Computational protocol: On the occurrence of intracolonial genotypic variability in highly clonal populations of the hydrocoral Millepora platyphylla at Moorea (French Polynesia)

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Protocol publication

[…] Controls for the presence of null alleles and large allele dropout were performed with MICRO-CHECKER v.3.7. Multilocus genotypes (MLGs) were produced for each sample and compared within each colony to detect the occurrence of intracolonial genotypic variability. The genotype probability (GP) was estimated for each locus and for a combination of all loci using GENALEX v.6.5. Repeated multilocus genotypes were also identified in GENALEX and were considered as clone mates at GP < 0.001 (Table ). For the 51 sampled colonies of M. platyphylla that were subjected to multiple sampling, the most common genotype was retained as the main genotype. All additional genotypes within the same colony could result either from mosaicism (somatic mutations) or chimerism (fusion of two or more individuals). In previous studies, mosaic individuals were identified based on the number of divergent loci from the main genotype, i.e. only one or two loci (as in,) since mutations remain rare events. In contrast, a greater number of loci and allelic differences were expected in chimeras, i.e. when two genetically distinct colonies merge. Based on the stepwise mutation model of microsatellite markers, we estimated the number of repeat units that were added or subtracted during a mutation event. Divergent alleles from the main genotype caused by multiple-step mutations and large allele differences are most likely due to chimerism rather than somatic mutations. Stepwise mutations were identified over all loci for each deviating genotype and averaged per habitat and morphology (percentage of stepwise mutations).Bayesian clustering analyses have been used to identify chimeras based on their cluster assignment probability. Chimeras have to include genotypes that differ from the main genotype and belong to a different cluster,. Here, mosaic individuals and chimeras were identified based on a Bayesian clustering analysis using STRUCTURE. Clustering analyses were performed to ensure non-biased detection of deviating genotypes following the protocol used in Schweinsberg et al.. Initial STRUCTURE runs were used to determine the most likely number of clusters (K) in each population of M. platyphylla, i.e. within the five reef habitats: mid slope, upper slope, back reef, fringing reef and patch reef. Runs were performed with the default setting, a burn-in period of 50 000, 50 000 MCMC repeats and 10 iterations per K. The results were uploaded to STRUCTURE HARVESTER and the most likely K was retained for a second run in STRUCTURE with a burn-in period of 500 000, 500 000 MCMC repeats, 10 iterations and uniform prior setting. The results were once again uploaded to STRUCTURE HARVESTER and the resulting merged dataset was analysed to estimate cluster assignment. Based on our definitions of chimeras and mosaics using microsatellite data, we assumed that only fragments of the same colony having a genetic variation of at least 60%, whatever the number of divergent loci, were the result of chimerism. All other deviating genotypes were considered as mosaic colonies. […]

Pipeline specifications

Software tools GenAlEx, Structure Harvester
Application Population genetic analysis
Diseases Infertility