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36 results for “genomic inbreeding”
Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho bleekeri) using genome wide SNP markers
<p>Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF-seq)-based genotyping was performed for Sichuan taimen with 43 yearling individuals from 3 locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (average F=2.6×10-3±0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < 0.001) and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic-relatedness-guided breeding and conservation strategy for wild fish species without pedigree information records.</p>
Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population
Demographic events such as series of bottlenecks impact the genetic variation and adaptive potential of populations. European megafauna, such as wild boars (Sus scrofa), have experienced severe climatic and size fluctuations that have shaped their genetic variation. Habitat fragmentation as well as human-mediated translocations have further contributed to the complex demographic history of European wild boar. Danish wild boars represent an extreme case of a small and isolated population founded by four wild boars from Germany. Here, we explore the genetic composition of the Danish wild boar population in Klelund. We genotyped all 21 Danish wild boars that were recently transferred from the source population in Lille Vildmose into the Klelund Plantation to establish a novel wild boar population. We compared the Danish wild boars to high‐density single nucleotide polymorphism genotypes from a comprehensive reference set of 1263 wild and domesticated pigs, including 11 individuals from Ulm, one of two presumed founder locations in Germany. Our findings support the European wild background of the Danish population and no traces of gene flow with wild or domesticated pigs were found. The narrow genetic origin of the Danish wild boars is illustrated by extremely long and frequent runs of homozygous stretches in their genomes, indicative of recent inbreeding. This study provides the first insights into one of the most inbred wild boar populations globally established a century ago from a narrow base of only four founders. --
Data for: Genomic insights into inbreeding and adaptive divergence of trout populations to inform genetic rescue
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Data from: Genomes of Galápagos mockingbirds reveal the impact of island size and past demography on inbreeding and genetic load in contemporary populations
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Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population
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Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho bleekeri) using genome wide SNP markers
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Data from: Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon
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Data from: Demographic history and inbreeding in two declining sea duck species inferred from whole genome sequence data
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An evaluation of inbreeding measures using a whole genome sequenced cattle pedigree
<p>The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (F<sub>UNI</sub>) or on the genomic relationships (F<sub>GRM</sub>) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (F<sub>HOM</sub>), homozygous-by-descent segments (F<sub>HBD</sub>), runs-of-homozygosity (F<sub>ROH</sub>) or on the known genealogy (F<sub>PED</sub>) was better at capturing whole genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies. The results indicate that F<sub>UNI</sub> and F<sub>GRM</sub> might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus specific inbreeding measures or at low marker density, the ranking of the methods can also change as F<sub>HBD </sub>makes better use of the information from neighbouring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, F<sub>PED</sub> was uncorrelated with locus specific homozygosity.</p>
Data from: Genomic analysis reveals depression due to both individual and maternal inbreeding in a free-living mammal population
There is ample evidence for inbreeding depression manifested as a reduction in fitness or fitness-related traits in the focal individual. In many organisms, fitness is not only affected by genes carried by the individual, but also by genes carried by their parents, for example if receiving parental care. While maternal effects have been described in many systems, the extent to which inbreeding affects fitness directly through the focal individual, or indirectly through the inbreeding coefficients of its parents, has rarely been examined jointly. The Soay sheep study population is an excellent system in which to test for both effects, as lambs receive extended maternal care. Here, we tested for both maternal and individual inbreeding depression in three fitness-related traits (birthweight and weight and hindleg length at 4 months of age) and three fitness components (first-year survival, adult annual survival and annual breeding success), using either pedigree-derived inbreeding or genomic estimators calculated using ~37 000 SNP markers. We found evidence for inbreeding depression in 4-month hindleg and weight, first-year survival in males, and annual survival and breeding success in adults. Maternal inbreeding was found to depress both birthweight and 4-month weight. We detected more instances of significant inbreeding depression using genomic estimators than the pedigree, which is partly explained through the increased sample sizes available. In conclusion, our results highlight that cross-generational inbreeding effects warrant further exploration in species with parental care and that modern genomic tools can be used successfully instead of, or alongside, pedigrees in natural populations.
Population genomics of an Octopus species identify oceanographic barriers and inbreeding patterns: Demultiplexed reads of 71 Octopus insularis individuals
<p>Coastal marine ecosystems are highly productive and important for global fisheries. To mitigate over-exploitation and to establish efficient conservation management plans for species of economic interest, it is necessary to identify the oceanographic barriers that condition divergence and gene flow between populations with those species, and that determine their relative amounts of genetic variability. Here, we present the first population genomic study of an <em>Octopus</em> species, <em>Octopus</em> <em>insularis</em>, which was described in 2008 and is distributed in coastal and oceanic island habitats in the tropical Atlantic Ocean, Gulf of Mexico and the Caribbean Sea. Using genomic data, we identify the South Equatorial current as the main barrier to gene flow between southern and northern parts of the range, followed by discontinuities in the habitat associated with depth. We find that genetic diversity of insular populations significantly decreases after colonization from the continental shelf, also reflecting low habitat availability. Using demographic modelling, we find signatures of a stronger population expansion for coastal relative to insular populations, consistent with estimated increases in habitat availability since the Last Glacial Maximum. The direction of gene flow is coincident with unidirectional currents and bidirectional eddies between otherwise isolated populations. Together, our results show that oceanic currents and habitat breaks are determinant in the diversification of coastal marine species where adults have a sedentary behavior but paralarvae are dispersed passively, shaping standing genetic variability within populations. Lower genetic diversity within insular populations implies that these are particularly vulnerable to current human exploitation and selective pressures, calling for the revision of their protection status.</p>
The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species
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Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data
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Data from: Genomic analysis reveals depression due to both individual and maternal inbreeding in a free-living mammal population
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Genomic and fitness consequences of inbreeding in an endangered carnivore
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Data from: Exploring tree-like and non-tree-like patterns using genome sequences: an example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh.
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An evaluation of inbreeding measures using a whole genome sequenced cattle pedigree
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Population genomics of an Octopus species identify oceanographic barriers and inbreeding patterns: Demultiplexed reads of 71 Octopus insularis individuals
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Genomic inbreeding and population structure of northern pike (Esox lucius) in Xinjiang, China
<p>Northern pike (Esox lucius) is originally only distributed in the Irtysh River, and now spread into many habitats in Xinjiang, China. A total of four populations were collected from north to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a small lake nearby Ulungu River (LJD) and Bosten Lake (LBO). We estimated population genomic parameters, performed gene flow analysis, and estimated the effective population size of each population.</p>
Data from: Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens
Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bacillus thuringiensis (Bt) resistance. We developed 350-bp double-digest restriction-site associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection and inbreeding in this nonmodel insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily a result of the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, in which more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated line, we generated a dense intraspecific linkage map containing three PCR-based and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups, but this clustering was not statistically significant. Overall, we have confirmed and extended the general expectations for reduced genetic diversity in laboratory colonies, provided tools for further genomic analyses and produced highly homozygous genomic DNA for future whole genome sequencing of H. virescens.
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