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The persistence of small populations is influenced by the degree and cost of inbreeding, with the degree of inbreeding depending on whether close-kin mating is passively or actively avoided. Few studies have simultaneously studied these factors. We examined inbreeding in a small, isolated population of westslope cutthroat trout using extensive genetic and demographic data. Passive inbreeding avoidance was low, with predicted lifetime dispersal of approximately 36 and 74 m for females and males, respectively. Additionally, we found limited evidence for active inbreeding avoidance during reproduction. Relatives remained spatially clustered into adulthood, and observed relatedness among mate pairs was greater than expected under random mating by 0.09, suggesting that inbreeding is a concern in this population. Further, we examined sex-specific inbreeding depression throughout the life cycle and provide evidence for inbreeding depression in some fitness components, including family size, juvenile survival and reproductive success. Our results suggest that, in an at-risk trout population, limited passive and active inbreeding avoidance lead to a higher degree of inbreeding than expected under random mating. Observed inbreeding, along with evidence for fitness reduction due to inbreeding depression, could put the population at a heightened risk of decline or extirpation. [ABSTRACT FROM AUTHOR]

Emerging infectious diseases (EIDs) not only cause catastrophic declines in wildlife populations but also generate selective pressures that may result in rapid evolutionary responses. One such EID is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal and has reduced the average lifespan of individuals by around 2 years, likely causing strong selection for traits that reduce susceptibility to the disease, but population decline has also left Tasmanian devils vulnerable to inbreeding depression. We analysed 22 years of data from an ongoing study of a population of Tasmanian devils on Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether size traits or susceptibility to DFTD were under inbreeding depression. We found a positive phenotypic relationship between head width and susceptibility to DFTD, but this was not underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship between body weight and susceptibility to DFTD, and there was evidence for a negative genetic correlation between susceptibility to DFTD and body weight. There was additive genetic variance in susceptibility to DFTD, head width and body weight, but there was no evidence for inbreeding depression in any of these traits. These results suggest that Tasmanian devils have the potential to respond adaptively to DFTD, although the realised evolutionary response will critically further depend on the evolution of DFTD itself. [ABSTRACT FROM AUTHOR]

ABSTRACT Objective Methods Results Conclusion We investigated inbreeding effects on longevity and fertility in the House of Habsburg, one of the principal royal dynasties of Europe.A total number of 124 Habsburg marriages, involving 107 men and 124 women, in the period of approximately 1450–1800 were considered for the analysis. Kinship and inbreeding coefficients were computed from genealogical information, which included more than 8000 individuals.We found a significant negative association between age of death and inbreeding coefficient (F) in those women who had children (regression coefficient b = −1.06, p = 0.0008). This result led us to investigate possible inbreeding effects on maternal mortality in the period of 4 weeks after the childbirth. A strong inbreeding depression on maternal survival was detected through the Kaplan–Meier curve for groups of women with different level of inbreeding (log‐rank test p = 0.0001) and the Cox proportional hazards regression analysis (hazard ratio = 2.36, p = 0.0008). Effect on fertility was also found as more inbred women had longer interbirth intervals (b = 154.66, p = 0.022). Effects of male or female inbreeding on the number of children per woman were not detected through zero‐inflated regression models suggesting that reproductive compensation might be occurring among the more inbred and less‐fecund women.The effect of inbreeding in adulthood in the Habsburg lineage was at least as important as that previously reported on prereproductive survival. To our knowledge, our results are the first evidence of an inbreeding effect on maternal mortality in humans. [ABSTRACT FROM AUTHOR]

Background: Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1 Mb (genome), between 1 and 2 Mb - FROH 1−2; 2–4 Mb FROH 2−4 or > 8 Mb FROH >8) and excess homozygosity (FSNP). Results: The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1−2, r = 0.20 with FROH 2−4 and r = 0.28 with FROH 4−8). Meanwhile, the FPed had a moderate correlation with FSNP (r = 0.47) and high correlation with FROH >8 (r = 0.58) and FROH−genome (r = 0.60). The FROH−genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH−genome (r = 0.55) and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2−4 to 0.37 for FROH 1−2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traits ranged from 0.12 to 0.51 for FPed, 0.19–0.59 for FGRM, 0.21–0.58 for FROH−genome, and 0.19–0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49–1.97% for FGRM, 0.34–2.2% for FROH−genome, and 0.50–1.62% for FSNP per 1% of inbreeding. The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits. Conclusions: The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait. [ABSTRACT FROM AUTHOR]

Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long‐term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation‐impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics‐informed conservation can reduce the genetic load whilst reducing the loss of genome‐wide diversity. Genomics‐informed management is likely to become instrumental in maintaining the long‐term viability of zoo populations. see also the Perspective by Evelyn L. Jensen, Rachel Gray & Joshua M. Miller [ABSTRACT FROM AUTHOR]

Genetic architecture of yield and yield contributing characters of five crosses in chickpea were performed by generation mean analysis. Non-significant χ2 values were noted for plant weight at harvest (PWH), number of pods per plant (NPd/P) and number of seeds per plant (NS/P) in cross-2; for number of secondary branches at first flower (NSBFF) and number of secondary branches at maximum flower (NSBMF) in cross-3 and for number of primary branches at maximum flower (NPBMF) in cross-4. Among these, PWH in cross-2; NSBFF and NSBMF in cross-3 and NPBMF in cross-4 were also non-significant regarding C and D scales. Non-significant scale coupled with non-significant χ2 values indicated only additive-dominance relationship for those characters and crosses that would likely be helpful in doing successful breeding plan easily for the development of potential lines in chickpea. Gene effects viz., additive [d], dominance [h], additive × additive [i] and dominance × dominance [l] were significant for different crosses and characters indicating involvement of additive, dominance, additive × additive and dominance × dominance gene interactions in the control of these traits. Most of the studied characters exhibited duplicate type of epistasis therefore, recurrent selection for these traits is suggested. Effective factor (K1) was less than one for all the characters and crosses indicating minimum one group of gene controlled the characters. Both broad (h2b) and narrow (h2n) sense heritability in majority cases were found to be high which indicates that selection for high heritability showing traits is likely to be effective. Mid-parent (MP) and better-parent (BP) heterosis found to be non-significant in maximum cases. All the characters and crosses showed non-significant inbreeding depression (ID) indicating a good sign for further genetic work. [ABSTRACT FROM AUTHOR]

Inbreeding depression is a key factor regulating the evolution of self-fertilization in plants. Despite predictions that inbreeding depression should evolve with selfing rates as deleterious alleles are increasingly exposed and removed by selection, evidence of purging the genetic load in wild populations is equivocal at best. This discordance could be explained, in part, if the load underlying inbreeding depression is subject to soft selection, i.e., the fitness of selfed individuals depends on the frequency and density of selfed vs. outcrossed individuals in the population. Somewhat counterintuitively, this means that populations with contrasting mutation load can have similar fitness. Soft selection against selfed individuals may be expected when there is inbreeding depression for competitive ability in density-regulated populations. We tested population-level predictions of inbreeding depression in competitive ability by creating a density series of potted plants consisting of either purely outcrossed, purely selfed, or mixed (50% outcrossed, 50% selfed) seed of the mixed-mating biennial Sabatia angularis (Gentianaceae) representing ecological neighborhoods. Focusing on the growth and survival of juveniles, we show that mean plant size is independent of neighborhood composition when resources are limiting, but greatest in outcrossed neighborhoods at low densities. Across a range of densities, this manifests as stronger densitydependence in outcrossed populations compared to selfed or mixed ones. We also found significantly greater size inequalities among individuals in mixed neighborhoods, even at high densities where mean juvenile size converged, a key signature of asymmetric competition between outcrossed and selfed individuals. Our work illustrates how soft selection could shelter the genetic load underlying inbreeding depression and its demographic consequences. [ABSTRACT FROM AUTHOR]

Inbreeding depression, the reduced fitness of inbred relative to outbred individuals was described more than two centuries ago, long before the development of population genetics. Its impact is central to evolutionary ecology and the evolution of mating systems, in particular self-fertilization in hermaphrodites. In the first half of the 20th century, population genetics revealed a mechanism for inbreeding depression through homozygosity. Numerous theoretical studies have modeled inbreeding depression as a function of genetic architecture and analyzed how it varies with population selfing rates. A major concept in these models is purging, i.e., the purging of recessive deleterious mutations through inbreeding. Consequently, inbreeding depression is expected to decrease with increasing population selfing rates. Along with these theoretical studies, many experimental studies, particularly on plants, have measured inbreeding depression using experimental crosses or directly in the field. The results of these studies have revealed that the evolutionary ecology of inbreeding depression is difficult to capture and that empirical data do not exactly match model predictions, specifically purging efficacy. In addition, the lability of inbreeding depression in natural populations can qualitatively affect the selective role of inbreeding depression in the evolution of mating systems. Recently, several studies have demonstrated the role of epigenetics in shedding new light on the dynamics of inbreeding depression in natural populations. This review provides a general overview of the studies on inbreeding depression and how various angles can help capture its selective role in natural populations. [ABSTRACT FROM AUTHOR]

Inbreeding impairs the cognitive abilities of humans, but its impact on cognition in other animals is poorly studied. For example, environmental stress (e.g. food limitation and extreme temperatures) often amplifies inbreeding depression in morphological traits, but whether cognition is similarly affected is unclear. We, therefore, tested if a higher temperature (30°C versus 26°C) during development exacerbates any difference in inhibitory control between inbred (f = 0.25) and outbred guppies (Poecilia reticulata). Inhibitory control is an aspect of cognition that is often measured in vertebrates using a detour test, in which animals have to navigate around a transparent barrier to reach a reward. We also tested if inbreeding and temperature affect 'boldness', which is a putative personality trait in guppies. Inbreeding lowered inhibitory control of guppies raised at the higher temperature but not those raised at the control temperature. Inbred fish were significantly less bold than outbred fish. In addition, males, but not females, raised at the higher temperature had significantly lower inhibitory control. There was no effect of temperature on the boldness of either sex. Our study is among the first to test if experimentally induced inbreeding impairs cognition in a non-domesticated vertebrate. We show that both inbreeding and higher temperatures during development can affect the behaviour and cognitive abilities of fish. These findings are noteworthy given the twin threats of rising global temperatures and more frequent inbreeding as habitat fragmentation reduces population sizes. [ABSTRACT FROM AUTHOR]

Inbreeding depression is likely to play an important role during biological invasion. But relatively few studies have investigated the fitness of selfed and outcrossed offspring in self-incompatible invasive plants in natural environments in their introduced range. Moreover, the majority of studies on inbreeding depression have investigated self-compatible species with mixed mating, and less is known about the intensity of inbreeding depression in outcrossing selfincompatible species. Here, we address these questions experimentally by comparing selfed and outcrossed progeny of purple loosestrife (Lythrum salicaria) over four growing seasons, including three under field conditions in a freshwater marsh in southern Ontario, Canada, a region where L. salicaria is highly invasive. The tristylous mating system of L. salicaria involves disassortative mating among floral morphs enforced by trimorphic incompatibility. However, owing to partial incompatibility, self-fertilized seed can be obtained by manual self-pollination thus facilitating comparisons of selfed and outcrossed progeny. We compared progeny with and without intraspecific competition from selfed or outcrossed neighbours and examined the influence of breeding treatment and competition on fitness correlates by measuring a range of life-history traits including: proportion of seeds germinating, days to germination, survival, proportion of plants flowering, time to flowering, vegetative mass, and inflorescence number and mass. We analysed data for each trait using functions from time series estimates of growth and two multiplicative estimates of fitness. We detected varying intensities of inbreeding depression for several traits in three of the four years of the experiment, including inflorescence mass and reproductive output. Cumulative inbreeding depression over four years averaged d = 0.48 and 0.68, depending on the method used to estimate multiplicative fitness. The competition treatments did not significantly affect plant performance and the magnitude of inbreeding depression. Given the primarily outcrossing mating system of L. salicaria populations, the detection of inbreeding depression for several key life-history traits was as predicted by theory. Our results suggests that biparental inbreeding and low selfing in colonizing populations may have significant effects on demographic parameters such as population growth. [ABSTRACT FROM AUTHOR]

Anthropogenic activities are causing a steep decline of wildlife populations. Increased inbreeding in shrinking populations can substantially curb individual fitness and population viability. One potentially important but largely ignored component of inbreeding depression may be cognitive decline. Cognition affects an animal's capacity to respond to environmental disturbance, which, in the face of global change, may make the difference between persistence and extinction. While the effects of inbreeding on cognitive performance have been relatively well documented in humans, they remain largely unexplored in natural populations. Here we review the current (limited) knowledge on whether and how inbreeding impinges on animals' cognitive abilities. Insights into the relationship between inbreeding and cognition could prove valuable not only for comprehending the development and evolution of cognition but also for conservation. [ABSTRACT FROM AUTHOR]

Estimates of the influence of inbreeding on the fitness of wild animals can guide genetic conservation in rare species. Conservation genetics is important in Mexican wolves (Canis lupus baileyi) because the current population descended from 7 founders and mean inbreeding is relatively high. As an endangered subspecies, Mexican wolves are actively managed using select conflict avoidance measures and by placing captive‐born foster pups into wild litters. We obtained data on inbreeding coefficients of wolf pups and adults based on a pedigree dating to 1957 and data on reproduction for wild wolf packs during 1998–2022. We estimated trends in inbreeding coefficients and the associations between dam, sire, and pup inbreeding coefficients and pup recruitment to age 9 months, and assessed 3 components of recruitment: probability of producing a litter, number of pups produced, and recruitment conditional on successful reproduction. We generated estimates using generalized linear mixed models and bootstrapped estimates of confidence intervals. Mean inbreeding coefficients were high (0.227, SD = 0.047) in the wild population, but we detected no significant evidence of an increase during 2010–2022. Overall, the net associations of dam, sire, and pup inbreeding coefficients with our primary fitness metric, pup recruitment to age 9 months, did not differ from zero. While high inbreeding coefficients are a concern for the long‐term recovery of the subspecies, the stable level of inbreeding, lack of evidence for inbreeding depression, high pup production (5.1 pups/litter, SD = 1.64), and rapid population growth (384% increase from 2010–2022) indicate that inbreeding has not prevented rapid progress towards recovery goals under current management practices. [ABSTRACT FROM AUTHOR]

The most important step in plant breeding is the correct selection of parents, and it would be wise to use heterotic groups for this. The purpose of this study is to analyse yield and its components as well as genetic diversity in line × tester wheat populations. It also seeks to present a coherent framework for the isolation of early superior families and the development of heterotic groups in bread wheat. F1 and F2 generations of 51 genotypes, including 36 combinations between 12 lines and three testers and 15 parents, were evaluated for yield and its components in a three-replication experiment according to the randomized block design. Line × tester analysis of variance, general and specific combining abilities, heterosis, heterobeltiosis and inbreeding depression were calculated. Heterotic groups created based on general and specific combining abilities were compared with each other. The results showed that there was sufficient genetic variation in the population and that further genetic calculations could be made. The selections made based on general and specific combining abilities, heterosis values and average performance of genotypes without heterotic grouping indicated different genotypes for each feature. The creation of heterotic groups made it possible to select genotypes that were superior in terms of all the criteria listed. It was concluded that heterotic groups created based on specific combining abilities may be more useful for breeding studies. [ABSTRACT FROM AUTHOR]

Abstract Background Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1 Mb (genome), between 1 and 2 Mb - FROH 1−2; 2–4 Mb FROH 2−4 or > 8 Mb FROH >8) and excess homozygosity (FSNP). Results The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1−2, r = 0.20 with FROH 2−4 and r = 0.28 with FROH 4−8). Meanwhile, the FPed had a moderate correlation with FSNP (r = 0.47) and high correlation with FROH >8 (r = 0.58) and FROH−genome (r = 0.60). The FROH−genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH−genome (r = 0.55) and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2−4 to 0.37 for FROH 1−2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traits ranged from 0.12 to 0.51 for FPed, 0.19–0.59 for FGRM, 0.21–0.58 for FROH−genome, and 0.19–0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49–1.97% for FGRM, 0.34–2.2% for FROH−genome, and 0.50–1.62% for FSNP per 1% of inbreeding. The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits. Conclusions The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.

Abstract Genetic architecture of yield and yield contributing characters of five crosses in chickpea were performed by generation mean analysis. Non-significant χ2 values were noted for plant weight at harvest (PWH), number of pods per plant (NPd/P) and number of seeds per plant (NS/P) in cross-2; for number of secondary branches at first flower (NSBFF) and number of secondary branches at maximum flower (NSBMF) in cross-3 and for number of primary branches at maximum flower (NPBMF) in cross-4. Among these, PWH in cross-2; NSBFF and NSBMF in cross-3 and NPBMF in cross-4 were also non-significant regarding C and D scales. Non-significant scale coupled with non-significant χ2 values indicated only additive-dominance relationship for those characters and crosses that would likely be helpful in doing successful breeding plan easily for the development of potential lines in chickpea. Gene effects viz., additive [d], dominance [h], additive × additive [i] and dominance × dominance [l] were significant for different crosses and characters indicating involvement of additive, dominance, additive × additive and dominance × dominance gene interactions in the control of these traits. Most of the studied characters exhibited duplicate type of epistasis therefore, recurrent selection for these traits is suggested. Effective factor (K1) was less than one for all the characters and crosses indicating minimum one group of gene controlled the characters. Both broad (h2 b) and narrow (h2 n) sense heritability in majority cases were found to be high which indicates that selection for high heritability showing traits is likely to be effective. Mid-parent (MP) and better-parent (BP) heterosis found to be non-significant in maximum cases. All the characters and crosses showed non-significant inbreeding depression (ID) indicating a good sign for further genetic work.

Abstract Background Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders, which may be confused with pathologies of environmental etiology. Results We present a data mining framework specifically designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates. Conclusions The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.

Many parasite species use multiple host species to complete development; however, empirical tests of models that seek to understand factors impacting evolutionary changes or maintenance of host number in parasite life cycles are scarce. Specifically, one model incorporating parasite mating systems that posits that multihost life cycles are an adaptation to prevent inbreeding in hermaphroditic parasites and thus preclude inbreeding depression remains untested. The model assumes that loss of a host results in parasite inbreeding and predicts that host loss can evolve only if there is no parasite inbreeding depression. We provide the first empirical tests of this model using a novel approach we developed for assessing inbreeding depression from field-collected parasite samples. The method compares genetically based selfing rate estimates to a demographic-based selfing rate, which was derived from the closed mating system experienced by endoparasites. Results from the hermaphroditic trematode Alloglossidium renale , which has a derived two-host life cycle, supported both the assumption and the prediction of the mating system model, as this highly inbred species had no indication of inbreeding depression. Additionally, comparisons of genetic and demographic selfing rates revealed a mixed mating system that could be explained completely by the parasite's demography (i.e., its infection intensities). [ABSTRACT FROM AUTHOR]

Ecosourcing seed of 'local genetic stock' for ecological restoration has been practiced in New Zealand for about 50 years. However, we believe that it has become unnecessarily restrictive. Ecosourcing ensures plants used for restoration are adapted to local conditions and maintains current distributional patterns. It also restricts genetic diversity, confines species to their historic range, and reduces the conservation options for threatened species. For example, New Zealand tree species, the life form most frequently used in restoration plantings, have low population genetic differentiation and high net migration of alleles throughout their range. Therefore, very little is gained through restrictive ecosourcing of tree seed. Furthermore, avoidance of the danger of inbreeding depression and widening the scope for closer environmental matching, argues for larger rather smaller source areas. Climate change, extinctions across multiple trophic levels, habitat loss and fragmentation, spread of invasive species, and novel habitats have completely altered the contemporary biotic landscape. Conservation needs to engage with these changes if it is to protect and restore ecosystems. Restrictive ecosourcing is counter-productive as it limits utilising genotypic, phenotypic and ecotypic diversity, and thus the evolutionary potential of indigenous species and ecosystems. It also reduces opportunities to protect biodiversity when populations are small, and limits response to climate change. A new approach is needed. We recommend that phylogeographic patterns and biogeographic boundaries be used to set nine broad ecosourcing regions and, within these regions, phenotypic adaptation to particular environments be used as a guide to seed selection. This more relaxed approach to ecosourcing will improve restoration outcomes through increasing species and genetic diversity, reducing the detrimental effects of inbreeding and promoting the genetic rescue of populations of threatened species. Examples of adopting an eco-evolutionary approach to ecosourcing are provided for the early-successional coloniser Kunzea ericoides and late-successional conifer species. [ABSTRACT FROM AUTHOR]

Abstract Genetic rescue—an increase in population fitness following the introduction of new alleles—has been proven to ameliorate inbreeding depression in small, isolated populations, yet is rarely applied as a conservation tool. A lingering question regarding genetic rescue in wildlife conservation is how long beneficial effects persist in admixed populations. Using data collected over 40 years from 1192 endangered Florida panthers (Puma concolor coryi) across nine generations, we show that the experimental genetic rescue implemented in 1995—via the release of eight female pumas from Texas—alleviated morphological, genetic, and demographic correlates of inbreeding depression, subsequently preventing extirpation of the population. We present unequivocal evidence, for the first time in any terrestrial vertebrate, that genetic and phenotypic benefits of genetic rescue remain in this population after five generations of admixture, which helped increase panther abundance (> fivefold) and genetic effective population size (> 20-fold). Additionally, even with extensive admixture, microsatellite allele frequencies in the population continue to support the distinctness of Florida panthers from other North American puma populations, including Texas. Although threats including habitat loss, human-wildlife conflict, and infectious diseases are challenges to many imperiled populations, our results suggest genetic rescue can serve as an effective, multi-generational tool for conservation of small, isolated populations facing extinction from inbreeding.

Abstract Background The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1–2 Mb), FROH2 (2–4 Mb), FROH3 (4–8 Mb), FROH4 (8–16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. Results The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. Conclusions Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

ABSTRACT: In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (Fped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (Fhat1, Fhat2, Fhat3), VanRaden's first method (FVR1, with observed allele frequencies, and FVR0.5, when allele frequencies are set to 0.5), and one based on runs of homozygosity (Froh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from −0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (Fhat1) to 40.62 kg (Fhat3), 1.18 kg (Fhat2) to 1.70 kg (Fhat3), 0.90 kg (Fhat2) to 1.45 kg (Froh and Fhat3), 0.19 (Fped) to 0.34 d (Fhat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.

Cotton is a valuable industrial fiber crop grown in many regions worldwide. Four cotton (Gossypium hirsutum L.) cultivars, i.e., Ishonch, Navbakhor-2, C-6524, and Tashkent-6, and their F1-2 diallel hybrids’ cultivation comprised a randomized complete block design with a factorial arrangement and four replications during 2019–2021 in the Tashkent Region, Uzbekistan. Significant (P ≤ 0.01) differences were notable among the parental genotypes and their F1 hybrids for boll weight and seed cotton yield. The parental cultivars Ishonch and Navbakhor-2 and their F1 diallel hybrids showed more stability and performed better than other genotypes. Broad-sense heritability estimates were the highest for boll weight and seed cotton yield while lowest for bolls per plant. Based on this trait’s yield, heritability, and variability, the inbreeding depression was positive in the F2 populations Ishonch × Navbakhor-2 and Navbakhor-2 × Tashkent-6. According to yield, the cultivars Ishonch, Navbakhor-2, and Tashkent-6 were outstanding as positive donors. [ABSTRACT FROM AUTHOR]

Induced homologous tetraploid oysters are typically derived from a limited number of effective parents, with subsequent breeding steps likely to cause inbreeding, which may cause their own production performance to decline. To explore the performance of inbreeding, we established outbred (F0) and inbred lines (F1 and F2) in tetraploid Pacific oyster. Cleavage rate, shell height, survival rate, and total weight were compared. Inbreeding coefficients in F0, F1, and F2 were 0, 0.25, and 0.375, respectively. The results showed that there was no significant difference in cleavage rate between outbred line and inbred lines. The F1 showed distinct growth and survival depression only at larval stage, but no depression at grow-out stage. F1 growth and survival IDC values at larval stage were − 1.29% to 0.03% and − 0.31% to 0.01%, respectively. However, depressed growth and survival rate appeared in almost all F2 growth cycle; F2 growth and survival IDC values were − 1.10% to − 0.78% and − 3.14% to − 4.51% in larval stage and − 0.48% to − 0.25% and − 0.79% to − 0.64% in grow-out stage, respectively. Growth and survival rate at Longkou and Qingdao sites showed no depression in the F1 line during grow-out stage. The results indicate that inbreeding depressed growth and in particular survival in tetraploid oysters. With increased inbreeding levels, depressed growth and survival became more distinct. We provided important insights on the inbred lines construction and further breeding of tetraploid oysters. [ABSTRACT FROM AUTHOR]

It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes and low levels of genetic polymorphisms. To understand the genetic mechanisms of long-term persistence in threatened species, we determined the whole genome sequences of akame (Lates japonicus), which has survived for a long time with extremely low genetic variations. Genome-wide heterozygosity in akame was estimated to be 3.3 to 3.4 × 10−4/bp, one of the smallest values in teleost fishes. Analysis of demographic history revealed that the effective population size in akame was around 1,000 from 30,000 years ago to the recent past. The relatively high ratio of nonsynonymous to synonymous heterozygosity in akame indicated an increased genetic load. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions, including genes involved in immunity, synaptic development, and olfactory sensory systems, have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, suggesting adaptive evolution to temperate waters after the speciation of akame and its close relative, barramundi (Lates calcarifer). Our results indicate that the functional genetic diversity likely contributed to the long-term persistence of this species by avoiding the harmful effects of the population size reduction. [ABSTRACT FROM AUTHOR]

In guava (Psidium guajava), the impact of self-pollination on the quantitative traits of the fruits is not fully understood, necessitating further investigation. This study aimed to estimate the effects of selfing on fruit traits in S1 and S2 inbred families of guava and to explore potential impacts on genetic diversity. Eighteen S1 families were generated through selfing of progenies from biparental crosses, and ten S2 families were produced by selfing superior genotypes from S1 families. The experiment was conducted at the Experimental Station of Ilha Barra do Pomba, in the municipality of Itaocara-Rio de Janeiro, Brazil. It utilized a randomized complete block design, with three replications and ten plants per plot. Evaluated traits included fruit weight, length, diameter, length-diameter ratio, endocarp thickness, mesocarp thickness, pulp weight, and soluble solids content. The data underwent individual analysis of variance, yielding predicted mean trait values for S1 and S2 generations, alongside correlation and homozygosity estimates. Genetic diversity was assessed using Mahalanobis distance and UPGMA cluster analysis, and comparative box plots between inbred populations were created for the evaluated traits. Box plot analysis revealed symmetry in most evaluated traits, suggesting uniformity in the data due to the selfing strategy. Analysis of variance indicated statistically significant differences in all traits, highlighting variability between populations S1 and S2. Fruit and pulp weights exhibited high homozygosity levels, with values of 90.86 and 102.59 respectively, linked to increased fruit traits in the S2 population, indicating their importance in the fixation of favorable alleles. Fruit weight, length, and diameter, endocarp thickness, and mesocarp thickness showed strong correlations, exceeding 0.70. Genetic diversity assessment via Mahalanobis distance indicated a decrease in genetic variability, evidenced by fewer groups in S2 compared to the S1 population. However, this reduction did not noticeably affect the average performance of the S2 population. The results indicate that the two generations of self-pollination did not negatively affect the phenotypic values of the evaluated traits. [ABSTRACT FROM AUTHOR]

Inbreeding depression refers to the reduced performance arising from increased homozygosity, a phenomenon that is the reverse of heterosis and exists among plants and animals. As a natural self-pollinated crop with strong heterosis, the mechanism of inbreeding depression in rice is largely unknown. To understand the genetic basis of inbreeding depression, we constructed a successive inbreeding population from the F2 to F4 generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each generation. The expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle, 11 for primary branches, and 12 for secondary branches, and these loci constitute the main correlation between heterosis and inbreeding depression. However, the genetic basis of inbreeding depression is also distinct from that of heterosis, such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected depression. Noticeably, two-locus interactions may change the extent and direction of the depression effects of the target loci, and overall interactions would promote inbreeding depression among generations. Using an F2:3 variation population, the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after inbreeding. We found inconsistent or various degrees of background depression from the F2 to F3 generation assuming different genotypes of the target locus, which may affect the actual depression effect of the locus due to epistasis. The results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms, which expand our understanding of the whole-genome architecture of inbreeding depression. [ABSTRACT FROM AUTHOR]

Background: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1–2 Mb), FROH2 (2–4 Mb), FROH3 (4–8 Mb), FROH4 (8–16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. Results: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. Conclusions: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle. [ABSTRACT FROM AUTHOR]

Inbreeding depression (ID) is a major selective force during mating system evolution primarily contributed by highly to partially recessive deleterious mutations. Theories suggest that transient genetic association with fitness alleles can be important in affecting the evolution of alleles that modify the selfing rate during its sweep. Nevertheless, empirical tests often focus on the pre- existing genetic association between selfing rate and ID maintained under mutation--selection balance. Therefore, how this standing genetic association is affected by key factors and its impacts on the evolution of selfing remain unclear. I show that as the selection coefficient of deleterious mutations increases, the association between selfing rate and ID declines from positive to negative. These results predict that association between selfing and ID tends to be negative in populations with low selfing rates, while positive in highly selfing populations. Using population genetic and quantitative genetic models, I show that standing genetic associations between selfing rate and fitness alleles can significantly impact the evolution of the mean selfing rate of a population. I present better metrics of population-level ID, which can be calculated based on the correlation coefficient between individual selfing rate and the fitness of selfed and outcrossed offspring. [ABSTRACT FROM AUTHOR]

In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (F ped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (F hat1 , F hat2 , F hat3), VanRaden's first method (F VR1 , with observed allele frequencies, and F VR0.5 , when allele frequencies are set to 0.5), and one based on runs of homozygosity (F roh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from −0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (F hat1) to 40.62 kg (F hat3), 1.18 kg (F hat2) to 1.70 kg (F hat3), 0.90 kg (F hat2) to 1.45 kg (F roh and F hat3), 0.19 (F ped) to 0.34 d (F hat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful. [ABSTRACT FROM AUTHOR]

The aim of this paper is to present methods for estimating inbreeding and inbreeding effects using genome data and to give an overview of previous results in dairy cattle populations. Arrays with 50,000 single nucleotide polymorphisms (SNPs) evenly distributed across the genome are predominantly used in cattle population studies. The genome-based methods make it possible to localize the clusters and size of the homozygous segments ("runs of homozygosity", ROH) created by inbreeding on the genome, which enables further analyses of the genomic inbreeding coefficient (FROH), the mapping of inbreeding effects, the allele effects in the ROH and the development of the ROH in ancestral generations. Another way to calculate genomic inbreeding coefficients is to use the individual SNPs. This method can lead to an overestimation of genomic inbreeding and inbreeding depression, as homozygous SNP genotypes are not necessarily identical-by-descent. If the ROH clusters and their detrimental effects on the breeding traits in a cattle population are known, then the expected distribution of ROH and their expected effects on performance depression can be predicted for each animal and its progeny. Most studies on genomic inbreeding have been performed in Holstein populations. A 1% increase in FROH was associated with an inbreeding depression in 305-day milk yield of 20 - 61 kg milk, while fat and protein yield showed an inbreeding depression of 1.3 - 1.7 kg and 1.2 - 2.5 kg, respectively. In phenotypic standard deviations of the traits, this corresponds to a decrease of 2.393%, 2.306% and 3.021%. The fertility traits experienced less inbreeding depression with 0.825% of the phenotypic standard deviation in comparison to milk performance. Disease incidences showed inbreeding depression with a 1% increase in FROH by 2.530% of the phenotypic standard deviation. The different lengths of the ROH segments showed very different trends for inbreeding depression depending on the traits and the respective population. The identified ROH regions with significant inbreeding depression were distributed across different chromosomal clusters and the effects varied greatly in size. A concentration on a few chromosomes or clusters was not found for any trait. Only a small number of loci in ROH exhibited pleiotropic effects on inbreeding depression. With the introduction of genomic selection, a faster fixation of loci and higher inbreeding increase occurs. Therefore, efficient inbreeding management is necessary for cattle populations. This can be improved by denser SNP sets. [ABSTRACT FROM AUTHOR]

Increasing levels of inbreeding with the loss of genetic diversity have been observed since years and are therefore the subject of scientific research for many decades and the resulting consequences for the economically important performance, health and functional traits in dairy cattle breeding. The aim of this study was therefore to review methods and previous findings on inbreeding effects in dairy cattle populations based on pedigree data from the literature. Negative effects of inbreeding (inbreeding depression) are well documented for breeding traits in livestock populations. An increase in the inbreeding coefficient based on pedigree data by 1% was associated with a decrease in the phenotypic trait value by 0.13% of the mean or by 0.59% of the phenotypic standard deviation. A reduction of inbreeding depression (purging) can occur when, as a result of selection, the individuals affected by stronger inbreeding depression in their survival and reproductive rate are increasingly impaired or used less frequently in breeding and thus alleles with negative effects on fitness are lost in the population. If sufficiently deep pedigree data are available, it becomes possible to show effects of reduced inbreeding depression using ancestral inbreeding coefficients. Across all studies, the estimated value for the ancestral inbreeding depression Fa_Kal according to Kalinowski et al. (2000) was -1.272% of the phenotypic standard deviation, for the new inbreeding Fa_New according to Kalinowski et al. (2000) -0.866% of the phenotypic standard deviation and the interaction between F and Fa_Bal (Ballou, 1997) -7.063% of the phenotypic standard deviation. This shows that purging of the inbreeding depression by selection was not detectable for all traits investigated, as the inbreeding depression was higher for ancestral inbreeding than for new inbreeding or the inbreeding depression associated with the interaction of the classical inbreeding coefficient with Fa_Bal. For the 305-day milk yield traits of the cows, there was clear evidence of purging of inbreeding depression in the Holsteins in the Netherlands and a reduction of inbreeding depression in the Holsteins in Ireland. However, for fertility and longevity traits, there was no reduction in inbreeding depression due to selection. It is therefore important to minimize the increase in ancestral and new inbreeding. In this way, a reduction in selection progress through inbreeding depression can also be prevented. [ABSTRACT FROM AUTHOR]

Statistical inferences about inbreeding depression are often derived from analyses with low power and a high risk of failing to detect inbreeding depression. That risk is widely appreciated by scientists familiar with the relevant statistical and genetical theory, but may be overlooked and underappreciated by decision-makers. Consequently, there is value in demonstrating this risk using a real example. We use data from the wolf population on Isle Royale to demonstrate the difficulty of making reliable statistical inferences about inbreeding depression. This wolf population is known—by other methods—to have gone effectively extinct due to deleterious genetic processes associated with inbreeding. Beyond that demonstration, we use two case-studies—wolves on Isle Royale and vaquita (porpoises) from the Gulf of California, Mexico—to show how statistical inferences about inbreeding depression can affect conservation decisions. According to most decision theory, decisions depend importantly on: 1) probabilities that certain states exist (e.g. inbreeding depression is present) and 2) the utility assigned to various outcomes (e.g. the value of acting to mitigate inbreeding when it is present). The probabilities are provided by statistical inference; whereas utilities are almost entirely determined by normative values and judgements. Our analysis suggests that decisions to mitigate inbreeding depression are often driven more by utilities (normative values) than probabilities (statistical inferences). As such, advocates for mitigating inbreeding depression will benefit from better communicating to decision-makers the value of populations persisting and the extent to which decisions should depend on normative values. [ABSTRACT FROM AUTHOR]

Simple Summary: Deleterious recessive alleles causing inbreeding depression may be eliminated from populations through purifying selection facilitated by inbreeding. Providing evidence of this phenomenon (i.e., inbreeding purging) is of great interest for conservation biologists and animal breeders. Ballou's ancestral inbreeding coefficient ( F B A L − A N C ) is one of the most widely used pedigree-based measurements to detect inbreeding purging, but the theoretical basis has not been fully established. In this report, the author gives a mathematical formulation of F B A L − A N C and proposes a new method for estimation based on the obtained formula. A stochastic simulation suggests that the new method could reduce the variance of estimates, compared to the conventional gene-dropping simulation. Inbreeding is unavoidable in small populations. However, the deleterious effects of inbreeding on fitness-related traits (inbreeding depression) may not be an inevitable phenomenon, since deleterious recessive alleles causing inbreeding depression might be purged from populations through inbreeding and selection. Inbreeding purging has been of great interest in conservation biology and animal breeding, because populations manifesting lower inbreeding depression could be created even with a small number of breeding animals, if inbreeding purging exists. To date, many studies intending to detect inbreeding purging in captive and domesticated animal populations have been carried out using pedigree analysis. Ballou's ancestral inbreeding coefficient ( F B A L − A N C ) is one of the most widely used measurements to detect inbreeding purging, but the theoretical basis for F B A L − A N C has not been fully established. In most of the published works, estimates from stochastic simulation (gene-dropping simulation) have been used. In this report, the author provides a mathematical basis for F B A L − A N C and proposes a new estimate by hybridizing stochastic and deterministic computation processes. A stochastic simulation suggests that the proposed method could considerably reduce the variance of estimates, compared to ordinary gene-dropping simulation, in which whole gene transmissions in a pedigree are stochastically determined. The favorable property of the proposed method results from the bypass of a part of the stochastic process in the ordinary gene-dropping simulation. Using the proposed method, the reliability of the estimates of F B A L − A N C could be remarkably enhanced. The relationship between F B A L − A N C and other pedigree-based parameters is also discussed. [ABSTRACT FROM AUTHOR]

Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree‐based inbreeding coefficients. However, with the development of single‐nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression. The aim of the study was to analyse inbreeding depression in 6 growth and 2 reproductive traits in the Asturiana de los Valles cattle breed using both genealogical and molecular information. The pedigree group comprised 225,848 records and an average equivalent number of complete generations of 2.3. The molecular data comprised genotypes of 2693 animals using the Affymetrix medium‐density chip. Using the pedigree information, three different inbreeding coefficients were estimated for the genotyped animals: the full pedigree coefficient (FPED), and the recent and ancient inbreeding coefficients based on the information of the last three generations (FPED<3G) and until the last three generations (FPED>3G), respectively. Using the molecular data, seven inbreeding coefficients were calculated. Four of them were estimated based on runs of homozygosity (ROH), considering (1) the total length (FROH), (2) segments shorter than 4 megabases (FROH<4), (3) between 4 and 17 megabases (FROH4‐17), and (4) longer than 17 Mb (FROH>17). Additionally, the three inbreeding coefficients implemented in the Plink software (FHAT1‐3) were estimated. Inbreeding depression was estimated using linear mixed‐effects model with inbreeding coefficients used as covariates. All analysed traits (birth weight, preweaning average daily gain, weaning weight adjusted at 180 days, carcass weight, calving ease, age at first calving, calving interval) showed a statistically significant non‐zero effect of inbreeding depression estimated from the pedigree group, except for the Postweaning Average Daily Gain trait. When inbreeding coefficients were based on the genomic group, statistically significant inbreeding depression was observed for two traits, Preweaning Average Daily Gain and Weaning Weight based on FROH, FROH>17, and FHAT3 inbreeding coefficients. Nevertheless, similar to inbreeding depression estimated based on pedigree information, estimates of inbreeding depression based on genomic information had no relevant economic impact. Despite this, from a long‐term perspective, genotyped data could be included to maximize genetic progress in genetic programs following an optimal genetic contribution strategy and to consider individual inbreeding load instead global inbreeding. ROH islands were identified on chromosomes 2, 3, 8, 10, and 16. Such regions contain several candidate genes for growth development, intramuscular fat, body weight and lipid metabolism that are related to production traits selected in Asturiana de los Valles breed. [ABSTRACT FROM AUTHOR]

Inbreeding is thought to be a key adverse factor impacting the genetic quality of seeds in seed production populations and the inbreeding degree (i.e., selfing or outcrossing rate) of seed production populations have been extensively assessed through mating system analysis. The adverse effect of inbreeding on seed quality traits in seed production populations under open-pollination conditions has not yet been clearly described. In this study, the open-pollinated seeds were collected from 26 mother trees in a 58-year-old seed tree stand. Three seed quality traits, including thousand-seed weight (TSW), germination rate (GR), and germination potential (GP), were measured, and the seeds from eight of 26 families with significant differences in seed quality traits were genotyped through twelve microsatellite markers. In addition, the seeds and sprouts (germinated seeds) from six families were genotyped to reveal the effect of inbreeding on seed germination. The three seed quality traits significantly differed among families (p < 0.001). The multilocus outcrossing rate (tm = 0.889) and single-locus outcrossing rate (ts = 0.648) of overall seeds indicated apparent selfing (11.1%) and biparental inbreeding (24.0%). The outcrossing rate in the sprout group (tm = 0.919, ts = 0.788) was higher than that in the seed group (tm = 0.833, ts = 0.646), and the difference in ts between groups was different from zero under the 95% confidence interval (0.024–0.260), suggesting that inbreeding negatively affected seed germination. Linear regression demonstrated that TSW was positively correlated with tm and ts, while GR was negatively related to tm−ts and positively related to ts, implying that seed mass (development) was probably more affected by self-fertilization, but germination capacity was more influenced by biparental inbreeding. The inbreeding depression (ID) of TSW was estimated to be 26.3% with a 0.1 decrease in tm, while that of GR was estimated to be 8.4% with a 0.1 decrease in ts. These results suggest that the IDs during seed development and the germination stage of Masson pine were nonignorable and that more attention to outcrossing rate should be paid to the establishment and management of Masson pine seed production. [ABSTRACT FROM AUTHOR]

Aim: Inbreeding is thought to affect the morphometric parameters leading to lower health status among the progeny. The present study was aimed to investigate the repercussions of inbreeding on anthropometric traits, namely height, weight and body mass index (BMI). Subjects and methods: The survey was conducted in two North Indian cities and total 813 individuals were randomly recruited from inbred and outbred families. The morphometric parameters of the subjects were measured using standard methods, BMI was calculated and categorized into underweight, normal weight and overweight. Family pedigrees were drawn and degree of inbreeding in terms of the inbreeding coefficient (F) was calculated. Results: A significant decline in morphometric measures was observed among inbred individuals as compared to outbred ones. The mean differences (95% CI) were found significant for various inbred and first cousin categories as compared to outbred subjects (p < 0.05). We found the increased frequency of underweight individuals corresponding to the degree of inbreeding for different types of inbred categories (p = 2.086 × 10−9) and also for different subtypes of first cousin unions corresponding to their sex-linked inbreeding coefficients (p = 5.2 × 10−5). The regression slope and correlation coefficient revealed a fitness decline and depression in anthropometric measures (p < 0.05) with the increase in 'F' for all inbred groups and first cousin categories. Conclusions: The present research confirms the adverse effects of inbreeding on morphometric parameters among inbred subjects. It has novelty in shedding light on the hitherto unreported differences in the consequences of inbreeding among different types of first cousin unions. Highlights: Consanguinity acts as a risk factor among humans resulting in poor health status. This empirical study deals with the effect of inbreeding on anthropometric measures. Significant decrease in morphometric traits was observed among inbred individuals. The risk for poor health status was found proportional to the degree of inbreeding. We also reported the differences in inbreeding effects for various first cousin unions for the very first time. [ABSTRACT FROM AUTHOR]

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g. at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria : Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions. [ABSTRACT FROM AUTHOR]

Most flowering plants require animal pollination and are visited by multiple pollinator species. Historically, the effects of pollinators on plant fitness have been compared using the number of pollen grains they deposit, and the number of seeds or fruits produced following a visit to a virgin flower. While useful, these methods fail to consider differences in pollen quality and the fitness of zygotes resulting from pollination by different floral visitors. Here we show that, for three common native self-compatible plants in Southern California, super-abundant, non-native honeybees (Apis mellifera L.) visit more flowers on an individual before moving to the next plant compared with the suite of native insect visitors. This probably increases the transfer of self-pollen. Offspring produced after honeybee pollination have similar fitness to those resulting from hand self-pollination and both are far less fit than those produced after pollination by native insects or by cross-pollination. Because honeybees often forage methodically, visiting many flowers on each plant, low offspring fitness may commonly result from honeybee pollination of self-compatible plants. To our knowledge, this is the first study to directly compare the fitness of offspring resulting from honeybee pollination to that of other floral visitors.

Inbreeding depression is a key factor regulating the evolution of self-fertilization in plants. Despite predictions that inbreeding depression should evolve with selfing rates as deleterious alleles are increasingly exposed and removed by selection, evidence of purging the genetic load in wild populations is equivocal at best. This discordance could be explained, in part, if the load underlying inbreeding depression is subject to soft selection, i.e., the fitness of selfed individuals depends on the frequency and density of selfed vs. outcrossed individuals in the population. Somewhat counterintuitively, this means that populations with contrasting mutation load can have similar fitness. Soft selection against selfed individuals may be expected when there is inbreeding depression for competitive ability in density-regulated populations. We tested population-level predictions of inbreeding depression in competitive ability by creating a density series of potted plants consisting of either purely outcrossed, purely selfed, or mixed (50% outcrossed, 50% selfed) seed of the mixed-mating biennial Sabatia angularis (Gentianaceae) representing ecological neighborhoods. Focusing on the growth and survival of juveniles, we show that mean plant size is independent of neighborhood composition when resources are limiting, but greatest in outcrossed neighborhoods at low densities. Across a range of densities, this manifests as stronger density-dependence in outcrossed populations compared to selfed or mixed ones. We also found significantly greater size inequalities among individuals in mixed neighborhoods, even at high densities where mean juvenile size converged, a key signature of asymmetric competition between outcrossed and selfed individuals. Our work illustrates how soft selection could shelter the genetic load underlying inbreeding depression and its demographic consequences.

Inbreeding depression, the reduced fitness of inbred relative to outbred individuals was described more than two centuries ago, long before the development of population genetics. Its impact is central to evolutionary ecology and the evolution of mating systems, in particular self-fertilization in hermaphrodites. In the first half of the 20th century, population genetics revealed a mechanism for inbreeding depression through homozygosity. Numerous theoretical studies have modeled inbreeding depression as a function of genetic architecture and analyzed how it varies with population selfing rates. A major concept in these models is purging, i.e., the purging of recessive deleterious mutations through inbreeding. Consequently, inbreeding depression is expected to decrease with increasing population selfing rates. Along with these theoretical studies, many experimental studies, particularly on plants, have measured inbreeding depression using experimental crosses or directly in the field. The results of these studies have revealed that the evolutionary ecology of inbreeding depression is difficult to capture and that empirical data do not exactly match model predictions, specifically purging efficacy. In addition, the lability of inbreeding depression in natural populations can qualitatively affect the selective role of inbreeding depression in the evolution of mating systems. Recently, several studies have demonstrated the role of epigenetics in shedding new light on the dynamics of inbreeding depression in natural populations. This review provides a general overview of the studies on inbreeding depression and how various angles can help capture its selective role in natural populations.

ABSTRACT: This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity. We also generated inbreeding coefficients based on the generational inbreeding for recent and old pedigree inbreeding, for different run-of-homozygosity length classes, and for recent and old homozygous-by-descent segment-based inbreeding. Estimates on the liability scale revealed significant evidence of inbreeding depression for reproductive-disease traits, with an increase in total pedigree and genomic inbreeding showing a notable effect for recent inbreeding. However, we found inconsistent evidence for inbreeding depression for mastitis or any metabolic diseases. Notably, in Holsteins, the probability of developing displaced abomasum decreased with inbreeding, particularly for older inbreeding. Estimates of disease probability for cows with low, average, and high inbreeding levels did not significantly differ across any inbreeding coefficient and trait combination, indicating that although inbreeding may affect disease incidence, it likely plays a smaller role compared with management and environmental factors.

Corn germplasm with different mesocotyl elongation was characterized for High Valleys in Mexico by estimating the general combinatory aptitude (GCA), specific combinatory aptitude (SCA), heterosis (H), inbreeding depression (ID) and principal component aptitude (PCA), with the purpose of directing the improvement for deep sowing. The hypothesis was that the parents and crosses of mesocotyl present variability in seedling and adult plant traits based on deep sowing. The 36 F1 and F2 crosses—derived from nine parents, three with short mesocotyl (S), three medium (M) and three long (L), obtained through Griffing diallel II—plus the parents were planted in sand beds and polyethylene bags in a greenhouse during the spring–summer cycles of 2021 and 2022. The following traits were measured: length of mesocotyl (LM), length of coleoptile, total seedling dry matter and 10 cob traits in addition to total dry matter. In 11 of the 14 traits, there was a positive and significant correlation (p ≤ 0.05) between the GCA of the parents and their LM. The highest SCA, H and ID (p ≤ 0.05) were for crosses L × L for all the traits measured. When comparing the GCA/SCA proportions, this relation varied from 0.76 to 0.97, which points to practically equal additive effects with those of dominance; however, in parents and L × L crosses, this relation was on average 0.94, 1.07 in M × M, 0.22 in S × S and 0.36 in L × S. In both F1 and F2, the variation was explained by two principal components: 89.5% for GCA and 73.4% for SCA. In both generations, the parents with higher GCA were H-48, HS-2 and Promesa, the three with long mesocotyl, while those with the highest GCA were crosses between these three hybrids.

Background Cassava is an outcrossing, highly heterozygous plant that is reported to suffer from inbreeding depression. However, unraveling recessive traits and exploring additive genes would require a limited level of inbreeding for the genetic improvement of cassava. Method The impact of inbreeding depression (ID) on agronomic and biotic tolerance of cassava was evaluated using the S 1 progenies of five African cassava varieties (TMS 30572, TME 419, TMS 98/0505, TMS 01/1371, and TMS 98/0002) at the seedling and clonal evaluation stages. Results At both trial stages, the effects of ID were severe on average performance of fresh root yield and fresh foliage yield; moderate on harvest index, dry matter content, vigor, and tolerance to cassava mosaic disease, cassava bacterial blight, and cassava anthracnose diseases; and less severe on plant height. Further examination of S 1 families using molecular markers showed varying levels of heterozygosity at several loci across the genome. In addition, the degree of heterozygosity and ID varied by the S 1 family. The TMS 01/1371 family showed the lowest degree of heterozygosity and ID on the average performance of different agronomic attributes, indicating that inbreeding may be strategically explored in this family to increase genetic gain and identify useful recessive traits. Lastly, the observed depression from inbreeding was higher in seedling evaluation than in clonal evaluation trials for fresh root yield, fresh foliage yield, harvest index, and dry matter content. Conclusion S 1 individuals showing relatively low heterozygosity based on SNP data were selected as parents to advance genetic gain in cassava. Generally, reduced heterozygosity was prominent in traits with severe ID impacts on average phenotypic performance. Our results highlight the relative importance of exploring non-additive genetic effects and transgressive segregations for favorable allele combinations in cassava improvement.

Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.

Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.

Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients (F) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different F and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on F based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator. [ABSTRACT FROM AUTHOR]

This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity. We also generated inbreeding coefficients based on the generational inbreeding for recent and old pedigree inbreeding, for different run-of-homozygosity length classes, and for recent and old homozygous-by-descent segment-based inbreeding. Estimates on the liability scale revealed significant evidence of inbreeding depression for reproductive-disease traits, with an increase in total pedigree and genomic inbreeding showing a notable effect for recent inbreeding. However, we found inconsistent evidence for inbreeding depression for mastitis or any metabolic diseases. Notably, in Holsteins, the probability of developing displaced abomasum decreased with inbreeding, particularly for older inbreeding. Estimates of disease probability for cows with low, average, and high inbreeding levels did not significantly differ across any inbreeding coefficient and trait combination, indicating that although inbreeding may affect disease incidence, it likely plays a smaller role compared with management and environmental factors. [ABSTRACT FROM AUTHOR]

Conservation is prioritized based on accepted taxa. As a consequence, a conservation incentive exists to emphasize inter‐population differences to define taxa, potentially leading to taxonomic inflation. But stressing the uniqueness of threatened populations has the side effect of hindering conservation actions that promote inter‐population gene flow, such as genetic rescue. These actions may be of critical importance for severely inbred populations involved in extinction vortices, for which an inflated taxonomy can become a conservation trap. Here, we exemplify this scenario with the western capercaillie (Tetrao urogallus, Phasianidae) population in the Cantabrian Mountains, described and legally listed as a subspecies not supported by recent molecular data. The Cantabrian capercaillie population is Critically Endangered after a long‐lasting decline and a recent demographic collapse. It shows clear signs of inbreeding depression, including striking clutch size decreases as well as reduced hatchability and chick survival. This critical situation could be alleviated through a genetic rescue, but this possibility is hindered by inertias rooted in the putative uniqueness of the Cantabrian capercaillie. It had been previously argued that poor taxonomy could hamper conservation, through the oblivion of populations deserving, but not having, a taxonomic status. We show that taxonomic inflation can also become an obstacle for effective conservation. [ABSTRACT FROM AUTHOR]