Data from "Parentage analysis of conservation translocations in the endangered, self-incompatible shrub Pseudoziziphus celata reveals reproductive constraints, variable survival, and a case for genetics-driven conservation"

This dataset contains the data and code required to replicate analyses in Edwards et al. “Parentage analysis of conservation translocations in the endangered, self-incompatible shrub Pseudoziziphus celata reveals reproductive constraints, variable survival, and a case for genetics-driven conservation”Christine E. Edwards1*, Burgund Bassüner1, Aaron S. David2, Noah Dell1, Caitlyn J. Foye1,3, Sterling Herron2, Stephanie Koontz2,4, Cheryl Peterson5, Stacy A. Smith2,6, Carl W. Weekley2, Brigette Williams1,7, and Eric S. Menges2IntroductionIn this study, we used genetic data and parentage analysis to understand how reproductive dynamics, variation in survival, and the use of genetic data to guide translocation design have shaped the genotypic composition and genetic diversity of 12 translocated populations of Florida ziziphus. We developed a panel of all known wild genotypes of Florida ziziphus to serve as our panel of potential parents. For translocations completed prior to 2011, we sampled all individuals that survived from the time of planting until sampling in 2011, whereas for translocations conducted after 2011, we collected material and genotyped it before conducting the translocations. We genotyped all individuals using 12 microsatellites, conducted parentage analysis, identified the maternal and paternal parents, analyzed the genotypic composition and genetic diversity for each translocated population, and analyzed whether the offspring produced by different parental combinations varied in survival time. The goals of this study were to understand: 1) whether the seeds produced were derived only from the genotypes in the ex situ collection or whether other wild genotypes also served as parents, 2) whether parental pairs varied in compatibility and reproductive output over time by analyzing the relative proportions of each full-sib group in the translocations, 3) whether the offspring from different parental pairs varied in survival time, and 4) whether MLGs varied in their ability to serve as maternal and paternal parents. Finally, an additional goal was to understand the effects of incorporating genetic data into the design of reintroductions by comparing the genetic diversity and genotypic composition of early translocations conducted before the genetic study was initiated to those in which genetic data was generated prior to conducting the translocations and used in the translocation design.Datasets:The first dataset includes genotypic data at 12 microsatellite loci for a panel of all known wild genotypes of Florida ziziphus to serve as our panel of potential parents. The genotypic data are in the form of allele sizes at the loci, whose names are listed in the first row. The name and DNA sequences for the microsatellite loci are listed in Table S1 of the manuscript. The sample names are in column 1 and take the format of “unique sample code—mlg number.”The second data file includes genotypic data in genodive format for all 1120 translocated individuals included in the study. For translocations completed prior to 2011, we sampled all individuals that survived from the time of planting until sampling in 2011, whereas for translocations conducted after 2011, we collected material and genotyped it before conducting the translocations. The data set includes genotypic data (in the format of microsatellite allele sizes) for all individuals at 12 microsatellites (with locus name and primer information included in table S1 of the manuscript). Population codes are as listed in Table 1 in the manuscript. This data file was used both to calculate genetic diversity metrics and conduct parentage analysis.The final dataset includes both survival data (coded as 0/1) and a unique code for each full-sib group. The data contain the following columns:intro_yr = the year the reintroduction was conductedintro_type = Whether the population is an introduction (intro) or augmentation (aug)genotype = result of parentage analysis, listing mlgs that were identified as parentsRgenotype = individual code assigned to each full-sib group for analysis in Rplant_id = sample id, corresponding the ids in the genotype filesurvival = number of years the individual survivedLastLiving = year in which the individual was last observed aliveLiving = 0/1 indicating whether the plant is currently dead (0) or alive (1)Popcode = population name as indicated in Table 1 of the manuscript.,