Bioregional boundaries and genomically-delineated stocks in snapper (Chrysophrys auratus) from southeastern Australia

Abstract

Marine species often exhibit genetic discontinuities concordant with biogeographic boundaries, frequently occurring due to changes in ocean circulation, bathymetry, coastline topography and temperature. Here we used 10,916 single nucleotide polymorphisms (SNPs) to assess the concordance between population genomic differentiation and coastal biogeography in the fishery important snapper (Chrysophrys auratus) across southeastern Australia. Additionally, we investigated whether spatial scales of assessment and management of snapper align with evidence from population genomics. Across 488 snapper samples from 11 localities between the west coast of South Australia and the south coast of New South Wales, we detected genomic structure concordant with the region three biogeographic provinces. We also detected fine-scale genetic structuring relating to spatial variation in spawning and recruitment dynamics, as well as temporal stability in the genomic signal associated with two important spawning grounds. The current management boundaries in the region coincided with either the genetic breaks at bioregional boundaries or with local-scale variation. Our study highlights the value of population genomic surveys in species with high dispersal potential for uncovering stock boundaries and demographic variation related to spawning and recruitment. It also illustrates the importance of marine biogeography in shaping population structure in commercial species with high dispersal potential.

Strong philopatry in an estuarine‐dependent fish

“…This boundary coincides with species distribution limits, as well as population structuring for several species (Colgan, 2016), including an east-west divergence previously identified for A. butcheri and other sparids such as snapper, Chrysophrys auratus (Bertram et al, 2023;Burridge & Versace, 2006). The genetic differentiation present across Victorian locations is explained by the presence and convergence of strong ocean currents found across south-eastern Australia (i.e.…”

Estimation of effective population size and effective number of breeders in an abundant and heavily exploited marine teleost

“…Population genomic work has shown that the Australian locations selected in this study are represented by two geographically and genetically isolated snapper populations, known as the south-west (Bertram et al 2022) and the south-east (Bertram et al 2023) stocks. Muscle samples were obtained from 202 0+ aged YOY snapper recruits from the south-west stock (Cockburn Sound), as well as 202 YOY from the south-east stock (Port Phillip Bay; Table 1, Fig.…”

“…Here we utilized tissue samples taken from snapper belonging to two genetically distinct and geographically isolated stocks in southern Australia that were originally sampled for stock assessment purposes and for population genetic structure work (Conron et al 2020, Fairclough et al 2021, Bertram et al 2022, Bertram et al 2023). For the two stocks, both single-cohort YOY and adults of mixed ages were available for effective size estimation, allowing us to generate estimates of both N b in a single reproductive cycle and generational N e using the LD N e method.…”

Connecting the dots: applying multispecies connectivity in marine park network planning

“…Unlike microsatellites, which are assumed to be selectively neutral, SNPs can be neutral or adaptive. Given that variation under local environmental selection may bias demographic inferences, we used datasets from which putatively adaptive variants had already been removed (as described in Barceló et al 2021, Bertram et al 2022, Pratt et al 2022, Bertram et al 2023. Based on these requirements, we identified suitable highquality datasets for five species (Figure 2, Table 1).…”

“…Although these species provide only a snapshot of the diversity of connectivity patterns expected across our study region, they encompass both active dispersal strategies (bottlenose dolphins and common dolphins, herein 'active dispersers'), and advection-driven larval dispersal strategies (nerites, limpets, and snapper, herein 'larval' dispersers). Although snapper has a relatively long pelagic larval stage, our categorisation is an oversimplification because the species is also known to move during juvenile and/or adult stage (for details see Bertram et al 2022, Bertram et al 2023. Our study taxa include key species for MPA design in South Australia because of their priority status in conservation management plans and fishery stock assessments.…”