DOI: 10.5061/dryad.s1b07
title: Data from: Looking into the black box: simulating the role of self-fertilization and mortality in the genetic structure of Macrocystis pyrifera

description: Patterns of spatial genetic structure (SGS), typically estimated by
 genotyping adults, integrate migration over multiple generations and
 measure the effective gene flow of populations. SGS results can be
 compared with direct ecological studies of dispersal or mating system to
 gain additional insights. When mismatches occur, simulations can be used
 to illuminate the causes of these mismatches. Here we report a SGS and
 simulation-based study of self-fertilization in Macrocystis pyrifera, the
 giant kelp. We found that SGS is weaker than expected in M. pyrifera, and
 used computer simulations to identify selfing and early mortality rates
 for which the individual heterozygosity distribution fits that of the
 observed data. Only one (of three) population showed both elevated kinship
 in the smallest distance class and a significant negative slope between
 kinship and geographic distance. All simulations had poor fit to the
 observed data unless mortality due to inbreeding depression was imposed.
 This mortality could only be imposed for selfing, as these were the only
 simulations to show an excess of homozygous individuals relative to the
 observed data. Thus, the expected data consistently achieved
 non-significant differences from the observed data only under models of
 selfing with mortality, with best fits between 32-42% selfing. Inbreeding
 depression ranged from 0.70-0.73. The results suggest that
 density-dependent mortality of early life stages is a significant force in
 structuring Macrocystis populations, with few highly-homozygous
 individuals surviving. The success of these results should help to
 validate simulation approaches even in data-poor systems, as a means to
 estimate otherwise difficult-to-measure life-cycle parameters.
description: Carpinteria
 Microsatellite DataMicrosatellite data in
 6-digit format, with individual ID, X and Y coordinates, and ten
 microsatellite markers. Missing data indicated by
 000000.Carp021612CNoMpy9.txtGoleta Microsatellite DataMicrosatellite data in 6-digit format, with individual ID, X and Y coordinates, and ten microsatellite markers. Missing data indicated by 000000.Gol021612CNoMpy9MDDrop.txtMohawk Microsatellite DataMicrosatellite data in 6-digit format, with individual ID, X and Y coordinates, and ten microsatellite markers. Missing data indicated by 000000.Moh021612CNoMpy9.txtR script to calculate summary statistics from microsatellite dataScript calculates mean number of alleles per locus, observed heterozygosity, expected heterozygosity, and Fis. Input files are microsatellite data only, with alleles separated into separate columns (i.e. 10 loci are presented in 20 columns, with no headers or other columns).Summary Stats.RR script to simulate one generation of inbreedingScript simulates selfing, and creation of full-sibling, half-sibling, and first cousins in proportions ranging from 0 to 100%. Input files are microsatellite data only, with alleles separated into separate columns (i.e. 10 loci are presented in 20 columns, with no headers or other columns).All Crosses 082412.R