DOI: 10.5061/dryad.w9ghx3fm3
title: Data from: Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote northwest Australia

description: 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.
description: 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) &lt;7, call rate &gt;0.35, minimum allele frequency
 &gt;0.00075 for <i>Isopora </i>and<i>
 &gt;</i>0.0017 for <i>Acropora</i> (further<i>
 </i>details of DArT-seq protocol in Appendix B).
description: This submission includes five files 
 <b>aspera_DArT_Report_34304_SNPs.xlsx</b>: Excel
 file with two row data from 34,304 SNPs called for all <i>Acropora
 aspera</i> 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 
 <b>bruegs_DArT_Report_23165_SNPs.xlsx</b>: Excel
 file with two row data from 23,165 SNPs called for all <i>Isopora
 brueggemanni </i>samples. Includes information of each loci provided
 by DArT propriety pipeline (as above for aspera). 
 <b>aspera_all_Kimberley_585_loci.xlsx</b>: Excel file in
 GenAlEx format for 585 SNPs used to delineate clusters in the entire
 <i>Acropora aspera </i>data set. Also, second worksheet
 includes the summary statistics for each locus for each
 lineage. 
 <b>aspera-c_Kimberley_2898_loci.xlsx</b>: 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. 
 <b>bruegs_Kimberley_2132_loci.xlsx</b>: Excel file in GenAlEx
 format for 2,132 SNPs used for population genetics analysis of
 561<i>Isopora brueggemanni </i>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.