Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data

Abstract

Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.

Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (Haliotis laevigata), along a longitudinal environmental gradient

“…We found no evidence of genomewide diversity loss as might have been expected if populations were overexploited and experienced recent, severe and prolonged bottlenecks (Allendorf et al., ). In fact, diversity levels in greenlip abalone are comparable with red abalone from California (Wit & Palumbi, ), blacklip abalone from southeast Australia (Miller et al., ) and Roe's abalone from southwestern Australia (L. B. Beheregaray et al. unpublished data).…”

Evaluating methods to visualize patterns of genetic differentiation on a landscape

“…The combination of decreasing cost and increasing throughput of DNA sequencing has transformed many fields. This is especially true of landscape genetics, where improved access to sequencing has enabled increasingly ambitious studies that sample larger landscapes as well as more individuals across the landscape than was possible just a few years ago (e.g., Miller et al., ; Pagani et al., ; Roffler et al., ). For instance, for a growing number of species, it is now possible to observe landscape‐scale patterns of genetic differentiation, which represent long‐term records of evolutionary history.…”

The First Isolation and Characterisation of the Protist Labyrinthula sp. in Southeastern Australia

“…; Miller et al. ) of southeast Australia. Whether temporal or climatic variations influence biogeographical distribution of Labyrinthula needs to be investigated.…”

“…For instance, it is known that marine flora and fauna in southeast Australia display strong regional genetic variations that suggest a lasting physical barrier to dispersal was present historically, and through several sea level change periods (Sinclair et al 2016). These barriers resulted in what are known to be three biogeographical provinces (Peronian to the east, Flindersian to the south and west, and Maugean to the southeast) with clearly observed genetic variations that persist in both marine flora (Sinclair et al 2016) and fauna (Charlton-Robb et al 2015;DiBattista et al 2014;Miller et al 2016) of southeast Australia. Whether temporal or climatic variations influence biogeographical distribution of Labyrinthula needs to be investigated.…”