Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration
Ontology highlight
ABSTRACT:
SUBMITTER: Smeds L
PROVIDER: S-EPMC10848878 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity (i.e., adaptive potential) to respond to ecological stressors. We are interested in how the variation captured in protein-coding genes fluctuates relative to overall genomic diversity and whether smaller populations suffer greater costs due to their genetic load of deleterious mutations compared with larger populations. We analyzed individual whole-genome sequences (N = 74) from three different populations of Montezuma quail (Cyrtonyx montezumae), a small ground-dwelling bird that is sustainably harvested in some portions of its range but is of conservation concern elsewhere. Our historical demographic results indicate that Montezuma quail populations in the United States exhibit low levels of genomic diversity due in large part to long-term declines in effective population sizes over nearly a million years. The smaller and more isolated Texas population is significantly more inbred than the large Arizona and the intermediate-sized New Mexico populations we surveyed. The Texas gene pool has a significantly smaller proportion of strongly deleterious variants segregating in the population compared with the larger Arizona gene pool. Our results demonstrate that even in small populations, highly deleterious mutations are effectively purged and/or lost due to drift. However, we find that in small populations the realized genetic load is elevated because of inbreeding coupled with a higher frequency of slightly deleterious mutations that are manifested in homozygotes. Overall, our study illustrates how population genomics can be used to proactively assess both neutral and functional aspects of contemporary genetic diversity in a conservation framework while simultaneously considering deeper demographic histories.
| S-EPMC8210801 | biostudies-literature
Project description:Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%-24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.
| S-EPMC8896455 | biostudies-literature
Project description:Sarcoptic mange, a parasitic disease caused by the mite Sarcoptes scabiei, is regularly reported on wolves Canis lupus in Scandinavia. We describe the distribution and transmission of this parasite within the small but recovering wolf population by analysing 269 necropsy reports and performing a serological survey on 198 serum samples collected from free-ranging wolves between 1998 and 2013.The serological survey among 145 individual captured Scandinavian wolves (53 recaptures) shows a consistent presence of antibodies against sarcoptic mange. Seropositivity among all captured wolves was 10.1 % (CI. 6.4 %-15.1 %). Sarcoptic mange-related mortality reported at necropsy was 5.6 % and due to secondary causes, predominantly starvation. In the southern range of the population, seroprevalence was higher, consistent with higher red fox densities. Female wolves had a lower probability of being seropositive than males, but for both sexes the probability increased with pack size. Recaptured individuals changing from seropositive to seronegative suggest recovery from sarcoptic mange. The lack of seropositive pups (8-10 months, N?=?56) and the occurrence of seropositive and seronegative individuals in the same pack indicates interspecific transmission of S. scabiei into this wolf population.We consider sarcoptic mange to have little effect on the recovery of the Scandinavian wolf population. Heterogenic infection patterns on the pack level in combination with the importance of individual-based factors (sex, pack size) and the north-south gradient for seroprevalence suggests low probability of wolf-to-wolf transmission of S. scabiei in Scandinavia.
| S-EPMC4962404 | biostudies-literature
Project description:Natural populations are becoming increasingly fragmented which is expected to affect their viability due to inbreeding depression, reduced genetic diversity and increased sensitivity to demographic and environmental stochasticity. In small and highly inbred populations, the introduction of only a few immigrants may increase vital rates significantly. However, very few studies have quantified the long-term success of immigrants and inbred individuals in natural populations. Following an episode of natural immigration to the isolated, severely inbred Scandinavian wolf (Canis lupus) population, we demonstrate significantly higher pairing and breeding success for offspring to immigrants compared to offspring from native, inbred pairs. We argue that inbreeding depression is the underlying mechanism for the profound difference in breeding success. Highly inbred wolves may have lower survival during natal dispersal as well as competitive disadvantage to find a partner. Our study is one of the first to quantify and compare the reproductive success of first-generation offspring from migrants vs. native, inbred individuals in a natural population. Indeed, our data demonstrate the profound impact single immigrants can have in small, inbred populations, and represent one of very few documented cases of genetic rescue in a population of large carnivores.
| S-EPMC5054837 | biostudies-literature
Project description:Quantification of loss of haplotype diversity in the highly inbred Scandinavian wolf population
| PRJEB44869 | ENA
Project description:Bardet-Biedl syndrome (BBS) is a defining ciliopathy, notable for extensive allelic and genetic heterogeneity, almost all of which has been identified through sequencing. Recent data have suggested that copy-number variants (CNVs) also contribute to BBS. We used a custom oligonucleotide array comparative genomic hybridization (aCGH) covering 20 genes that encode intraflagellar transport (IFT) components and 74 ciliopathy loci to screen 92 unrelated individuals with BBS, irrespective of their known mutational burden. We identified 17 individuals with exon-disruptive CNVs (18.5%), including 13 different deletions in eight BBS genes (BBS1, BBS2, ARL6/BBS3, BBS4, BBS5, BBS7, BBS9, and NPHP1) and a deletion and a duplication in other ciliopathy-associated genes (ALMS1 and NPHP4, respectively). By contrast, we found a single heterozygous exon-disruptive event in a BBS-associated gene (BBS9) in 229 control subjects. Superimposing these data with resequencing revealed CNVs to (1) be sufficient to cause disease, (2) Mendelize heterozygous deleterious alleles, and (3) contribute oligogenic alleles by combining point mutations and exonic CNVs in multiple genes. Finally, we report a deletion and a splice site mutation in IFT74, inherited under a recessive paradigm, defining a candidate BBS locus. Our data suggest that CNVs contribute pathogenic alleles to a substantial fraction of BBS-affected individuals and highlight how either deletions or point mutations in discrete splice isoforms can induce hypomorphic mutations in genes otherwise intolerant to deleterious variation. Our data also suggest that CNV analyses and resequencing studies unbiased for previous mutational burden is necessary to delineate the complexity of disease architecture.
| S-EPMC4974085 | biostudies-literature
Project description:The major histocompatibility complex (MHC) has an integral role in the immune system, and hence diversity at its genes may be of particular importance for the health of populations. In large populations, balancing selection maintains diversity in MHC genes, but theoretical expectations indicate that this form of selection is absent or inefficient in small populations. We examine the level of diversity at three MHC class II loci in the wolf population of Scandinavia, a population naturally recolonized with a genetic contribution from as few as three founders, and in four neighbouring wolf populations. In the Scandinavian wolf population, two alleles were found for each locus and the distribution of alleles is compatible with their linkage into two haplotypes. Changes in the level of heterozygosity over time since recolonization demonstrate the effects of the proposed arrival of an immigrant wolf. The maintenance of diversity is shown to be compatible with a neutral, random allocation of alleles, in conjunction with crossing between packs. A total of 15 DRB1, seven DQA and 10 DQB1 alleles are found in four neighbouring wolf populations, with substantial sharing across populations. Even in these larger populations, bottlenecks and fragmentation with consequent genetic drift are likely to have resulted in few indicators for balancing selection and significant differentiation of populations.
| S-EPMC1691861 | biostudies-other
Project description:Abstract Wolves (Canis lupus) can exert top‐down pressure and shape ecological communities through the predation of ungulates and beavers (Castor spp.). Therefore, understanding wolf foraging is critical to estimating their ecosystem‐level effects. Specifically, if wolves are consumers that optimize tradeoffs between the cost and benefits of prey acquisition, changes in these factors may lead to prey‐switching or negative‐density dependent selection with potential consequences for community stability. For wolves, factors affecting cost and benefits include prey vulnerability, risk, reward, and availability, which can vary temporally. We described the wolf diet by the frequency of occurrence and percent biomass and characterized the diet using prey remains found in wolf scats on Isle Royale National Park, Michigan, USA, during May–October 2019 and 2020. We used logistic regression to estimate prey consumption over time. We predicted prey with temporal variation in cost (availability and/or vulnerability) such as adult moose (Alces alces), calf moose, and beaver (Castor canadensis) to vary in wolf diets. We analyzed 206 scats and identified 62% of remains as beaver, 26% as moose, and 12% as other species (birds, smaller mammals, and wolves). Adult moose were more likely to occur in wolf scats in May when moose are in poor condition following winter. The occurrence of moose calves peaked during June–mid‐July following birth but before calf vulnerability declined as they matured. By contrast, beaver occurrence in wolf scat did not change over time, reflecting the importance of low‐handling cost prey items for recently introduced lone or paired wolves. Our results demonstrate that the wolf diet is responsive to temporal changes in prey costs. Temporal fluctuation in diet may influence wolves' ecological role if prey respond to increased predation risk by altering foraging or breeding behavior. We analyzed wolf diet from scats in relation to optimal foraging. We found 62% of remains as beaver, 26% as moose, and 12% as other (birds, smaller mammals, and wolves). The contents of wolf scat changed over time. Wolf diet is plastic and responsive to temporal changes in prey acquisition cost as predicted by optimal foraging theory.
| S-EPMC10019911 | biostudies-literature
Project description:Variation in gene expression profiles was determined between mouse inbred strains in hindlimb muscle tissue. Strains under investigation were: C57Bl/6, C57Bl/10, CBA, DBA2, and BALB/c. Keywords: other
2003-12-10 | GSE662 | GEO
Project description:Stress leads to physiologic dysfunction and cardiometabolic disease. Allostatic load score (ALS) measures stress-induced cardiovascular, metabolic, and inflammatory biomarkers. We estimated the odds of high ALS by reason for and age at immigration, duration of American residence, number of children, and socioeconomic status in 193 African immigrants (male: 65%, age 41 ± 10 y (mean ± Standard Deviation (SD)), range 22-65 y). ALS was calculated with High-ALS defined as ALS ≥ 3.0 and Low-ALS defined as ALS < 3.0. Oral glucose tolerance tests (OGTT) were performed, the cardiovascular disease (CVD) risk estimated, and TNF-α, an inflammatory cytokine, measured. Logistic regression was used to estimate odds of High-ALS. In the High- and Low-ALS groups, ALS were 4.0 ± 1.2 vs. 1.3 ± 0.7, diabetes prevalence: 14% vs. 4%, CVD risk: 23% vs. 8%, TNF-α levels: 15 ± 9 vs. 11 ± 6 pg/mL, respectively (all p ≤ 0.01). Immigrants were more likely to be in the High-ALS group if their reason for immigration was work or asylum/refugee (OR 2.18, p = 0.013), their age at immigration was ≥30 y (OR 3.28, p < 0.001), their duration of residence in United States was ≥10 y (OR 3.16, p = 0.001), or their number of children was ≥3 (OR 2.67, p = 0.019). Education, income, health insurance, marital status, and gender did not affect High-ALS odds. Factors adversely influencing allostatic load and cardiometabolic health in African immigrants were age at and reason for immigration, duration of residence in America, and number of children.
| S-EPMC7345091 | biostudies-literature