Population genomic analysis reveals genetic structure and thermal-tolerant genotypes in remnant Tasmanian giant kelp populations

Giant kelp, Macrocystis pyrifera, is a foundation species that forms dense forests of complex physical habitat and supports coastal biodiversity, productivity, and other essential ecosystem services. Tasmanian coasts have suffered a massive decline in giant kelp forests due to changes in regional oceanography and environmental conditions, but efforts are being made to restore these disappearing populations using identification and selective breeding for lineages that are more tolerant to warmer temperatures. Here, we used gametophytes that originated from remnant populations collected at three sites in northeastern and three sites in southeastern Tasmania to determine the genetic structure of the giant kelp population via genotyping-by-sequencing (GBS) and assembled a draft genome from a Tasmanian giant kelp sporophyte individual. Previous research identified seven strain lines that were tolerant to warm temperatures, and we used the GBS data to test whether genotypes were associated with warm tolerance. Kelps from the north were genetically distinct from the southern ones, with much lower gene flow between regions than within regions. These results revealed that giant kelp populations from Tasmania are more genetically structured than previously thought. Two loci were significantly associated with warm temperature tolerance. They are population-specific: the alternative allele from one of the loci was found only in the northern populations, while the other was found in the southern populations. This could suggest that thermal tolerance is adapting locally or drifting given large changes in population demography, but further research is needed to confirm this hypothesis. Our research sheds light on genetic patterns in this critical habitat-forming kelp and will help inform conservation management, including selective breeding.