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457 results for “Inbreeding”
Density dependence maintains long-term stability despite increased isolation and inbreeding in the Florida Scrub-Jay
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Epistasis, inbreeding depression and the evolution of self-fertilization
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Data from: Contrasting patterns of inbreeding and inbreeding depression in co-occurring spotted turtle and eastern box turtle populations
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Why don't all animals avoid inbreeding?
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Epistasis, inbreeding depression and the evolution of self-fertilization
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Inbreeding depression in artificial selection lines of Ipomoea purpurea
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An inbreeding perspective on the effectiveness of wildlife population defragmentation measures: A case study on wild boar (Sus scrofa) of Veluwe, The Netherlands
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Data from: Inbreeding depression affects the growth of seedlings of an African timber species with a mixed mating reproductive system, Pericopsis elata (Harms) Meeuwen
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Data from: Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
<p>Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition; characteristics that can affect the severity of inbreeding depression. We utilised extensive long-term data on more than 3100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic<sub> </sub>estimates of realised inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than non-inbred individuals. Inbreeding depression, measured as the decline in fitness related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.</p>
Data from: Sexually-selected male weapon is associated with lower inbreeding load but higher gender load in the bulb mite
<p>Elaborate sexually selected ornaments and armaments are costly but increase the reproductive success of their bearers (usually males). It has been postulated that high-quality males can invest disproportionately more in such traits, making those traits honest signals of genetic quality. However, genes associated with such traits may have sexually antagonistic effects on fitness. Here, using a bulb mite <i>Rhizoglyphus robini</i>, a species in which a distinct dimorphism exists between males in the expression of a sexually selected weapon, we compare inbreeding and gender load between lines derived from armed fighters and unarmed scramblers. After four generations of sib-mating, inbreeding depression for female fitness was significantly lower in fighter-derived lines compared to scrambler-derived lines, suggesting that fighter males had significantly higher genetic quality. However, outbred females from fighter-derived lines had significantly lower fitness compared to outbred females from scrambler-derived lines, demonstrating significant gender load associated with the presence of a sexually selected male weapon. Our results imply that under outbreeding, genetic benefits of mating with bearers of elaborate sexually selected traits might be swamped by the costs of decreased fitness of female progeny due to sexually antagonistic effects.</p>
Inbreeding and disease avoidance in a free‐ranging koala population
<p>Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk, and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether female koalas make mate choices based on [1] relatedness, and [2] chlamydial disease in available mates. We found no evidence that female koalas based their mate choice on the relative relatedness of available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas based their mate choice on the chlamydial disease status of available mates. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At-risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.</p>
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>
Heterozygosity–fitness correlations reveal inbreeding depression in neonatal body size in a critically endangered rock iguana
Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.
Data from: Bottlenecks and inbreeding depression in autotetraploids
Inbreeding depression is dependent on the ploidy of populations and can inhibit the evolution of selfing. While polyploids should generally harbor less inbreeding depression than diploids at equilibrium, it has been unclear whether this pattern holds in non-equilibrium conditions following bottlenecks. We use stochastic individual based simulations to determine the effects of population bottlenecks on inbreeding depression in diploids and autotetraploids, in addition to cases where neo-autotetraploids form from the union of unreduced gametes. With a ploidy-independent dominance function based on enzyme kinetics, inbreeding depression is generally lower in autotetraploids for fully and partially recessive mutations. Due to the sampling of more chromosomes during reproduction, bottlenecks generally reduce inbreeding depression to a lesser extent in autotetraploids. All else being equal, population bottlenecks may have ploidy dependent effects for another reason – in some cases mating between close relatives temporarily increases inbreeding depression in autotetraploids by increasing the frequency of the heterozygous genotype harboring the most harmful mutations. When neo-autotetraploids are formed by few individuals, inbreeding depression is dramatically reduced, given extensive masking of harmful mutations following whole genome duplication. This effect persists as nascent tetraploids reach mutation-selection-drift balance, providing a transient period of permissive conditions favoring the evolution of selfing.
Severe inbreeding depression is predicted by the "rare allele load" in Mimulus guttatus
<p>Most flowering plants are hermaphroditic and experience strong pressures to evolve self‐pollination (automatic selection, reproductive assurance). Inbreeding depression (ID) can oppose selection for selfing, but it remains unclear if ID is typically strong enough to maintain outcrossing. To measure the full cost of sustained inbreeding on fitness, and its genomic basis, we planted highly homozygous, fully genome‐sequenced inbred lines of yellow monkeyflower (<i>Mimulus guttatus)</i> in the field next to outbred plants from crosses between the same lines. The cost of full homozygosity is severe: 65% for survival, 86% for lifetime seed production. Accounting for the unmeasured effect of lethal and sterile mutations, we estimate that the average fitness of fully inbred genotypes is only 3–4% that of outbred competitors. The genome sequence data provides no indication of simple overdominance, but the number of rare alleles carried by a line, especially within rare allele clusters nonrandomly distributed across the genome, is a significant negative predictor of fitness measurements. These findings are consistent with a deleterious allele model for ID. High variance in rare allele load among lines and the genomic distribution of rare alleles both suggest that migration might be an important source of deleterious alleles to local populations.</p>
Data from: Bayesian quantification of ecological determinants of outcrossing in natural plant populations: computer simulations and the case study of biparental inbreeding in English yew
The mating system is a central parameter of plant biology because it shapes their ecological and evolutionary properties. Therefore, determining ecological variables that influence the mating system is important for a deeper understanding of the functioning of plant populations. Here, using old concepts and recent statistical developments, we propose a new statistical tool to make inferences about ecological determinants of outcrossing in natural plant populations. The method requires co-dominant genotypes of seeds collected from maternal plants within different locations. Using extensive computer simulations, we demonstrated that the method is robust to the issues expected for real-world data, including the Wahlund effect, inbreeding and genotyping errors such as allele dropout and allele misclassification. Furthermore, we showed that the estimates of ecological effects and outcrossing rates can be severely biased if genotyping errors and genetic differentiation are not treated explicitly. Application of the new method to the case study of a dioecious tree (Taxus baccata) allowed revealing that female trees that grow in lower local densities have a greater tendency towards mating with relatives. Moreover, we also demonstrated that biparental inbreeding is higher in populations that are characterised by a longer mean distance between trees and a smaller mean trunk perimeter. We found these results to agree with both the theoretical predictions and the history of English yew.
Inbreeding depression in a sexually selected weapon and the homologue in females
<p>Theory predicts that traits with heightened condition-dependence, such as sexually selected traits, should be affected by inbreeding to a greater degree than other traits. The presence of environmental stress may compound the negative consequences of inbreeding depression. In this study we examined inbreeding depression across multiple traits and whether it increased with a known form of environmental stress. We conducted our experiment using both sexes of the sexually dimorphic leaf-footed cactus bug, <em>Narnia femorata </em>(Hemiptera: Coreidae). Adult male cactus bugs have enlarged hind legs used as weapons in male-male contests; these traits, and their homologue in females, have been previously found to exhibit high condition-dependence. In this study, we employed small developmental group size as an environmental stress challenge. Nymph <em>N. femorata</em> aggregate throughout their juvenile stages, and previous work has shown the negative effects of small group size on survivorship and body size. We found evidence of inbreeding depression for survival and seven out of the eight morphological traits measured, in both sexes. Inbreeding depression was higher for the size of the male weapon and the female homolog. Additionally, small developmental group size negatively affected survival to adulthood. However, small group size did not magnify the effects of inbreeding on morphological traits. These findings support the hypothesis that traits with heightened condition-dependence exhibit higher levels of inbreeding depression.</p>
Evolution of selfing syndrome and its influence on genetic diversity and inbreeding: A range-wide study in Oenothera primiveris.
<p><strong>Premise of the study:</strong> To avoid inbreeding depression plants have evolved diverse breeding systems to favor outcrossing such as self-incompatibility. However, changes in biotic and abiotic conditions can result in selective pressures that lead to a breakdown in self-incompatibility. The shift to increased selfing is commonly associated with reduced floral features, lower attractiveness to pollinators, and increased inbreeding. In this study, we tested the hypothesis that the loss of self-incompatibility, a shift to self-fertilization (autogamy), and concomitant evolution of the selfing syndrome (reduction in floral traits associated with cross-fertilization) will lead to increased inbreeding and population differentiation in <em>Oenothera primiveris</em>. Across its range, this species exhibits a shift in its breeding system and floral traits from a self-incompatible population with large flowers to self-compatible populations with smaller flowers.</p> <p><strong>Methods:</strong> We conducted a breeding system assessment, evaluated floral traits in the field and under controlled conditions, and measured population genetic parameters using RADseq data. </p> <p><strong>Key results:</strong> Our results reveal a bimodal transition to the selfing syndrome from the west to the east of the range of <em>O. primiveris</em>. This shift includes variation in the breeding system, mating system, a reduction in floral traits (flower diameter, herkogamy, and scent production), a shift to greater autogamy, reduced genetic diversity, and increased inbreeding.</p> <p><strong>Conclusions:</strong> The observed variation highlights the importance of range-wide studies to understand breeding system variation and the evolution of the selfing syndrome within populations and species.</p>
Inbreeding and kinship coefficients of parents of sperm competition experiment with lake char (Lake Geneva 2017/18)
<p>A total of 14 lake char (<em>Salvelinus umbla</em>) were genotyped in the same library using ddRADsequencing. The data includes 14 gzipped .fastq files generated using 2 lanes of sequencing on an Illumina HIseq 2500 and the final dataset with the final estimates of kinship and inbreeding. For each individual, the fastq files of the 2 sequencings lanes were merged after demultiplexing using <em>process_radtags</em> (Stacks 1.48). We provide the bash and R scripts that we used. There are no legal or ethical considerations regarding the above-mentioned data.</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. --
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