Data from: Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis
Cite this dataset
Huanel, Oscar R. et al. (2022). Data from: Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis [Dataset]. Dryad. https://doi.org/10.5061/dryad.v41ns1rzw
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.
This data file includes genotypes for 2,232 single nucleotide polymorphisms (SNPs) in 687 individuals of Gracilaria chilense collected from 36 populations across the South Pacific Ocean, including New Zealand, Chatham Island, Perú, and Chile. The genetic data were obtained with ddRAD next-generation sequencing. Gracilaria chilense is a red alga presenting a typical haploid-diploid sexual life cycle and both and both haploids gametophytes and diploids sporophytes can be sampled jointly in population reproducing sexually. The species has the capacity to reproduce asexually by cuttings. Samples were collected from both rocky shores (i.e., attached individuals resulting from spore settlement, and therefore from sexual reproduction) and soft bottoms (i.e., free-floating thalli propagating vegetatively) when available. Gracilaria chilense is one of the few red algae that have been domesticated, and cultivated farms, populated almost exclusively by free-floating thalli propagating vegetatively, are commonly encountered in Chile.
The first row of the vcf data file corresponds to sample ID that includes codes for: sampled country (NZ: New Zealand, PE: Peru, and CH: Chile) and locality (codes for localities are as in associated Table 1), ploidy (2n= diploid and n= haploid), and in each locality a unique code for each individual.
Table 1: Location of the 36 Gracilaria chilensis sampling localities in the South Pacific. The country, sampling locality and bioregion, type of population (attached or free-floating), position and number of haploids and diploids sampled are indicated. Bioregions are indicated in bold, following the New Zealand Coastal Biogeographic Regions Classification map (available at https://www.doc.govt.nz/documents/conservation/marine-and-coastal/marine-protected-areas/coastal-marine-habitats-marine-protected-areas.pdf, the Peru-Chile biogeographic classification of Camus (2001).
Fondo Nacional de Desarrollo Científico y Tecnológico, Award: 1090360
Fondo Nacional de Desarrollo Científico y Tecnológico, Award: 1170541
Agence Nationale de la Recherche, Award: ANR-10-BTBR-04