Multilocus genotypes from all sites

This file contains multilocus genotypes generated by fragment analysis of PCR amplicon using an ABI 3730 with an internal size standard (Genescan LIZ-500, Applied Biosystems, CA). Electropherograms were visualized and allele sizes were called using GENEMAPPER v 4.0 (Applied Biosystems, CA). Samples that failed to amplify more than 2 of 11 loci were excluded from the analysis. Alleles are labeled by their 3-digit fragment size. Alleles are concatenated for each locus giving a 6-digit genotype for each primer. Missing data is coded as "0".Sample names contain a two-digit code for the year followed by an underscore and a four-digit identifier for each colony sampled. Together this 6-digit number provides a unique identifier for each sample

Figure5_CnidarianTreeNetwick

Bayesian genealogy of ten cnidarian species studied, based on partial COI sequences (approx. 700 bp) in Newick format

ScirokoResultsAllforDryad

ScirokoResultsAllforDrya

Assessment of Host-Associated Genetic Differentiation among Phenotypically Divergent Populations of a Coral-Eating Gastropod across the Caribbean

<div><p>Host-associated adaptation is emerging as a potential driver of population differentiation and speciation for marine organisms with major implications for ecosystem structure and function. <em>Coralliophila abbreviata</em> are corallivorous gastropods that live and feed on most of the reef-building corals in the tropical western Atlantic and Caribbean. Populations of <em>C. abbreviata</em> associated with the threatened acroporid corals, <em>Acropora palmata</em> and <em>A. cervicornis</em>, display different behavioral, morphological, demographic, and life-history characteristics than those that inhabit other coral host taxa, indicating that host-specific selective forces may be acting on <em>C. abbreviata</em>. Here, we used newly developed polymorphic microsatellite loci and mitochondrial cytochrome b sequence data to assess the population genetic structure, connectivity, and demographic history of <em>C. abbreviata</em> populations from three coral host taxa (<em>A. palmata</em>, <em>Montastraea</em> spp., <em>Mycetophyllia</em> spp.) and six geographic locations across the Caribbean. Analysis of molecular variance provided some evidence of weak and possibly geographically variable host-associated differentiation but no evidence of differentiation among sampling locations or major oceanographic regions, suggesting high gene flow across the Caribbean. Phylogenetic network and Bayesian clustering analyses supported a hypothesis of a single panmictic population as individuals failed to cluster by host or sampling location. Demographic analyses consistently supported a scenario of population expansion during the Pleistocene, a time of major carbonate reef development in the region. Although further study is needed to fully elucidate the interactive effects of host-associated selection and high gene flow in this system, our results have implications for local and regional community interactions and impact of predation on declining coral populations.</p> </div

Median joining network for <i>cyt b</i> haplotypes from a sample of 130 <i>Coralliophila abbreviata</i>.

<p>Circles represent individual haplotypes. The size of the circle is proportional to the frequency of the haplotype in the sample and branch lengths are proportional to the number of mutational steps (range: 1–3). Small black circles represent missing/theoretical haplotypes.</p

Map of sampling localities across the greater Caribbean.

<p>Dashed line represents the major regional break tested, between the eastern and western Caribbean.</p

Global characteristics of five polymorphic microsatellite loci for <i>Coralliophila abbreviata</i>.

<p>Shown, for each locus, are the forward (F) and reverse (R) primer sequences, repeat motif, size range of alleles in base pairs (bp), global sample size (<i>N</i>), number of observed alleles (<i>N</i>_a), observed (<i>H</i>_O) and expected (<i>H</i>_E) heterozygosities, fixation index (<i>F</i>_IS), and uncorrected <i>P</i>-value for test of departure from Hardy Weinberg Equilibrium (<i>P</i>_HW). Loci correspond to GenBank accession numbers HM156485, HM156486, HM156490–HM156492.</p

AMOVA results for tests of host-associated differentiation among populations of <i>Coralliophila abbreviata</i> using mtDNA and microsatellite (msats) data.

<p>Populations were defined by host taxon (i.: ACR, MON) or host and locality (ii.–iv.: FL ACR, FL MON, BAH ACR [msats only], NAV ACR, NAV MON, CUR ACR [msats only], CUR MON, SVG ACR, SVG MON). <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047630#s3" target="_blank">Results</a> for microsatellite data represent the weighted averages over all loci.</p><p>Bold values were significant (α = 0.05) before Bonferroni correction for multiple comparisons,</p>*<p>indicates significance after correction.</p

Genetic diversity indices, neutrality test statistics, and mismatch distribution parameters for mitochondrial <i>cyt b</i> sequences of <i>Coralliophila abbreviata</i> collected from Florida (FL), Navassa (NAV), St. Vincent and the Grenadines (SVG), Curacao (CUR), Panama (PAN), as well as all individuals combined (GLOBAL).

<p>Genetic diversity indices: <i>N</i>, sample size; <i>N</i>_h, number of haplotypes; <i>N</i>_p, number of polymorphic sites; <i>h</i>, haplotype diversity; <i>π</i>, nucleotide diversity. Neutrality statistics: <i>D</i>, Tajima's statistic (Tajima 1989); <i>F</i>_S, Fu's statistic (FU 1997). Mismatch distribution: <i>τ</i> (tau), time since beginning of expansion in mutational units; θ₀ and θ₁, initial and final population size estimators, respectively; <i>P</i> (SSD), probability of sum of squared deviations; Rg, raggedness statistic (Harpending 1994); <i>P</i> (Rg), probability of Rg.</p>*<p><i>P</i><0.01.</p>**<p><i>P</i><0.001.</p

Sample sizes of <i>Coralliophila abbreviata</i> by coral host and locality for mitochondrial cytochrome b sequences (mtDNA) and microsatellite markers (Msats).

<p>Sample sizes of <i>Coralliophila abbreviata</i> by coral host and locality for mitochondrial cytochrome b sequences (mtDNA) and microsatellite markers (Msats).</p