DOI: 10.5061/dryad.76hdr7t7c
title: Experimental test of the fitness effects of divergent marine-freshwater chromosomal inversions in stickleback under different salinity conditions

description: Chromosomal inversions are a type of structural variant that have long
 interested evolutionary biologists because of their potential role in
 local adaptation and speciation. However, direct experimental evidence for
 the fitness consequences of inversions is rare, limiting our ability to
 dissect the evolutionary forces associated with the spread and maintenance
 of inversions in natural populations. We tackle this knowledge gap by
 studying the fitness effects of three chromosomal inversions that
 consistently differ between marine and freshwater populations of
 threespine sticklebacks (Gasterosteus aculeatus). Using controlled
 laboratory crosses, we tested whether inversion genotype influences
 fitness (measured as survival, standard length, and body condition) across
 two salinity treatments (freshwater vs saltwater). In both the freshwater
 and the saltwater treatments, there were no deviations from Mendelian
 ratios at any of the three inversions. This suggests that there are no
 intrinsic deleterious effects of these inversions, in contrast to
 observations from other systems. Overall, there was no effect of inversion
 genotype on standard length or body size across the two salinity
 treatments for the chromosome XI and XXI inversions. For the chromosome I
 inversion, heterozygotes had a slightly lower body condition in the
 freshwater treatment. Together, these results suggest that the fitness
 effects of these inversions are not strongly influenced by salinity and
 that other selective forces might be involved in their evolution. More
 broadly, these findings highlight the importance of performing empirical
 tests of fitness effects of chromosomal inversions to better explain their
 spread and maintenance in nature.
description: # Experimental test of the fitness effects of divergent marine-freshwater
 chromosomal inversions in stickleback under different salinity conditions
 Dataset DOI: [10.5061/dryad.76hdr7t7c](10.5061/dryad.76hdr7t7c) ##
 Description of the data and file structure This data was collected based
 on lethal sampling of experimental crosses from a marine population of
 threespine sticklebacks. For each individual, measurements of body size,
 which correspond to standard length and weight, were determined.
 Additionally, individuals were genotyped to determine the orientation at
 the chromosomal inversion of interest (i.e., chromosome I, chromosome XI,
 or chromosome XXI) and sex.  ### Files and variables #### File:
 cross_data_stickleback_F2.csv **Description:** This file includes
 information about the F2 crosses, which are used for the analysis. #####
 Variables * parent.cross: F1 cross from where a female and male were used
 to generate an F2 cross * tank.parents: Tank where the F1 parents were
 housed * Cross: Name of the F2 cross, which derives from the parent cross
 name followed by a replicate. For example, chrI_03_01 means that this is
 the first replicate of an F2 cross derived from the third F1 cross of a
 chromosome I inversion * cross.date: Date when the F2 cross was made *
 n.larvae: Number of larvae before the F2 clutch was split #### File:
 genotype_and_size_data_stickleback_F2.csv **Description:** This file
 includes the genotype and body size information of the sampled
 individuals.  ##### Variables * Tank: Tank where the individual was hosted
 * ID: Individual identifier * Inversion: Target chromosomal inversion.
 Each individual has only one chromosomal inversion of interest, which can
 be either chromosome I, XI, or XXI. At the chromosomal inversion of
 interest, an individual can be freshwater homozygote (F), heterozygote
 (H), or marine homozygote (M). At the other two inversions, the individual
 is always a marine homozygote (M) * Family: F1 cross that was used to
 generate the F2 cross from which an individual derives from. This is the
 same as parent.cross for the file above. * Cross: Name of the F2 cross.
 This is the same as the column Cross for the file above * System:
 Indicates which salinity treatment an individual was exposed to. FWS2
 refers to the freshwater treatment, whereas SW refers to the saltwater
 treatment * chrI: Genotype at the chromosome I inversion -  freshwater
 homozygote (F), heterozygote (H), or marine homozygote (M). Missing values
 are indicated as "NA" * chrXI: Genotype at the chromosome XI
 inversion -  freshwater homozygote (F), heterozygote (H), or marine
 homozygote (M). Missing values are indicated as "NA" * chrXXI:
 Genotype at the chromosome XXI inversion -  freshwater homozygote (F),
 heterozygote (H), or marine homozygote (M). Missing values are indicated
 as "NA" * Sex: Sex based on PCR genotyping -  female (F) or male
 (M). Missing values are indicated as "NA" * Date: Date when the
 individual was euthanized * SL: Standard length described as the length
 from the most anterior point of the snout to the attachment of the caudal
 fin in millimeters * Weight: Weight in grams * Comments: Any remarks that
 were observed during the measuring process * Gravid: If a female was
 observed to be gravid, Yes. Otherwise, No * Suggestion: A value of
 "Remove" was added if the individual was cataloged to have
 developmental abnormalities during the sampling. These individuals were
 excluded from the analysis to test for the association of inversion
 genotype and body size. Empty cells indicate that the individual was not
 removed from this analysis ## Code/software #### File:
 analyses_fitness_effects_inversions_sticklebacks_F2.R
 **Description:** This R script contains the code used for the analysis of
 the previously described data. The script is divided into three sections
 1. Survival analysis: In this section, it is explored whether there is
 differential survival between families and/or salinity treatment. Here, it
 is also tested if there is an effect of age on overall survival. Age was
 calculated as the number of days between when the cross was made and the
 sampling date. 2. Genotype frequencies: In this section, the genotype
 frequencies were calculated for each chromosomal inversion and plotted
 while separating by salinity treatment. The frequency data was then used
 to compare genotype frequencies between the salinity treatments (1) and
 the expected 1:2:1 Mendelian ratio using a Chi-square test (2). 3. Testing
 the effect of genotype and salinity treatment on body size: In this
 section, it is explored whether there is an effect of inversion genotype
 across the salinity treatments for the body size measurements of standard
 length and body condition. The latter corresponds to the residual of the
 cubic root of weight regressed onto standard length. In this section,
 linear mixed models were used, and the results were plotted using the
 estimated marginal means associated with those models.