Fine‐Scale Population Structure, High Gene Flow and Local Adaptation in Australasian Snapper (Chrysophrys auratus) in New Zealand

Abstract

Understanding how populations are structured and adapt to their local environment is critical for developing effective management strategies. We used the commercially and culturally valued marine teleost Chrysophrys auratus (the Australasian snapper) as an exemplar of a high‐gene‐flow species to study genetic structure, population connectivity, and local adaptation. We performed whole‐genome sequencing of 382 individuals across 13 sample locations, covering the range of the species in New Zealand. We find that snapper consist of two genetic clusters with low levels of genetic differentiation (FST = 0.0031): a northeastern (NE) and a southwestern (SW) cluster, with genetic discontinuities around the Tauroa and Mahia Peninsulas. We further observe widespread admixture and dispersal events, which are indicative of ongoing gene flow, in particular around the areas of the genetic discontinuities near the Tauroa and Mahia Peninsulas. Selection scans identified 25 regions of interest (ROIs) throughout the genome. The haplotype‐based statistic XP‐nSL was used to identify which genetic cluster each ROI was most likely under selection, 12 and 13 ROIs for the NE and SW clusters, respectively. The identification of candidate genes with similar molecular functions provided tentative evidence of polygenic adaptation to local environments. Finally, we discuss how monitoring genetic variation contributes to fisheries management by maintaining genetic diversity and resilience in commercial fish. These insights into genetic structure, connectivity, genetic diversity, and local adaptation are critical for protecting species under increased pressure from anthropogenic threats like fishing and climate change, and are thus directly applicable to fisheries management.