Abstract
The macroalga Macrocystis pyrifera (“giant” or “bladder” kelp) plays a vital role in cold‐temperate marine ecosystems but faces increasing threats from ongoing environmental change. Understanding its population diversity and connectivity is essential for predicting future range shifts and assessing the ecological consequences of such shifts in both present and novel ranges. Here, we used high‐resolution genotyping‐by‐sequencing (GBS) to investigate the population structure of M. pyrifera within and among populations in Aotearoa (New Zealand), Lutruwita (Tasmania), and Falkland Islands/Malvinas. Our results showed New Zealand and Tasmanian populations are more closely related to each other than to those from the Falklands, consistent with isolation by distance. Fine‐scale population structure was detected within each of the three regions, especially New Zealand, where we could pinpoint genetically unique populations down to tens of kilometers. Our research provides insights on fine‐scaled giant kelp diversity and connectivity patterns across three regions in the Southern Hemisphere, which contrast with previous studies that used traditional genetic markers, and will aid future conservation of this ecologically and economically important taxon.