Inbreeding avoidance and cost in a small, isolated trout population
Data files
Sep 14, 2024 version files 976.48 KB
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Belletal_trout_inbreeding_2024_demographic_data.csv
140.56 KB
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Belletal_trout_inbreeding_2024_genotypic_data.csv
834.03 KB
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README.md
1.90 KB
Abstract
The persistence of small populations is influenced by the degree and cost of inbreeding, with the degree of inbreeding depending on whether close-kin mating is passively or actively avoided. Few studies have simultaneously studied these factors. We examined inbreeding in a small, isolated population of westslope cutthroat trout using extensive genetic and demographic data. Passive inbreeding avoidance was low, with predicted life-time dispersal of approximately 36 and 74 m for females and males, respectively. Additionally, we found limited evidence for active inbreeding avoidance during reproduction. Relatives remained spatially clustered into adulthood, and observed relatedness among mate pairs was greater than expected under random mating by 0.09, suggesting that inbreeding is a concern in this population. Further, we examined sex-specific inbreeding depression throughout the life-cycle and provide evidence for inbreeding depression in some fitness components, including family size, juvenile survival, and reproductive success. Our results suggest that, in an at-risk trout population, limited passive and active inbreeding avoidance lead to a higher degree of inbreeding than expected under random mating. Observed inbreeding, along with evidence for fitness reduction due to inbreeding depression, could put the population at a heightened risk of decline or extirpation.
Access datasets on Dryad: https://doi.org/10.5061/dryad.fj6q5743h
Description of the data and file structure
We provide two datasets: 1) demographic data for all capture events (Belletal_trout_inbreeding_2024_demographic_data.csv) and 2) genotype data with genetic IDs that correspond to IDs in the demographic dataset (Belletal_trout_inbreeding_2024_genotypic_data.csv).
1) Demographic data column descriptions
- CMR: Whether the sample was collected during a marking (Cap) or recapture (Recap) run for the two years (2017 and 2018) that within year mark recapture was conducted.
- Location: Whether the sample was collected below or above the isolation barrier. The population of interest and all analyses focus on the above barrier samples.
- Section: The 40 m section that the fish was collected in. The sections start at 0 for the first section above the isolation barrier, and then proceed in increments of 40 m until the upstream barrier (e.g., 0, 40, 80…).
- Length: The fish total length in mm.
- PIT: The PIT tag number either inserted into the body cavity of the fish on the first capture, or scanned on subsequent captures.
- DOY: Day of the year.
- Year
- GenID: ID for the genetic sample. This aligns with the GenID in the genotypic data.
2) Genotypic data column descriptions
- GenID: ID for the genetic sample. This aligns with the GenID in the demographic data.
- WCT_138699_65: Sex identification marker where 11 indicates a female and 12 indicates a male.
- Remaining columns: All remaining columns are different SNP markers and the values are the associated genotypes.
Code
JAGS scripts are provided for the mate selection model (mate_selection_conditional_poisson.txt) and the survival model (cjs_inbreeding_procb.txt). JAGS is required to run these scripts.