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Segregation distorters (SDs) are genetic elements that distort the Mendelian segregation ratio to favor their own transmission and are able to spread even when they incur fitness costs on organisms carrying them. Depending on the biology of the host organisms and the genetic architecture of the SDs, the population dynamics of SDs can be highly variable. Inbreeding is considered an effective mechanism for inhibiting the spread of SDs in populations, and can evolve as a defense mechanism against SDs in some systems. However, we show that inbreeding in the form of selfing in fact promotes the spread of SDs acting as pollen killers in a toxin-antidote system in hermaphroditic plants by two mechanisms: (i) By reducing the effective recombination rate between killer and antidote loci in the two-locus system and (ii) by increasing the proportion of SD alleles in individual flowers, rather than in the general gene-pool. We also show that in rice (Oryza sativa L.), a typical hermaphroditic plant, all molecularly characterized SDs associated with pollen killing were involved in population hybridization and have introgressed across different species. Paradoxically, these loci, which are associated with hybrid incompatibility and can be thought of as Bateson-Dobzhansky-Muller incompatibility loci are expected to reduce gene-flow between species, in fact cross species boundaries more frequently than random loci, and may act as important drivers of introgression.

Cancer is a leading cause of death in domestic dogs. Deaths due to cancer vary widely among breeds, providing an opportunity for testing the multi-stage model of carcinogenesis. This model underpins evolutionary and basic studies of cancer suppression and predicts a linear increase in cancer with breed size, an expectation complicated by bigger breeds having a shorter lifespan (decreasing risk). Using three independent datasets, the weight and lifespan of breeds provided a good fit of lifetime cancer mortality to the multi-stage model, the fit suggesting many canine cancers are initiated by four driver mutations. Of 85 breeds in more than one dataset, only flat-coated retriever showed significantly elevated cancer mortality, with Scottish terrier, Bernese mountain dog and bullmastiff also showing notable risk (greater than 50% over expected). Analysis of breed clades suggested terriers experience elevated cancer mortality. There was no evidence that the lower mass-specific metabolic rate of larger breeds reduced cancer risk. Residuals indicated increased breed inbreeding shortened expected lifespan, but had no overall effect on cancer mortality. The results provide a baseline for identifying increased breed risk for specific cancers and demonstrate that, unless selection promotes increased cancer suppression, the evolution of larger longer-lived animals leads to a predictable increased cancer risk.

ABSTRACT In recent decades, the integration of horses (Equus ferus) in European rewilding initiatives has gained widespread popularity due to their potential for regulating vegetation and restoring natural ecosystems. However, employing horses in conservation efforts presents important challenges, which we here explore and discuss. These challenges encompass the lack of consensus on key terms inherent to conservation and rewilding, the entrenched culture and strong emotions associated with horses, low genetic diversity and high susceptibility to hereditary diseases in animals under human selection, as well as insufficient consideration for the social behaviour of horses in wild‐living populations. In addition, management of wild‐living horses involves intricate welfare, ethics and legislative dimensions. Anthropocentric population‐control initiatives may be detrimental to horse group structures since they tend to prioritise individual welfare over the health of populations and ecosystems. To overcome these challenges, we provide comprehensive recommendations. These involve a systematic acquisition of genetic information, a focus on genetic diversity rather than breed purity and minimal veterinary intervention in wild‐living populations. Further, we advise allowing for natural top‐down and bottom‐up control – or, if impossible, simulating this by culling or non‐lethal removal of horses – instead of using fertility control for population management. We advocate for intensified collaboration between conservation biologists and practitioners and enhanced communication with the general public. Decision‐making should be informed by a thorough understanding of the genetic makeup, common health issues and dynamics, and social behaviour in wild‐living horse populations. Such a holistic approach is essential to reconcile human emotions associated with horses with the implementation of conservation practices that are not only effective but also sustainable for the long‐term viability of functional, biodiverse ecosystems, while rehabilitating the horse as a widespread wild‐living species in Europe. [ABSTRACT FROM AUTHOR]

Ecological and evolutionary changes are likely to occur rapidly when outcrossing populations experience pollinator loss. However, the number and identify of plant traits that will respond to this form of selection, as well as the overall predictability of evolutionary responses, remain unclear. We experimentally evolved 20 large replicate populations of Mimulus guttatus for 10 generations under three treatments: pure outcrossing, mixed mating (10% outcrossing) and pure selfing. These populations were founded from the same genetically diverse and outcrossing natural population. After 10 generations, all measured traits evolved with flower size, phenology, and reproductive traits diverging consistently among mating system treatments. Autogamy increased dramatically in the selfing treatment, but the magnitude of adaptation only becomes clear once inbreeding depression is factored out. Selfing treatment plants evolved reduced stigma-anther separation, and also exhibited declines in flower size and per-flower reproductive capacity. Flower size also declined in selfing populations but this was drivenmainly by inbreeding depression and cannot be attributed to adaptation towards the selfing syndrome. Generally, the mixed mating populations evolved trait values intermediate to the fully selfing and outcrossing populations. Overall, our experimental treatments reiterated differences that have been documented in interspecific comparisons between selfing and outcrossing species pairs. Given that such contrasts involve species separated by thousands or even millions of generations, it is noteworthy that large evolutionary responses were obtained from genetic variation segregating within a single natural population. [ABSTRACT FROM AUTHOR]

Commercial livestock producers need to prioritize genetic progress for health and efficiency traits to address productivity, welfare, and environmental concerns but face challenges due to limited pedigree information in extensive multi‐sire breeding scenarios. Utilizing pooled DNA for genotyping and integrating seminal microbiome information into genomic models could enhance predictions of male fertility traits, thus addressing complexities in reproductive performance and inbreeding effects. Using the Angus Australia database comprising genotypes and pedigree data for 78,555 animals, we simulated percentage of normal sperm (PNS) and prolificacy of sires, resulting in 713 sires and 27,557 progeny in the final dataset. Publicly available microbiome data from 45 bulls was used to simulate data for the 713 sires. By incorporating both genomic and microbiome information our models were able to explain a larger proportion of phenotypic variation in both PNS (0.94) and prolificacy (0.56) compared to models using a single data source (e.g., 0.36 and 0.41, respectively, using only genomic information). Additionally, models containing both genomic and microbiome data revealed larger phenotypic differences between animals in the top and bottom quartile of predictions, indicating potential for improved productivity and sustainability in livestock farming systems. Inbreeding depression was observed to affect fertility traits, which makes the incorporation of microbiome information on the prediction of fertility traits even more actionable. Crucially, our inferences demonstrate the potential of the semen microbiome to contribute to the improvement of fertility traits in cattle and pave the way for the development of targeted microbiome interventions to improve reproductive performance in livestock. [ABSTRACT FROM AUTHOR]

The “dark honeybee” Apis mellifera mellifera, originally the dominating subspecies of the Western honeybee in Central and Northern Europe, is currently threatened by extinction in Austria and its conservation breeding program is carried out by two breeding associations in Salzburg (AMZ – Austrian Mellifera Breeders) and Tyrol (breeding association Kauns-Kaunerberg). In this study, genetic diversity (genomic inbreeding FROH, number of homozygosity segments NROH), the relationship structures and foreign gene proportions in samples from the two Mellifera breeding associations were examined in comparison to A.m.carnica samples using the high-density 70k SNP Illumina® Honey Bee Genotyping Array. The mean Carnica gene-proportion (C-line gene proportion) in the two Mellifera samples was originally 32.4 to 34.4%. By excluding hybridized queens, this gene share was reduced to an average of 12.8–17.7%. In terms of genomic inbreeding, the Austrian Mellifera samples exhibited a mean FROH of 4.20% with maximum values of up to 17.2%. The results of this study clearly illustrated the problems conservation breeding programs in small populations are exposed to. We further demonstrated that the simultaneous consideration of multiple genetic descriptors such as FROH, NROH, ADMIXTURE and the kinship network NETVIEW is effective and practically usable in monitoring breeding programs, which can further be communicated in a way that is understandable to the practical breeders. [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]

Volunteer‐based roadkill monitoring schemes, including road carcass sampling, can represent considerable advances with respect to classical methods employed in conservation biology. We studied the genetic diversity, structure, and dynamics of the European polecat (Mustela putorius) across the Iberian Peninsula. We used samples of road carcasses collected by volunteers because this carnivore is an elusive species otherwise difficult to monitor with standard field protocols. We gathered 238 samples obtained from 2004 to 2022 from 13 different areas (8–31 samples/area). Using microsatellite loci, we identified 4 genetic units with gene flow among 3 of them in the Iberian Peninsula. The genetic variability was steadily low in 1 of the areas (Girona) for all the parameters evaluated. This area is also genetically isolated from the other studied areas. The inbreeding coefficient was significant in the north‐ and south‐Iberia units, and we did not detect a bottleneck signature in any of the 4 genetic units. Future conservation actions should consider the genetic dissimilarity among detected units and elucidate the ecological factors that have led to the observed genetic patterns. [ABSTRACT FROM AUTHOR]

Binturong (Arctictis binturong) is a threatened carnivore that inhabits the forests of South and Southeast Asia. Despite its wide range, binturong is relatively scarce across its habitat distribution and is currently under the threat of poaching and illegal trade. Captive breeding has unfortunately been conducted rather haphazardly with a lack of origin record maintained, implicating potential risks to the management such as inbreeding or genetic swamping. This study thus aims to characterise the phylogenetic relationship of Indonesian binturong within the context of Southeast Asian binturong and further probe the distinctness of lineages originating from Java, Sumatra, Indonesian Borneo, and Bangka using Cytochrome B (CytB) and Cytochrome C Oxidase Subunit 1 (CO1). Genetic distance, phylogram topology, and haplotype analysis of both encoding genes further corroborate the distinctness of Java, Borneo, and Bangka binturong from other binturong from Indochinese regions such as India, Laos, and Myanmar. Search for prospective single nucleotide polymorphism markers to discriminate island lineages consistently found that each Java, Bangka, and Bornean binturong be distinct from each other and other lineages, especially when assessed using haplotype-based clustering. Assigning binturong originated from Sumatra is nonetheless more complicated, suggesting the possibility. Our findings substantiated the much-needed systematic research of Southeast Asian binturong as ex-situ insurance population management grows in Indonesia and other parts of the world to protect the diversity of binturong lineages and their corresponding unique evolutionary history. [ABSTRACT FROM AUTHOR]

Invasive species often undergo demographic bottlenecks that cause a decrease in genetic diversity and associated reductions in population fitness. Despite this, they manage to thrive in novel environments. Investigating the effects of inbreeding and genetic bottlenecks on population fitness for invasive species is, therefore, key to understanding how they may survive in new environments. We used the blowfly Calliphora vicina (Sciences, Mathématiques et Physique, 1830, 2, 1), which is native to Europe and was introduced to Australia and New Zealand, to examine the effects of genetic diversity on population fitness. We first collected 59 samples from 15 populations across New Zealand and one in Australia, and used 20,501 biallelic SNPs to investigate population genomic diversity, structure and admixture. We then explored the impacts of repeated experimental bottlenecks on population fitness by creating inbred and outbred lines of C. vicina and measuring a variety of fitness traits. In wild‐caught samples, we found low overall genetic diversity, signals of genetic admixture and limited (<3%) genetic differentiation between North and South Island populations, with genetic links between the South Island and Australia. Following experimental bottlenecks, we found significant reductions in fitness for inbred lines. However, fitness effects were not felt equally across all phenotypic traits. Moreover, they were not enough to cause population collapse in any experimental line, suggesting that C. vicina (when under relaxed selection, as in laboratory settings) may be able to compensate for population bottlenecks even when highly inbred. Our results demonstrate the value of a tractable experimental system for investigating processes that may facilitate or hamper biological invasion. [ABSTRACT FROM AUTHOR]

Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise F ST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct. [ABSTRACT FROM AUTHOR]

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village‐based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011–0.043) and negligible inbreeding coefficients (FIS: −0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92–6.85 Mb, with short ROH segments (1–5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20–40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low‐inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features. [ABSTRACT FROM AUTHOR]

Background: Mating control is a crucial aspect of honeybee breeding. Instrumental insemination of queens gives the breeder maximum control over the genetic origin of the involved drones. However, in addition to the drones' descent, the breeder's control also extends over the number of drones to use for inseminations. Thus far, this aspect has largely been ignored in attempts to optimize honeybee breeding schemes. The literature provides some comparisons between single drone inseminations (SDI) and multi drone inseminations (MDI) but it is unclear whether the number of drones used in MDI is a relevant parameter for the optimization of honeybee breeding programs. Methods: By computer simulations, we investigated the effect of the number of drones per inseminated queen in breeding programs that relied on best linear unbiased prediction (BLUP) breeding values. We covered a range of 1 to 50 drones per queen and observed the developments of genetic gain and inbreeding over a period of 20 years. Hereby, we focused on insemination schemes that take the drones for one queen from a single colony. Results: SDI strategies led to 5.46% to 14.19% higher genetic gain than MDI at the cost of 6.1% to 30.2% higher inbreeding rates. The number of drones used in MDI settings had only a negligible impact on the results. There was a slight tendency that more drones lead to lower genetic gain and lower inbreeding rates but whenever more than five drones were used for inseminations, no significant differences could be observed. Conclusion: The opportunities to optimize breeding schemes via the number of drones used in inseminations are very limited. SDI can be a viable strategy in situations where breeders are interested in genetically homogeneous offspring or precise pedigree information. However, such strategies have to account for the fact that the semen from a single drone is insufficient to fill a queen's spermatheca, whence SDI queens will not build full-strength colonies. When deciding for MDI, breeders should focus on collecting enough semen for a succesful insemination, regardless of how many drones they need for this purpose. [ABSTRACT FROM AUTHOR]

Current rates of habitat degradation and climate change are causing unprecedented declines in global biodiversity. Studies on vertebrates highlight how conservation genomics can be effective in identifying and managing threatened populations, but it is unclear how vertebrate‐derived metrics of genomic erosion translate to invertebrates, with their markedly different population sizes and life histories. The Black‐veined White butterfly (Aporia crataegi) was extirpated from Britain in the 1920s. Here, we sequenced historical DNA from 17 specimens collected between 1854 and 1924 to reconstruct demography and compare levels of genomic erosion between extirpated British and extant European mainland populations. We contrast these results using modern samples of the Common Blue butterfly (Polyommatus icarus); a species with relatively stable demographic trends in Great Britain. We provide evidence for bottlenecks in both these species around the period of post‐glacial colonization of the British Isles. Our results reveal different demographic histories and Ne for both species, consistent with their fates in Britain, likely driven by differences in life history, ecology and genome size. Despite a difference, by an order of magnitude, in historical effective population sizes (Ne), reduction in genome‐wide heterozygosity in A. crataegi was comparable to that in P. icarus. Symptomatic of A. crataegi's disappearance were marked increases in runs‐of‐homozygosity (RoH), potentially indicative of recent inbreeding, and accumulation of putatively mildly and weakly deleterious variants. Our results provide a rare glimpse of genomic erosion in a regionally extinct insect and support the potential use of genomic erosion metrics in identifying invertebrate populations or species in decline. [ABSTRACT FROM AUTHOR]

Captive‐breeding programs are increasingly implemented to curb population declines but can have unintended negative effects on genetic diversity and phenotypes. Through an analysis of ~10 years of genetic monitoring, pedigree information, and phenotypic data, we evaluated a captive‐breeding program that uses adaptive management to reduce inbreeding and improve captive broodstock performance. A captive‐breeding program was established in 2012 to reintroduce spring‐run Chinook salmon to the southern edge of their range in California's San Joaquin River (SJR), using fish produced each year at the nearby Feather River Hatchery (FRH). We found that the SJR program adequately captured the genetic diversity of the FRH source population and that mate pairings guided by genetic relatedness reduced inbreeding. However, the SJR broodstock reared in captivity had smaller body size at maturity in comparison to the FRH source broodstock which matures at sea, but this effect disappeared when SJR juveniles were released from captivity to mature at sea. Phenotypic traits of SJR female parents also influenced reproductive performance; older mothers and those with smaller eggs had offspring with lower survival. These findings demonstrate that adaptive genetic monitoring and pedigree information can be powerful tools for reducing risks of captive breeding and evaluating program effectiveness. [ABSTRACT FROM AUTHOR]

Since European settlement of Australia, substantial areas of subtropical rainforest have been cleared. More recently, effort is being made to restore areas of this ecological community. The financial investment and increasing reliance on ecological restoration in biodiversity conservation justifies a need for better understanding of how to improve success at the genetic level. This research measures genetic diversity (allelic richness [Rs], expected heterozygosity [He], and inbreeding using Wright's coefficient [FIS]) for expected neutral DNA markers in three Australian subtropical rainforest trees—White booyong (Argyrodendron trifoliolatum), Watkin's fig (Ficus watkinsiana), and Native tamarind (Diploglottis australis). Wild and restored populations of these species were compared in two neighboring regions in Northeast New South Wales (the Tweed Caldera and the Big Scrub). There were no statistically significant differences in Rs or He between wild and restored populations for any of the target species. Inbreeding was significantly higher in one of the restored versus wild population comparisons: F. watkinsiana in the Tweed (restored F = 0.20; wild F = −0.02; p = 0.01). The comparable levels of genetic diversity observed in restored and wild populations targeted in this study are likely due to informed practitioner perspectives and practices, staged plantings over several years, and high genetic diversity and low genetic differentiation within source populations. [ABSTRACT FROM AUTHOR]

Premise Methods Results Conclusions The impact of inbreeding on biological processes is well documented in individuals with severe inbreeding depression. However, the biological processes influencing the adaptive growth of normal selfed individuals are unknown. Here, we aimed to investigate how inbreeding affects gene expression for adaptive growth of normal selfed seedlings from a self‐fertilizing parent in Chinese fir (Cunninghamia lanceolata).Using RNA‐seq data from above‐ and underground tissues of abnormal and normal selfed seedlings, we analyzed GO biological processes network. We also sequenced small RNAs in the aboveground tissues and measured the copy number variations (CNV) of the hub genes.Phenotypic fitness analysis revealed that the normal seedlings were better adapted than their abnormal counterparts. Upregulated differentially expressed genes (DEGs) were associated with development processes, and downregulated DEGs were mainly enriched in fundamental metabolism and stress response. Results of mRNA‐miRNA parallel sequencing revealed that upregulated target genes were predominantly associated with development, highlighting their crucial role in phosphorylation in signal transduction networks. We also discovered a moderate correlation (0.1328 < R2 < 0.6257) between CNV and gene expression levels for three hub genes (TMKL1, GT2, and RHY1A).We uncovered the key biological processes underpinning the growth of normal selfed seedlings and established the relationship between CNV and the expression levels of hub genes in selfed seedlings. Understanding the candidate genes involved in the growth of selfed seedlings will help us comprehend the genetic mechanisms behind inbreeding depression in the evolutionary biology of plants. [ABSTRACT FROM AUTHOR]

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic diversity and population structure of U.S. Polypay sheep using both pedigree- and genomic-based methods. Pedigree data from 193 Polypay flocks participating in the National Sheep Improvement Program (NSIP) were combined with pedigree records from USSES (n = 162,997), tracing back to the breed's origin. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip containing 51,867 single nucleotide polymorphisms (SNPs). Four subgroups were used for the pedigree-based analyses: 1) the current generation of animals born in 2020--2022 (n = 20,701), 2) the current generation with a minimum of four generations of known ancestors (n = 12,685), 3) only genotyped animals (n = 1,856), and 4) the sires of the current generation (n = 509). Pedigree-based inbreeding for the full population was 2.2%, with a rate of inbreeding of 0.22% per generation. Pedigree-based inbreeding, Wright's inbreeding, and genomic inbreeding based on runs of homozygosity were 2.9%, 1.3%, and 5.1%, respectively, for the genotyped population. The effective population size ranged from 41 to 249 for the pedigree-based methods and 118 for the genomic-based estimate. Expected and observed heterozygosity levels were 0.409 and 0.403, respectively. Population substructure was evident based on the fixation index (FST), principal component analysis, and model-based population structure. These analyses provided evidence of differentiation from the foundation flock (USSES). Overall, the Polypay breed exhibited substantial genetic diversity and the presence of a population substructure that provides a basis for the implementation of genomic selection in the breed. [ABSTRACT FROM AUTHOR]

Inbreeding, the mating of individuals that are related through common ancestry, is of central importance in evolutionary and conservation biology due to its impacts on individual fitness and population dynamics. However, while advanced genomic approaches have revolutionised the study of inbreeding in animals, genomic studies of inbreeding are rare in plants and lacking in fungi. We investigated global patterns of inbreeding in the prized edible porcini mushroom Boletus edulis using 225 whole genomes from seven lineages distributed across the northern hemisphere. Genomic inbreeding was quantified using runs of homozygosity (ROHs). We found appreciable variation both among and within lineages, with some individuals having over 20% of their genomes in ROHs. Much of this variation could be explained by a combination of elevation and latitude, and to a lesser extent by predicted habitat suitability during the last glacial maximum. In line with this, the majority of ROHs were short, reflecting ancient common ancestry dating back approximately 200–1700 generations ago, while longer ROHs indicative of recent common ancestry (less than approximately 50 generations ago) were infrequent. Our study reveals the inbreeding legacy of major climatic events in a widely distributed forest mutualist, aligning with prevailing theories and empirical studies of the impacts of historical glaciation events on the dominant forest tree species of the northern hemisphere. [ABSTRACT FROM AUTHOR]

Premise Methods Results Conclusions In hermaphroditic plants, the evolution of self‐fertilization is driven by two major forces; the cost of outcrossing or Fisher's automatic advantage of selfing and inbreeding depression. Seminal theoretical works have established that an inbreeding depression threshold of 0.5 governs the evolution. Below that threshold, selfing evolves, above that, outcrossing evolves. Does this threshold apply to cleistogamous plants?I developed a model using a Lloydian approach to analyze the evolution of cleistogamy.I showed that the inbreeding depression threshold does not apply in cleistogamous species, and that because cleistogamous (closed) flowers do not export pollen, Fisher's advantage of selfing is totally cancelled.In line with model predictions, I discuss the fact that cleistogamous species often exhibit low inbreeding depression in empirical studies. [ABSTRACT FROM AUTHOR]

Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically demographic history and environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analyzed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found a strong negative association between genetic diversity and extinction when considering only heterozygosity in models. However, this association disappeared when accounting for ecological covariates, suggesting a confounding between demography and genetics and a more complex role for heterozygosity in extinction risk. Modeling interactions between heterozygosity and demographic variables revealed that associations between extinction and heterozygosity were context-dependent. For example, extinction declined with increasing heterozygosity in large, but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in small populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting >25% increase in extinction beyond ecological factors in certain contexts. These results highlight that inferences about the importance of genetic diversity for population viability should not rely on genomic data alone but require investments in obtaining demographic and environmental data from natural populations. [ABSTRACT FROM AUTHOR]

The European Roller (Coracias garrulus), a long-distance migratory bird, faced a considerable decline in breeding pairs throughout Europe at the end of the 20th century. Due to conservation efforts and the installation of nesting boxes, the population of the European Roller in Serbia has made a remarkable recovery. Here, we used the variability of nucleotide sequences of the mitochondrial DNA (mtDNA) control region and 10 microsatellite loci to assess the genetic diversity and structuring, phylogeographic patterns and demographic history of this species using 224 individuals from Serbia. Our results showed moderate level of genetic diversity (HO = 0.392) and a slightly elevated level of inbreeding and homozygosity (FIS = 0.393). Genetic structuring based on microsatellite data indicated three genetic clusters, but without a clear spatial pattern. High haplotype diversity (Hd = 0.987) of the mtDNA control region sequences was detected, and neutrality tests indicated a recent demographic expansion. The phylogeographic analysis, which also included previously published sequences of the mtDNA control region, supported the subdivision into two distinct European and Asian haplogroups (ΦST = 0.712). However, the results of our study showed that a larger number of haplotypes sampled in Serbia are clustered in the Asian haplogroup as compared to previous studies, indicating a historically continuous distribution of this species and possibly a wider distribution of the subspecies Coracias garrulus semenovwi. Our results suggest that the European Roller population in Serbia is genetically stable, with no evidence of recent bottlenecks, and emphasize the importance of artificial nest boxes for promoting and maintaining population dynamics of European Rollers. [ABSTRACT FROM AUTHOR]

Background: The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. Results: HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20). Conclusions: Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations. [ABSTRACT FROM AUTHOR]

Summary It is generally accepted that kelp populations have a metapopulation structure. Most zoospores settle near to their parent individual, and infrequent but long‐distance dispersal of zoospores contributes to gene flow between local populations. Population genetic analysis of single nucleotide polymorphism genotyping by MIG‐seq (i.e. multiplexed inter‐simple sequence repeats genotyping by sequencing) was performed on the dominant kelp, Eisenia bicyclis, in two areas: Kitsunezaki (a sheltered area) and Shimoda (an exposed site). Regional scale analysis of genetic structure was conducted at six sites in Kitsunezaki and three sites in Shimoda. When viewed on a regional scale based on the inbreeding coefficient within the local population, the inbreeding ratio was higher in Shimoda than in Kitsunezaki, probably as a result of the limited vertical zonal distribution in the exposed environment. Vertically wide distribution in the sheltered environment apparently enabled frequent crossing among individuals in Kitsunezaki. By contrast, when viewed on a local scale based on the pairwise kinship coefficient (FST) between populations, gene flow among local populations in Shimoda occurred over a wide area, but was limited in Kitsunezaki. In Shimoda, genetic exchange between local populations, even if inbreeding is locally active, is likely to support metapopulation maintenance and rapid recovery of local populations. In Kitsunezaki, however, genetic exchange among local populations is limited within few 100 m, and the metapopulation structure will decline in the long term because of inbreeding depression. Local dispersal distance of zoospores was investigated based on parent–offspring analysis in the Kitsunezaki population, which revealed that zoospores mainly settled within 5 m of their parent. However, some zoospores traveled over 27 m within the 4 × 30 m study area. The present study shows the importance of examination at different spatial scales when investigating zoospore dispersal of laminarialean kelps. [ABSTRACT FROM AUTHOR]

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]

Background and Aim: Runs of homozygosity (ROH) is a biocomputational technique for identifying homozygous regions in the genomics of livestock. This study aimed to determine the ROH in Sumba Ongole (SO) bulls (n = 48) using the BovineSNP50K BeadChip. Materials and Methods: GenomeStudio 2.0 software was used to generate the BovineSNP50K BeadChip output. The ROH and ROH-based inbreeding coefficients (FROH) were determined using the detect RUNS R v4.1.0 package. Using the following filtering criteria, PLINK v1.90 software was used to perform genotype quality control: (1) Individuals and single-nucleotide polymorphism (SNPs) had call rates >0.95; (2) more than 0.05 was the minor allele frequency; (3) the list contained only SNPs linked to autosomes; and (4) SNPs that strongly deviated (p < 1e-6) from Hardy--Weinberg equilibrium were removed. Subsequently, 25,252 autosomal SNP markers were included in the ROH and FROH analyses. Results: In general, the number and length of ROH segments in pool animals were 149.77 ± 16.02 Mb and 486.13 ± 156.11 Mb, respectively. Furthermore, the ROH segments in the animals under study can be discriminated into two classes of 1-4 Mb (83.33%) and 4-8 Mb (16.67%). Subsequently, Bos taurus autosomes (BTA) 1, BTA6, and BTA14 had significant homozygous segments comprising 13 genes. Despite this, the average FROH in pool animals was 0.20 ± 0.06. Conclusion: These findings indicate that a recent inbreeding event in SO cattle occurred many generations ago. Furthermore, the candidate genes identified from the ROH analysis indicate phenotypic attributes associated with environmental adaptation and economic traits. [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]

Objective: The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens. Methods: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures. Results: A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (FROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified. Conclusion: This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions. [ABSTRACT FROM AUTHOR]

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self‐compatible hermaphrodites, the mating system (e.g., self‐fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (Ne). This can potentially accelerate genetic drift, particularly in small populations where self‐fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (Ne) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within‐population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and Ne estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within‐population genetic diversity. [ABSTRACT FROM AUTHOR]

Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage‐grouse (Centrocercus urophasianus) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome‐wide adaptive divergence among source and recipient populations. Observed genetic diversity (HO = 0.65) was higher in the recipient population than predicted had no augmentation occurred (HO = 0.58) but less than what was predicted by our model (HO = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index (FST) (143 genes) or local environmental variables (97 and 157 genes for each genotype–environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation. [ABSTRACT FROM AUTHOR]

Simple Summary: It is well known that highly inbred dogs are more prone to diseases than less inbred or outbred dogs. This is because inbreeding increases the number of bad mutations present in both paternal and maternal chromosomes (recessive mutations) of the dogs. Using the genome data from 392 dogs belonging to 83 breeds, we investigated the association between the abundance of recessive bad mutations and dog health. The frequency of visits to veterinary clinics for non-routine care was used as the measure of dog health. Our results revealed a highly significant positive relationship between the number of recessive harmful mutations and the degree of dog health. The dog breeds that required more veterinary care had two times higher harmful mutations than those that required less care. The results of this study could be useful for understanding the disease burden on breed dogs and as a guide for dog breeding programs. It is well known that highly inbred dogs are more prone to diseases than less inbred or outbred dogs. This is because inbreeding increases the load of recessive deleterious variants. Using the genomes of 392 dogs belonging to 83 breeds, we investigated the association between the abundance of homozygous deleterious variants and dog health. We used the number of non-routine veterinary care events for each breed to assess the level of morbidity. Our results revealed a highly significant positive relationship between the number of homozygous deleterious variants located within the runs of homozygosity (RoH) tracts of the breeds and the level of morbidity. The dog breeds with low morbidity had a mean of 87 deleterious SNVs within the RoH, but those with very high morbidity had 187 SNVs. A highly significant correlation was also observed for the loss-of-function (LoF) SNVs within RoH tracts. The dog breeds that required more veterinary care had 2.3 times more homozygous LoF SNVs than those that required less veterinary care (112 vs. 50). The results of this study could be useful for understanding the disease burden on breed dogs and as a guide for dog breeding programs. [ABSTRACT FROM AUTHOR]

The population of the Northwest Pre-Caspian saiga (Saiga tatarica tatarica) numbered about 800 000 individuals in the middle of the last century. There was a dramatic decline at the end of the 20th century, and by 2015 the numbers of this saiga population reached about five thousand animals. The results of microsatellite loci and of mtDNA control region analysis obtained for museum saiga samples from the Northwest Pre-Caspian population, collected at the peak of their numbers in the 1950s, are presented. We compared these data with our previous results for the samples collected during the population depression in the years 1999–2016. There were no noticeable differences in the mtDNA control region diversity between the museum and modern saiga samples. The most vivid genetic consequence of the severe decline in population numbers was a significant increase of the inbreeding coefficient (Fis) calculated from the microsatellite loci. [ABSTRACT FROM AUTHOR]

The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. In recent years, genomic selection (GS) has accelerated genetic gain in dairy cattle breeds worldwide. Despite the evident genetic progress, several dairy populations have also encountered challenges such as heightened inbreeding rates and reduced effective population sizes. The challenge has been to find a balance between achieving substantial genetic gain while managing genetic diversity within the population, thereby mitigating the negative effects of inbreeding depression. This study aims to elucidate the impact of GS on pedigree and genomic rates of inbreeding (ΔF) and coancestry (ΔC) in Nordic Jersey (NJ) and Holstein (NH) cattle populations. Furthermore, key genetic metrics, including the generation interval (L), effective population size (Ne), and future effective population size (FNe) were assessed between 2 time periods, before and after GS, and across distinct animal cohorts in both breeds: females, bulls, and approved semen-producing bulls (AI-sires). Analysis of ΔF and ΔC revealed distinct trends across the studied periods and animal groups. Notably, there was a consistent increase in yearly ΔF for most animal groups in both breeds. An exception was observed in NH AI-sires, which demonstrated a slight decrease in yearly ΔF. Moreover, NJ displayed minimal changes in yearly ΔC between the periods, whereas NH exhibited elevated ΔC values across all animal groups. Particularly striking was the substantial increase in yearly ΔC within the NH female population, surging from 0.02% to 0.39% between the periods. Implementation of GS resulted in a reduction of the generation interval across all animal cohorts in both NJ and NH breeds. However, the extent of reduction was more pronounced in males compared with females. This reduction in generation interval influenced generational changes in ΔF and ΔC. Bulls and AI-sires of both breeds exhibited reduced generational ΔF between periods, in contrast to females that demonstrated an opposing pattern. Between the periods, NJ maintained a relatively stable Ne (29.4 before and 30.3 after GS), whereas NH experienced a notable decline from 54.3 to 42.8. Female groups in both breeds displayed a negative Ne trend, whereas males demonstrated either neutral or positive Ne developments. Regarding FNe, NJ exhibited positive FNe development with an increase from 40.7 to 57.2. The opposite was observed in NH, where FNe decreased from 198.8 to 42.7. In summary, it was evident that the genomic methods could detect differences between the populations and changes in ΔF and ΔC more efficiently than pedigree methods. Implementation of GS yielded positive outcomes within the NJ population regarding the rate of coancestry but the opposite was observed with NH. Moreover, analysis of ΔC data hints at the potential to decrease future ΔF through informed mating strategies. Conversely, NH faces more pressing concerns, even though ΔF remains comparatively modest in contrast to what has been observed in other Holstein populations. These findings underscore the necessity of genomic control of inbreeding and coancestry with strategic changes in the Nordic breeding schemes for dairy to ensure long-term sustainability in the forthcoming years. [ABSTRACT FROM AUTHOR]

The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. The objective of this study was to assess the effect of using or not using the genotypes of the parents of a cow for imputing SNPs on the estimation of genomic inbreeding coefficients of cows. Imputation (i.e., genotyped plus imputed) genotypes from 68,127 Italian Holstein dairy cows registered in the Italian National Association of Holstein, Brown, and Jersey Breeders were analyzed. Cows were genotyped with the high-density (HD) Illumina Infinium BovineHD BeadChip and GeneSeek Genomic Profiler HD-150K, and the medium-density (MD) GeneSeek Genomic Profiler 3, GeneSeek Genomic Profiler 4, GeneSeek MD, and the Labogena MD. To assess differences among estimators, genomic inbreeding coefficients were estimated with 4 PLINK v1.9 estimators (F, F hat1 ,F hat2 , andF hat3), 2 genomic relationship matrix- (grm) based estimators (F grm and F grm2 , with the latter including also pedigree information), and one estimator of runs of homozygosity (ROH; F ROH). Assuming that the correct genomic inbreeding coefficients should be those estimated from genotyped SNPs, a comparison of the genomic inbreeding coefficients estimated either with the genotyped SNPs or the SNPs after imputation was made. Information on the presence or absence of genotypic information from sire, dam, and maternal grandsire during the imputation was investigated. Genomic inbreeding coefficients estimated with genotyped SNPs or SNPs after imputation were consistent for F, F hat3 , F grm2 , and F ROH , when at least one of the parents was genotyped. Biased (mainly higher) genomic inbreeding coefficients of imputation SNPs were observed in cows that were genotyped with MD SNP panels whose SNPs were poorly represented in the selected imputation SNP dataset and also did not have their parents genotyped, when compared with what would be expected based on actual genotype data. For cows genotyped with MD the estimators F hat1 , F hat2 , and F grm provided higher genomic inbreeding coefficients of imputation SNPs even with both parents and the maternal grandsire genotyped. Overall, F ROH was the most robust estimator, followed by F and F hat3. Our findings suggest that SNPs selection, parental genotyping and estimator should be considered for designing imputation strategies in dairy cattle for estimating genomic inbreeding with imputation SNPs. For computing genomic inbreeding coefficients, it is recommendable to have at least one parent genotyped and use an ROH-based estimator. [ABSTRACT FROM AUTHOR]

Human‐mediated habitat destruction has had a profound impact on increased species extinction rates and population declines worldwide. The coastal development in the United Arab Emirates (UAE) over the last two decades, serves as an example of how habitat transformation can alter the landscape of a country in just a few years. Here, we study the genomic implications of habitat transformation in the Critically Endangered Emirati Leaf‐toed Gecko (Asaccus caudivolvulus), the only endemic vertebrate of the UAE. We generate a high‐quality reference genome for this gecko, representing the first reference genome for the family Phyllodactylidae, and produce whole‐genome resequencing data for 23 specimens from 10 different species of leaf‐toed geckos. Our results show that A. caudivolvulus has consistently lower genetic diversity than any other Arabian species of Asaccus, suggesting a history of ancient population declines. However, high levels of recent inbreeding are recorded among populations in heavily developed areas, with a more than 50% increase in long runs of homozygosity within a 9‐year period. Moreover, results suggest that this species does not effectively purge deleterious mutations, hence making it more vulnerable to future stochastic threats. Overall, results show that A. caudivolvulus is in urgent need of protection, and habitat preservation must be warranted to ensure the species' survival. [ABSTRACT FROM AUTHOR]

Background: Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl. Results: In total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie. Conclusions: Our study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts. [ABSTRACT FROM AUTHOR]

Dominance refers to the effect of a heterozygous genotype relative to that of the two homozygous genotypes. The degree of dominance of mutations for fitness can have a profound impact on how deleterious and beneficial mutations change in frequency over time as well as on the patterns of linked neutral genetic variation surrounding such selected alleles. Since dominance is such a fundamental concept, it has received immense attention throughout the history of population genetics. Early work from Fisher, Wright, and Haldane focused on understanding the conceptual basis for why dominance exists. More recent work has attempted to test these theories and conceptual models by estimating dominance effects of mutations. However, estimating dominance coefficients has been notoriously challenging and has only been done in a few species in a limited number of studies. In this review, we first describe some of the early theoretical and conceptual models for understanding the mechanisms for the existence of dominance. Second, we discuss several approaches used to estimate dominance coefficients and summarize estimates of dominance coefficients. We note trends that have been observed across species, types of mutations, and functional categories of genes. By comparing estimates of dominance coefficients for different types of genes, we test several hypotheses for the existence of dominance. Lastly, we discuss how dominance influences the dynamics of beneficial and deleterious mutations in populations and how the degree of dominance of deleterious mutations influences the impact of inbreeding on fitness. [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]

Simple Summary: Genetic diversity plays a crucial role in determining the ability of populations to evolve. We investigated the genetic variation of the black-and-white snub-nosed monkey by integrating adaptive MHC genes and neutral microsatellites. We found that neutral loci exhibited high heterozygosity and a high degree of polymorphism, while MHC genes showed high heterozygosity and moderate polymorphism. Additionally, positive selection and trans-species evolution indicated that historical balancing selection might have sustained the MHC polymorphism. This study provides valuable scientific evidence and a reference for formulating or amending conservation strategies for black-and-white snub-nosed monkeys. Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species. [ABSTRACT FROM AUTHOR]

Simple Summary: Wild horses in the region around Dülmen in Westphalia, Germany, date back to the Middle Ages. These horses ranged the wooden and marsh area in small herds. The Dukes of Croÿ fenced these wild horses in 1856 in an area called Merfelder Bruch, near Dülmen, and managed this herd as a self-contained population. Stallions employed were from the Dülmen wild horse population and, in some breeding seasons, from other primitive horse populations. The Dülmen wild horse population has to cope with harsh natural conditions all year round. The Dülmen wild horse population consists of about 530 horses with around 380 mares. Each year, 2 to 3 stallions sire 50 to 60 foals. In the present study, we characterize, for the first time, the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations using a highly informative microsatellite marker set. We found a high degree of genetic diversity in the Dülmen wild horse population. Genetic distance measures, principal component analysis, and Bayesian cluster analyses clearly demarcated the Dülmen wild horse population from the other 17 horse populations studied here. In addition, data supported the hypothesis of an early genetic divergence of Dülmen wild horses. The Dülmen wild horse population appeared as an invaluable resource to study the evolution of domesticated horses. The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of −0.035. Pairwise genetic distances (FST, Nei's standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski's horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication. [ABSTRACT FROM AUTHOR]

Indicator models of sexual selection posit that females choose males on the basis of traits that reveal male genetic quality and thereby enjoy increased offspring production. Here, we report that females of the butterfly Eurema hecabe receive indirect benefits from choosing males based on their ultraviolet (UV) wing coloration, a heritable and condition-dependent trait in this species. We first used a large laboratory-bred pedigree to demonstrate a per-family association between inbreeding and male UV trait value. Females exerted choice for UV-bright males within this protocol, and the average male UV trait value increased over six consecutive generations, presumably due to such selection and despite an increasing rate of pedigree-wide inbreeding. We then experimentally imposed a standard strength of inbreeding upon lines of divergent male UV trait values. Inbreeding depressed the siring performance of low UV treatment males more severely and resulted in a marginal reduction of their UV brightness, which rebounded sharply following subsequent outcrossing. These findings are consistent with the ornament-based signaling of genetic quality as a function of underlying individual-level mutational load. [ABSTRACT FROM AUTHOR]

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources. [ABSTRACT FROM AUTHOR]

An increasing trend in ancestral and classical inbreeding coefficients as well as inbreeding depression for longevity were found in the German Brown population. In addition, the proportion of US Brown Swiss genes is steadily increasing in German Browns. Therefore, the aim of the present study was to analyze the presence and genomic localization of runs of homozygosity (ROH) in order to evaluate their associations with the proportion of US Brown Swiss genes and survival rates of cows to higher lactations. Genotype data were sampled in 2364 German Browns from 258 herds. The final data set included 49,693 autosomal SNPs. We identified on average 35.996 ± 7.498 ROH per individual with a mean length of 8.323 ± 1.181 Mb. The genomic inbreeding coefficient FROH was 0.122 ± 0.032 and it decreased to 0.074, 0.031 and 0.006, when genomic homozygous segments > 8 Mb (FROH>8), >16 Mb (FROH>16) and >32 Mb (FROH>32) were considered. New inbreeding showed the highest correlation with FROH>32, whereas ancestral inbreeding coefficients had the lowest correlations with FROH>32. The correlation between the classical inbreeding coefficient and FROH was 0.572. We found significantly lower FROH, FROH>4, FROH>8 and FIS for US Brown Swiss proportions <60% compared to >80%. Cows surviving to the 2nd, 4th, 6th, 8th, and 10th lactation had lower genomic inbreeding for FROH and up to FROH>32, which was due to a lower number of ROH and a shorter average length of ROH. The strongest ROH island and consensus ROH shared by 50% of the animals was found on BTA 6 at 85–88 Mb. The genes located in this genomic region were associated with longevity (NPFFR2 and ADAMTS3), udder health and morphology (SLC4A4, NPFFR2, GC and RASSF6), milk production, milk protein percentage, coagulation properties of milk and milking speed (CSN3). On BTA 2, a ROH island was detected only in animals with <60% US Brown Swiss genes. Genes within this region are predominantly important for dual-purpose cattle breeds including Original Browns. For cows reaching more than 9 lactations, an exclusive ROH island was identified on BTA 7 with genes assumed to be associated with longevity. The analysis indicated that genomic homozygous regions important for Original Browns are still present and also ROH containing genes affecting longevity may have been identified. The breeding of German Browns should prevent any further increase in genomic inbreeding and run a breeding program with balanced weights on production, robustness and longevity. [ABSTRACT FROM AUTHOR]

1. The Kaijiang duck is a native Chinese breed known for its excellent egg laying performance, killing-out percentage (88.57%), and disease resistance. The assessment of population genetic structure is the basis for understanding the genetics of indigenous breeds and for their protection and management. 2. In this study, whole-genome sequencing was performed on 60 Kaijiang ducks to identify genetic variations and investigate the population structure. Homozygosity (ROH) analysis was conducted to assess inbreeding levels in the population. 3. The study revealed a moderate level of inbreeding, indicated by an average inbreeding coefficient of 0.1043. This may impact the overall genetic diversity. 4. Genomic Regions of Interest identified included 168 genomic regions exhibiting high levels of autozygosity. These regions were associated with processes including muscle growth, pigmentation, neuromodulation, and growth and reproduction. 5. The significance of these pathways indicated their potential role in shaping the desirable traits of the Kaijiang duck. These findings provide insights into the genetic basis of the Kaijiang duck's desirable traits and can inform future breeding and conservation efforts. [ABSTRACT FROM AUTHOR]

Small and isolated populations are at risk of local extinction, either due to the reduction of genetic diversity or due to stochastic events. We assessed genetic diversity in populations of the red-spotted (Luscinia svecica svecica) and white-spotted bluethroat (L. s. cyanecula) subspecies from six European sites, focusing on a peripheral and declining, red-spotted population from Central Europe (Krkonoše Mountains, Czech Republic). Analysis of population structure using mitochondrial sequences (cytochrome b) and ddRAD genomic data revealed that the two subspecies form clearly defined clusters, but traces of possible admixture were found in three populations of the white-spotted bluethroat. Demographic history reconstruction indicates past population range expansion in both subspecies, while the occurrence of short (0.4 Mbp) runs of homozygosity (ROH) segments suggests possible inbreeding 50 to 200 generations ago. Interestingly, although established by a small number of individuals, the Krkonoše population show reduced genetic diversity in only one measure of summary statistics, possibly due to sustained gene flow. Correspondingly, nine highly homozygous genes were recovered within a 2.6-Mbp long ROH region on the Chr 5. Thus, we found only a small reduction of genetic diversity in a population facing extinction, contrary to the expectations for a geographically distant and small population. [ABSTRACT FROM AUTHOR]

Cultivated potatoes are incredibly diverse, ranging from diploid to pentaploid and encompass four different species. They are adapted to disparate environments and conditions and carry unique alleles for resistance to pests and pathogens. Describing how diversity is partitioned within and among these populations is essential to understanding the potato genome and effectively utilizing landraces in breeding. This task is complicated by the difficulty of making comparisons across cytotypes and extensive admixture within section petota. We genotyped 730 accessions from the US Potato genebank including wild diploids and cultivated diploids and tetraploids using Genotype-by-sequencing. This data set allowed us to interrogate population structure and diversity as well as generate core subsets which will support breeders in efficiently screening genebank material for biotic and abiotic stress resistance alleles. We found that even controlling for ploidy, tetraploid material exhibited higher observed and expected heterozygosity than diploid accessions. In particular group chilotanum material was the most heterozygous and the only taxa not to exhibit any inbreeding. This may in part be because group chilotanum has a history of introgression not just from wild species, but landraces as well. All group chilotanum, exhibits introgression from group andigenum except clones from Southern South America near its origin, where the two groups are not highly differentiated. Moving north, we do not observe evidence for the same level of admixture back into group andigenum. This suggests that extensive history of admixture is a particular characteristic of chilotanum. [ABSTRACT FROM AUTHOR]

Small island populations are vulnerable to genetic decline via demographic and environmental stochasticity. In the absence of immigration, founder effects, inbreeding and genetic drift are likely to contribute to local extinction risk. Management actions may also have a greater impact on small, closed populations. The demographic and social characteristics of a species can, however, delay the impact of threats. K'gari, a ~ 1 660 km2 island off the Australian east coast and UNESCO World Heritage Site (Fraser Island 1842–2023), supports an isolated population of approximately 70–200 dingoes that represent an ideal opportunity to explore the small island paradigm. To examine temporal and spatial patterns of genetic diversity in this population we analysed single nucleotide polymorphism (SNP) genotype data (72 454 SNPS) for 112 K'gari dingoes collected over a 25-year period (1996 to 2020). Genetic diversity was lower in K'gari dingoes than mainland dingoes at the earliest time point in our study and declined significantly following a management cull in 2001. We did not find any spatial genetic patterns on the island, suggesting high levels of genetic connectivity between socially discrete packs. This connectivity, combined with the social structure and behaviour of dingoes, may act in concert to buffer the population from the impacts of genetic drift in the short term. Nevertheless, a general decline in genetic variation via inbreeding and drift has occurred over the past 20 years which we suggest should be considered in any future management planning for the population. Monitoring patterns of genetic variation, together with a clearer understanding of the social ecology of K'gari dingoes, will aid in the development of measurable genetic targets set over ecologically meaningful timelines, and help ensure continued survival of this culturally important population. [ABSTRACT FROM AUTHOR]

Despite decades of field study, very little is known about the molecular ecology of gibbons, particularly as it relates to their ability to disperse across degraded and fragmentary landscapes. The critically endangered western black crested gibbon (Nomascus concolor) has been reduced to a small, fragmented population with about 1300 individuals. In the largest population genetic study of free‐ranging gibbons to date, we sampled 47 of these gibbons from 13 sites in China and generated 15 polymorphic autosomal microsatellite markers. We identify three population clusters of N. concolor in Yunnan centered in 1) the Wuliang and Ailao Mountains, 2) the Yongde Daxueshan Mountains, and 3) an isolated remnant near the border with Vietnam. Within the Wuliang Mountains, we identified four subclusters, three of which are bounded by high‐altitude rhododendron forest, and one that is isolated from the main population by ~2 km of degraded forest and pasture. Least‐cost path analysis and isolation by resistance modeling demonstrates that the population genetic distances among gibbons in Wuliangshan National Nature Reserve are significantly correlated with geographic paths that avoid use of high‐altitude rhododendron forest in favor of evergreen broadleaf forest. Although these gibbons have likely undergone reductions in heterozygosity from recent consanguineous mating, we suggest that their active avoidance of inbreeding on the population level maintains higher than expected levels of genetic diversity. This research provides new insights into how gibbons interact with heterogeneous environments and expands our understanding of their molecular ecology and conservation genetics. [ABSTRACT FROM AUTHOR]

Background: Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators ( , , , , and ), as well as two segment-based estimators of runs of homozygosity (ROH, ) and homozygous-by-descent (HBD, ). Functional implications were analyzed for the positional candidate genes located within the related genomic regions. Results: A total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs (), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of and , however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals. Conclusions: We successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations. [ABSTRACT FROM AUTHOR]