DOI: 10.5061/dryad.b5r86
title: Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system

description: Clonality and genetic structure of the coral Pocillopora damicornis sensu
 lato were assessed using five microsatellites in 12 populations from four
 islands of the Society Archipelago (French Polynesia) sampled in June
 2008. The 427 analysed specimens fell into 132 multilocus genotypes
 (MLGs), suggesting that asexual reproduction plays an important role in
 the maintenance of these populations. A haploweb analysis of ITS2
 sequences of each MLG was consistent with all of them being conspecific.
 Genetic differentiation was detected both between and within islands, but
 when a single sample per MLG was included in the analyses, the populations
 turned out to be nearly panmictic. These observations provide further
 evidence of the marked variability in reproductive strategies and genetic
 structure of P. damicornis throughout its geographic range; comparison
 with results previously obtained for the congeneric species Pocillopora
 meandrina underlines the importance of life history traits in shaping the
 genetic structure of coral populations.
description: FASTA alignment of ITS2
 haplotype sequencesIn this FASTA alignment,
 the two haplotype sequences of heterozygote XXX are named XXXa and XXXb,
 whereas the single haplotype sequence of homozygote YYY is called
 YYY.ITS2alignment.fasSequencher file of processed and assembled ITS2 chromatogramsIn this Sequencher 4.1.4 file, the forward and reverse ITS2 chromatograms of each individual were assembled into contigs. For each homozygote, the contig was checked and cleaned then received the name of the individual sequenced. For length-variant heterozygotes, the double peaks were called either manually or using Sequencher's "Call Secondary Peak..." function, then the two haplotypes were reconstructed by combining the information carried by the forward and reverse chromatograms using the program Champuru (see http://dx.doi.org/10.1111/j.1471-8286.2006.01355.x, http://dx.doi.org/10.1111/j.1471-8286.2007.01857.x, available online at http://jfflot.mnhn.fr/champuru/ and http://seqphase.mpg.de/champuru); the contig and reconstructed haplotypes of each such individual received the name of this individual followed with "H", "a" and "b", respectively. For heterozygotes having two alleles of equal lengths, we used SeqPHASE (http://dx.doi.org/10.1111/j.1755-0998.2009.02732.x, available online at http://seqphase.mpg.de/seqphase) and PHASE to infer their haplotypes; the contig of each such individual received the name of this individual followed with "H" then the number of heterozygous SNPs observed (i.e., the number of double peaks in the contig), whereas its two inferred haplotypes received its name followed with "a" or "b", respectively. Finally, some individuals had double peaks but their chromatograms were two noisy to reconstruct accurately the two sequences: rather than risking to reconstruct one erroneous haplotype, for each such individual we only kept the haplotype that could be reconstructed unambiguously; these contigs were named by appending "h" to the names of the individuals concerned.ITS2chromatograms.SPFMicrosatellitesGenotypes of all 427 specimens analysed (in a Genetix file)microsatellites.gtx