DOI: 10.5061/dryad.7vv50
title: Data from: The genetic basis and experimental evolution of inbreeding depression in Caenorhabditis elegans

description: Determining the genetic basis of inbreeding depression is important for
 understanding the role of selection in the evolution of mixed breeding
 systems. Here, we investigate how androdioecy (a breeding system
 characterized by partial selfing and outcrossing) and dioecy
 (characterized by obligatory outcrossing) influence the experimental
 evolution of inbreeding depression in Caenorhabditis elegans. We derived
 inbred lines from ancestral and evolved populations and found that the
 dioecious lineages underwent more extinction than androdioecious lineages.
 For both breeding systems, however, there was selection during inbreeding
 because the diversity patterns of 337 single-nucleotide polymorphisms
 (SNPs) among surviving inbred lines deviated from neutral expectations. In
 parallel, we also followed the evolution of embryo to adult viability,
 which revealed similar starting levels of inbreeding depression in both
 breeding systems, but also outbreeding depression. Under androdioecy,
 diversity at a neutral subset of 134 SNPs correlated well with the
 viability trajectories, showing that the population genetic structure
 imposed by partial selfing affected the opportunity for different forms of
 selection. Our findings suggest that the interplay between the disruptions
 of coevolved sets of loci by outcrossing, the efficient purging of
 deleterious recessive alleles with selfing and overdominant selection with
 outcrossing can help explain mixed breeding systems.
description: Genotype_dataThis file contains a table with genotypes of the individuals from populations (inbred and outbred) of generation 0 and 100.R.Simulation_inbreedingR script to simulate the haplotypes generated during inbreedingSNP_infoTable with SNP marker information, used in the simulation of inbreeding.hap_G0.A.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a androdioecious population from generation 0.hap_G0.A.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a androdioecious population from generation 0.hap_G0.D.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a dioecious population from generation 0.hap_G0.D.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a dioecious population from generation 0.hap_G100.A1.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a androdioecious population, replicate nº1, from generation G100.hap_G100.A1.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a androdioecious population, replicate nº1, from generation G100.hap_G100.A2.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a androdioecious population, replicate nº2, from generation G100.hap_G100.A2.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a androdioecious population, replicate nº2, from generation G100.hap_G100.A3.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a androdioecious population, replicate nº3, from generation G100.hap_G100.A3.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a androdioecious population, replicate nº3, from generation G100.hap_G100.D1.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a dioecious population, replicate nº1, from generation G100.hap_G100.D1.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a dioecious population, replicate nº1, from generation G100.hap_G100.D2.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a dioecious population, replicate nº2, from generation G100.hap_G100.D2.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a dioecious population, replicate nº2, from generation G100.hap_G100.D3.O_IVPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome IV haplotypes of a dioecious population, replicate nº3, from generation G100.hap_G100.D3.O_XPhased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a dioecious population, replicate nº3, from generation G100.