Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote northwest Australia

Management strategies designed to conserve coral reefs threatened by climate change need to incorporate knowledge of the spatial distribution of inter- and intra-specific genetic diversity. We characterised patterns of genetic diversity and connectivity using single nucleotide polymorphisms (SNPs) in two reef-building corals to explore the eco-evolutionary processes that sustain populations in northwest Australia. Our sampling focused on the unique reefs of the Kimberley; we collected the broadcast spawning coral Acropora aspera (n = 534) and the brooding coral Isopora brueggemanni (n = 612) across inter-archipelago (tens to hundreds of kilometres), inter-reef (kilometres to tens of kilometres) and within-reef (tens of metres to a few kilometres) scales. Initial analysis of A. aspera identified four highly divergent lineages that were co-occurring but morphologically similar. Subsequent population analyses focused on the most abundant and widespread lineage, Acropora asp-c. Although the overall level of geographic subdivision was greater in the brooder than in the spawner, fundamental similarities in patterns of genetic structure were evident. Most notably, limits to gene flow were observed at scales less than 35 kilometres. Further, we observed four discrete clusters and a semi-permeable barrier to dispersal that were geographically consistent between species. Finally, sites experiencing bigger tides were more connected to the metapopulation and had greater gene diversity than those experiencing smaller tides. Our data indicate that the inshore reefs of the Kimberley are genetically isolated from neighbouring oceanic bioregions, but occasional dispersal between inshore archipelagos is important for the redistribution of evolutionarily important genetic diversity. Additionally, these results suggest that networks of marine reserves that effectively protect reefs from local pressures should be spaced within a few tens of kilometres to conserve the existing patterns of demographic and genetic connectivity.
Methods
We extracted genomic DNA from coral specimens using a salting-out protocol modified from Cawthorn et al. (2011) and purified with Zymo-Spin I-96 filter plates. Genome-wide SNP data were generated using the next generation sequencing platform and the DArT-seq protocol. DArT-seq is similar to other site-associated restriction enzyme-based library preparation methods (e.g. RAD-seq) and is a widely applied approach for exploring population genetic structure in species that lack genome assemblies (DiBattista et al., 2017; Pazmino et al., 2017; Thomas et al., 2020). Sequencing was carried out on an Illumina Hiseq2500 using 75 cycle single-end reads. Raw reads were processed using DArT’s proprietary variant calling pipeline, DArTsoft-14. The call quality of the initial SNP data set was further assured by setting a cut-off of read depth per locus (coverage) <7, call rate >0.35, minimum allele frequency >0.00075 for Isopora and >0.0017 for Acropora (further details of DArT-seq protocol in Appendix B).