DOI: 10.5061/dryad.fj6q5743h
title: Inbreeding avoidance and cost in a small, isolated trout population

description: 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.
description: # Inbreeding avoidance and cost in a small, isolated trout population
 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.