DOI: 10.5061/dryad.rbnzs7hbt
title: Data from: Population genetics of a broadcast-spawning coral across a tropical-temperate transition zone reveals regional differentiation and isolation of high-latitude reefs

description: Aim: Genetic connectivity is a key component of species resilience to
 climate change in terms of recovery capacity following disturbance and
 capacity to disperse to novel locations as the climate warms and isotherms
 shift poleward. We aimed to strengthen our understanding of resilience in
 this context by characterizing patterns of connectivity and genetic
 diversity in a broadcast spawning coral across a tropical-temperate
 transition zone. We hypothesize genetic differentiation between tropical
 and temperate populations and decreasing genetic diversity with higher
 latitudes. Location: Western Australia (WA). Taxon: Turbinaria
 species complex. Turbinaria reniformis Oken, 1815 (Dendrophylliidae).
 Methods: Samples from 930 target corals were collected from ten locations
 between 13 - 32 o latitude spanning a 9° C mean temperature range. In-situ
 species identification of T. reniformis is hindered by morphological
 plasticity and homoplasy with sister species. We combined Sanger
 sequencing of two mitochondrial DNA markers and high-throughput genotyping
 by sequencing (GBS) to isolate a single genetic Turbinaria lineage from
 our dataset through which patterns of genetic flow and diversity along the
 WA coastline could be explored using population- and individual-based
 analyses. Results: Mitochondrial DNA sequence variation was low among
 Turbinaria samples and could not resolve individual species. Using GBS, we
 identified three genetically distinct lineages. Subsequent analyses within
 one of these lineages revealed strong spatial subdivision with 2-3 genetic
 clusters. While temperate populations were genetically diverged from more
 tropical sites, we did not observe declines in genetic diversity with
 latitude. Main Conclusions: Temperate coral populations in Western
 Australia are genetically isolated from their tropical counterparts.
 Tropical populations of T. ‘reniformis’ exhibit adequate connectivity.
 Shark Bay represents the current southern limit of the tropical population
 of T. ‘reniformis’. Interestingly, temperate T. ‘reniformis’ in this study
 exhibit some genetic resilience due to their relatively high genetic
 diversity, yet the strong patterns of genetic subdivision for this widely
 dispersing coral species potentially limit their resilience to future
 climate scenarios.
description: <i>In-situ</i> species identification of corals is
 difficult. At a species level, existing studies based on COI and rDNA show
 most species are polyphyletic (Shimpi, Patel, & Haldar, 2019) and
 there is a high level of genetic overlap amongst morphospecies and
 particularly between <i>T. mesenterina</i> and <i>T.
 reniformis</i> (Arrigoni et al., 2014). With this in mind, we
 included three general morphotypes in our collections -
 <i>Turbinaria reniformis</i>, <i>T.
 mesenterina</i>, and <i>T. frondens</i>; however,
 samples with morphotypes matching the descriptions for <i>T.
 conspicua</i>, <i>T. bifrons</i> and <i>T.
 stellulata</i> listed in Veron & Pichon (1980) and Veron
 (2000) were also included for comparison. Tissue samples from a total of
 930 colonies were collected on SCUBA at ten locations along the Western
 Australian coastline, spanning more than 18 degrees of latitude and a mean
 temperature range of 9°C (Figure 1). Samples of 2
 cm<sup>2</sup> were collected using side cutters, at least 5
 metres apart to avoid clone mates, but within
 100m<sup>2</sup>, and were preserved in 100% AR grade ethanol.
 In addition, eleven previously submitted Museum voucher specimens for
 <i>Turbinaria </i>were included in the study.<i>
 </i>Genomic DNA was extracted and purified using a Qiagen DNeasy
 Blood & Tissue kit (plate format) following the manufacturers
 protocol. Samples included 11 specimens previously accessioned at the WA
 Museum.
 <i>Genotyping-by-Sequencing</i> A
 subset of 536 samples were selected for reduced representation library
 sequencing. This subset of samples included representatives from each site
 and from varied morphotypes and COI haplotypes. In addition, ten Museum
 voucher specimens for <i>Turbinaria </i>that had suitable
 sequences for the COI analysis were included. Genome-wide single
 nucleotide polymorphism (SNP) data were generated at Diversity Arrays
 Technology (DArT; http://www.diversityarrays.com) using a GBS approach
 (DArTseq) with the PstI and HpaII restriction enzymes. Genomic DNA was
 processed in digestion/ligation reactions principally as per Kilian et al.
 (2012), but replacing a single PstI-compatible adaptor with the two
 different adaptors corresponding to different restriction enzyme
 overhangs. The PstI-compatible adapter included the Illumina flow cell
 attachment sequence, sequencing primer and barcode. The reverse adapter
 contained the flow cell attachment region and HpaII-compatible overhang
 sequence. Sequencing was carried out on two lanes of an Illumina Hiseq2500
 and processed using proprietary DArT analytical pipelines
 (DArTsoft14). <i>SNP QC and
 Filtering</i> All filtering steps and
 statistical analyses were implemented using R software, version 3.0.1
 unless noted (R Core Team, 2015). The initial genotype matrix of 546
 individuals across 88,743 binary SNPs was filtered using ‘DArTR’ (Gruber,
 Unmack, Berry, & Georges, 2018). We removed loci that deviated
 from Hardy-Weinberg equilibrium (after adjusting for multiple comparisons
 at FDR 0.05), with minor allele frequencies less than 0.05, with call
 rates less than 0.90, and with read depth less than 10x. We retained only
 one SNP locus where there was more than one locus per sequence tag to
 avoid issues associated with linkage disequilibrium. We also removed any
 individuals with poor data (&lt;90% call rate) and utilised a
 reproducibility statistic to filter out all loci with &lt; 0.90
 correct calls across individuals. Finally, to remove any possible symbiont
 data, we aligned all sequences to available symbiont genomes (Aranda et
 al., 2016; Lin et al., 2015; Liu et al., 2018; Shoguchi et al., 2013) and
 removed any loci with a blastn e-value below
 10-3.
 <i>Initial screening</i> The
 initial SNP dataset of 546 individuals representing a range of different
 <i>Turbinaria</i> species, demonstrated by a number of
 genetically distinct lineages within the genus
 <i>Turbinaria</i>. To refine the broad clustering of our
 samples into genetically independent lineages, and to identify a single
 genetic lineage through which we can explore patterns of gene flow and
 population genetic structure, we used individual-based principle
 components analysis with “ade4”<i> </i>(Dray & Dufour,
 2007) using Euclidean Distance matrices, and constructed a
 neighbour-Joining (NJ) tree based on Nei’s genetic distance in
 ‘poppr<i>’ </i>(Kamvar, Tabima, & Grünwald,
 2014).
description: See the ReadMe file attached.