DOI: 10.5061/dryad.7wm37pw2r
title: Strongly deleterious mutations influence reproducitve output and longevity in an endangered population

description: Inbreeding depression has been documented in various fitness traits in a
 wide range of species and taxa, however, the mutational basis is not yet
 well understood. We investigate how putatively deleterious variation
 influences fitness and is shaped by individual ancestry by sequencing
 complete genomes of 37 individuals in a natural arctic fox (Vulpes
 lagopus) population subjected to both inbreeding depression and genetic
 rescue. We find that individuals with high proportion of loss of function
 genotypes (LoFs), which are predicted to exert a strong effect on fitness,
 generally have lower lifetime reproductive success and live shorter lives
 compared with individuals with lower proportion of LoFs. We also find that
 juvenile survival is negatively associated with the proportion of
 homozygous missense genotypes and positively associated with genome wide
 heterozygosity. Our results demonstrate that homozygosity of strongly and
 moderately deleterious mutations can be an important cause of trait
 specific inbreeding depression in wild populations, and mark an important
 step towards making more informed decisions using applied conservation
 genetics.
description: # Strongly deleterious mutations influence reproducitve output and
 longevity in an endangered population
 [https://doi.org/10.5061/dryad.7wm37pw2r](https://doi.org/10.5061/dryad.7wm37pw2r) ## Description of the data and file structure The study is carried out on a natural population of arctic foxes in Sweden. We investigated how putatively deleterious mutations influenced individual fitness, whether an immigration event altered the proportion of deleterious mutations in the population and whether individual ancestry influenced fitness. For fitness traits, lifetime reproductive success, longevity, litter size and juvenile survival were used. Individual ancestry were based on whether foxes were of native origin or whether they had immigrant ancestry. These were also divided into different generations (F1-F4). The mutations were divided into three categories: synonymous, missense and loss of function mutations. We also controlled for sex, phase of the rodent cycle and natal den. Data is collected during July every summer and is collected by researchers, rangers from the county board administrations and volunteering field workers. Fitness traits are documented by identifying individual foxes based on their unique ear tag combinations as well as from genetical samples during pedigree construction. Moreover, snap trapping of rodents is carried out yearly at a fixed number of dens to estimate the phase of the rodent cycle. The dataset is structured in an excel-file with three sheets. Sheet 1 includes the genomic data, sheet 2 and 3 includes the demographic data. R-code is uploaded as a separate text-file. ### Files and variables #### File: Genomic\_demographic\_fitness\_data\_Nat\_Com.xlsx **Description:** Genomic (sheet 1) and demographic (sheet 2 and 3) datasets used in the study in order to evaluate the effect of genomic variation (sheet 1) and individual ancestry (sheet 2 and 3) on fitness. Missing values indicated as "NA" #### Variables genomic dataset (sheet 1) * **Column**: A **Entry**: ID **Value**: individual code * **Column**: B **Entry**: sex **Value**: f, m **Explanation**: Sex of each individual fox, f = female, m = male * **Column**: C **Entry**: phase born **Value**: high, low **Explanation**: The phase of the rodent cycle each individual fox was born during. High = high rodent abundance. Low = low rodent abundance * **Column**: D **Entry**: survival **Value**: 0,1 **Explanation**: First year survival for each individual fox. 1 = survival. 0 = non-survival * **Column**: E **Entry**: litter size **Value**: numerical **Explanation**: The average number of cubs each individual arctic fox that survived to adulthood produced in their litters * **Column**: F **Entry**: LRS **Value**: numerical **Explanation**: Lifetime reproductive success. The total number of cubs each individual fox that survived to adulthood produced during their lifetime * **Column**: G **Entry**: age **Value**: numerical **Explanation**: The number of years each individual fox that survived to adulthood lived * **Column**: H **Entry**: het/kb **Value**: numerical **Explanation**: Genome-wide heterozygosity as number of heterozygotes per kb for each individual fox * **Column**: I **Entry**: LoF hom **Value**: 0-1 **Explanation**: The proportion of loss of function genotypes in homozygous state in each individual fox * **Column**: J **Entry**: LoF het **Value**: 0-1 **Explanation**: The proportion of loss of function genotypes in heterozygous state in each individual fox * **Column**: K **Entry**: LoF tot **Value**: 0-1 **Explanation**: The proportion of loss of function alleles in each individual fox * **Column**: L **Entry**: missense hom **Value**: 0-1 **Explanation**: The proportion of missense genotypes in homozygous state in each individual fox * **Column**: M **Entry**: missense het **Value**: 0-1 **Explanation**: The proportion of missense genotypes in heterozygous state in each individual fox * **Column**: N **Entry**: missense tot **Value**: 0-1 **Explanation**: The proportion of missense alleles in each individual fox * **Column**: O **Entry**: syn hom **Value**: 0-1 **Explanation**: The proportion of synonymous genotypes in homozygous state in each individual fox * **Column**: P **Entry**: syn het **Value**: 0-1 **Explanation**: The proportion of synonymous genotypes in heterozygous state in each individual fox * **Column**: Q **Entry**: syn tot **Value**: 0-1 **Explanation**: The proportion of synonymous alleles in each individual fox * **Column**: R **Entry**: pop **Value**: Helagsfjällen, Vindelfjällen-Arjeplogsfjällen **Explanation**: The subpopulation that each indivdual fox was sampled from - **Column**: S **Entry**: ancestry **Value**: native, hybrid **Explanation**: Ancestry of each individual fox. Hybrid = first, second or third generation descendants of immigrants. * **Column**: T **Entry**: coverage **Value**: numerical **Explanation**: Mean depth of coverage for each individual fox #### Variables demographic dataset LRS & age (sheet 2) * **Column**: A **Entry**: ID **Value**: individual code - **Column**: B **Entry**: sex **Value**: f,m **Explanation**: Sex of each individual fox - **Column**: C **Entry**: phase born **Value**: high,low **Explanation**: The phase of the rodent cycle each individual fox was born during. High = high rodent abundance. Low = low rodent abundance - **Column**: D **Entry**: den **Value**: den ID **Explanation**: The den each individual fox was born in - **Column**: E **Entry**: ancestry **Value**: native, F1, F2-F3 **Explanation**: Ancestry of each individual fox. F1 = first generation offspring of immigrants. F2-F3 second and third generation offspring of immigrants - **Column**: F **Entry**: LRS **Value**: numerical **Explanation**: Lifetime reproductive success. The total number of cubs each individual fox that survived to adulthood produced during their lifetime - **Column**: G **Entry**: age **Value**: numerical **Explanation**: The number of years each individual fox that survived to adulthood lived - **Column**: H **Entry**: year born **Value**: numerical **Explanation**: The year each individual fox was born in #### Variables demographic dataset litters (sheet 3) - **Column**: A **Entry**: year **Value**: numerical **Explanation**: The year each litter was produced in - **Column**: B **Entry**: phase **Value**: high, low **Explanation**: The phase of the rodent cycle each litter was produced in. High = high rodent abundance. Low = low rodent abundance - **Column**: C **Entry**: den **Value**: den ID **Explanation**: The den each litter was produced in - **Column**: D **Entry**: litter size **Value**: numerical **Explanation**: The number of cubs produced in each litter - **Column**: E **Entry**: pair **Value**: pair combinations **Explanation**: The pair combination of each litter. nativeXnative = native litters. nativeXimmigrant = F1 hybrid litters. NativeXF1-F4 = F2-F5 litters backcrossed with native individuals. F1-F4XF1-F4 = F2-F5 litters that backcrossed with immigrant descendants.