Strongly deleterious mutations influence reproducitve output and longevity in an endangered population
Data files
Sep 16, 2024 version files 70.85 KB
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Genomic_demographic_fitness_data_Nat.xlsx
28.85 KB
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r-code.txt
5.95 KB
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README.md
7.20 KB
Abstract
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.
README: Strongly deleterious mutations influence reproducitve output and longevity in an endangered population
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.