DOI: 10.5061/dryad.v41ns1rzw
title: Data from: Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis

description: 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.
description: This data file includes
 genotypes for 2,232 single nucleotide polymorphisms (SNPs) in 687
 individuals of <em>Gracilaria chilense</em> 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. <em>Gracilaria chilense</em> 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. <em>Gracilaria
 chilense</em> 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
 <em>Gracilaria chilensis</em> 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). For more information about the data set and sampling strategy please contact Oscar Huanel (oscar.huanel@gmail.com) or Marie-Laure Guillemin (marielaure.guillemin@gmail.com).