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.

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).

This submission includes five files

• aspera_DArT_Report_34304_SNPs.xlsx: Excel file with two row data from 34,304 SNPs called for all Acropora aspera samples. Includes all ramets and information of each loci provided by DArT propriety pipeline.
  • CloneID: Unique identifier for the sequence in which the SNP marker occurs
  • SNP: This column contains the base position and base variant details in the SNP row, and is is blank in the Reference row.
  • SnpPosition: The position (zero indexed) in the sequence tag at which the defined SNP variant base occurs
  • CallRate: The proportion of samples for which the genotype call is either "1" or "1", rather than "-" (no call)
  • OneRatioRef: The proportion of samples for which the genotype score is "1", in the Reference allele row
  • OneRatioSnp: The proportion of samples for which the genotype score is "1", in the SNP allele row
  • FreqHomRef: The proportion of samples which score as homozygous for the Reference allele
  • FreqHomSnp: The proportion of samples which score as homozygous for the SNP allele
  • FreqHets: The proportion of samples which score as heterozygous.
  • PICRef: The polymorphism information content (PIC) for the Reference allele row
  • PICSnp: The polymorphism information content (PIC) for the SNP allele row
  • AvgPIC: The average of the polymorphism information content (PIC) of the Reference and SNP allele rows
  • AvgCountRef: The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the Reference allele row
  • AvgCountSnp: The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the SNP allele row
  • RepAvg: The proportion of technical replicate assay pairs for which the marker score is consistent
• bruegs_DArT_Report_23165_SNPs.xlsx: Excel file with two row data from 23,165 SNPs called for all Isopora brueggemanni samples. Includes information of each loci provided by DArT propriety pipeline (as above for aspera).
• aspera_all_Kimberley_585_loci.xlsx: Excel file in GenAlEx format for 585 SNPs used to delineate clusters in the entire Acropora aspera data set. Also, second worksheet includes the summary statistics for each locus for each lineage.
• aspera-c_Kimberley_2898_loci.xlsx: Excel file in GenAlEx format for 2,898 SNPs used for the population genetics analysis Aspera-c lineage of 169 genets. Includes georeferenced coordinates for location of each genet in last two columns. Also, second worksheet describes is the summary statistics for each locus for site and averaged across sites.
• bruegs_Kimberley_2132_loci.xlsx: Excel file in GenAlEx format for 2,132 SNPs used for population genetics analysis of 561Isopora brueggemanni genets. Includes georeferenced coordinates for location of each genet in last two columns.  Also, second worksheet describes the summary statistics for each locus for site and averaged across sites.