consistent with the results predicted by the theoretical model for different levels of clonality. These findings highlight that the investment in clonal growth could differ among populations of L. rodriguezii, confirming that the full distribution of FIS is a promising feature to take into account for the study of asexuality in natural populations. We discuss the implications of these results for the conservation of the rare deep water kelp L. rodriguezii.