Multi-locus microsatellite genotypes of Pocillopora acuta (Scleractinia: Pocilloporidae) in the Bolinao-Anda Reef Complex, Philippines

This repository contains genotype data and sampling metadata used for the manuscript "Shifts in coral clonality along a gradient of disturbance: insights on reproduction and dispersal of Pocillopora acuta". The dataset contains genotypes of 428 P. acuta colonies using 16 polymorphic microsatellite loci, colony sizes, in-transect locations of each coral, and geographic coordinates of reef sites. These were used to examine clonal richness and structure, population genetic differentiation, and demographic and genetic connectivity within the reef system. In the study, we estimated the relative contribution of sexual and asexual modes of reproduction to population maintenance, and inferred the species' spatial scale of realized dispersal all against a backdrop of varying levels of wave exposure. 

Methods
Four reef sites at 3–5 m depths, separated by distances of 5–22 km, were chosen to represent reefs adjacent to the municipalities of Bolinao (Malilnep/MLP, Lucero/LCR) and Anda (Cangaluyan/CLY, Caniogan/CNG). Each site was represented by an exhaustively sampled 400 m2 transect. Identified adult colonies (> 5 cm diameter, n = 451) of P. damicornis sensu lato (Veron and Pichon 1976) were photographed, measured, and mapped within the transect.A putative outgroup population of P. damicornis s.l. (n = 37) haphazardly sampled in a reef site in Gonzaga, Cagayan, located ~ 325 km northeast of the selected sites, was also examined.

Sixteen poymorphic microsatellite loci exhibiting robust amplification and polymorphism were used for genotyping (Magalon et al. 2004, Starger et al. 2008, Torda et al. 2013). Forward primers for all loci were labeled at the 5′-end with either of four fluorophores (6-FAM, VIC, PET, or NED) for allelic detection. Fragment analysis was performed on an ABI3730xl sequencer (Applied Biosystems) at the Philippine Genome Center core sequencing facility (University of the Philippines Diliman). Fragment sizes were manually checked in Geneious Prime v2020.0.3 using the Microsatellite Plug-in v1.4.6 (Kearse et al. 2012). Reamplification was performed for loci and individuals with missing data. Individuals with missing data after two rounds of repeat amplification were removed from further analyses. The multilocus dataset was checked for genotyping errors and evidence of stuttering, large allele drop-outs, and null alleles using Micro-checker v2.2.3 (Van Oosterhout et al. 2004).