Experimental test of the fitness effects of divergent marine-freshwater chromosomal inversions in stickleback under different salinity conditions
Data files
Aug 04, 2025 version files 121.59 KB
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analyses_fitness_effects_inversions_sticklebacks_F2.R
21.98 KB
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cross_data_stickleback_F2.csv
1.13 KB
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genotype_and_size_data_stickleback_F2.csv
93.47 KB
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README.md
5 KB
Abstract
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.
Dataset DOI: 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
- 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.
- 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).
- 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.