High Inbreeding Coefficient Research Articles

Does a coexisting congener of a mixed mating species affect the genetic structure and selfing rate via reproductive interference?

Reproductive interference is defined as an interspecific interaction that reduces fitness via mating processes. Although its ecological and evolutionary consequences have attracted much attention, how reproductive interference affects the population genetic structures of interacting species is still unclear. In flowering plants, recent studies found that self-pollination can mitigate the negative effects of reproductive interference. Selfing-biased seed production is expected to increase population-level inbreeding and the selfing rate, and limits gene flow via pollinator outcrossing among populations. We examined the population genetics of the mixed-mating annual herb Commelina communis f. ciliata, focusing on reproductive interference by the sympatric competing congener C. communis using microsatellite markers. First, we found that almost all C. c. f. ciliata populations had relatively high inbreeding coefficients. Then, comparing sympatric and allopatric populations, we found evidence that reproductive interference from a competing congener increased the inbreeding coefficient and selfing rate. Allopatric populations exhibit varied selfing rates while almost all sympatric populations exhibit extremely high selfing rates, suggesting that population selfing rates were also influenced by unexamined factors, such as pollinator limitation. Besides, our findings revealed that reproductive interference from a competing congener did not limit gene flow among populations. We present the first report on how reproductive interference affects the genetic aspects of populations. Our results suggested that the high selfing rate of C. c. f. ciliata promotes its sympatric distribution with C. communis, even in the presence of reproductive interference, although it is not clear whether reproductive interference directly causes the high selfing rate.

An evaluation of potential inbreeding depression in wild Mexican wolves

AbstractEstimates 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.

Genetic diversity in the traditional cultivars and wild ancestor of near-threatened Japanese iris (Iris ensata Thunb.)

Wild relatives of cultivars are crucial sources of genetic variation for further enhancement, yet they face potential threats due to contemporary environmental changes. Iris ensata var. spontanea, a wild progenitor of the Japanese iris cultivars (I. ensata var. ensata), is extensively cultivated in Japanese gardens, is distributed across mesic meadows and wetlands in Japan and East Asia. This species is currently threatened owing to habitat loss linked to land use alterations. We assessed genetic diversity and phylogenetic relationships in 32 wild accessions and the 14 principal Edo Group of Japanese iris cultivars, originally bred during the Edo period (1600–1868). In the phylogenetic tree, the cultivars formed a cluster with reduced inbreeding coefficients, suggesting a singular origin and interbreeding between the genetically distinct accessions. Conversely, wild accessions exhibited greater overall genetic diversity and higher inbreeding coefficients than cultivars, indicating frequent inbreeding within divergent natural populations. Our findings highlight the distinct genetic reservoirs of both wild accessions and Edo cultivars, although the former may face inbreeding challenges. Urgent conservation action is needed to ensure the genetic diversity of wild populations as natural resources.

Genetic variability and population genetic structure in the Caucasian Parsley Frog, Pelodytes caucasicus (Boulenger, 1896) based on microsatellite markers

The Caucasian Parsley Frog, Pelodytes caucasicus (Boulenger, 1896), is endemic to Caucasia, and its population is decreasing. Here, we present information on the genetic structure and diversity of populations from four provinces of Türkiye (Giresun, Trabzon, Rize, and Artvin) using microsatellite markers. Despite their small geographic range, the species’ populations showed moderate genetic differentiation, which could be a result of rapid genetic drift. Our results show that Trabzon and Giresun populations are genetically different from those of Rize and Artvin. We found considerably low genetic diversity in Artvin, Trabzon, and Giresun populations. The inbreeding co-efficient is also high in those localities (HO<HE). Despite low genetic diversity and a high inbreeding coefficient, we could not find any sign of a genetic bottleneck.

Population genomics of the endangered freshwater mussel, Arcidens wheeleri (Unionoidea: Unionidae: Anodontini), in the Little River, Arkansas, USA

ABSTRACT North America is a hotspot of freshwater mussel diversity. However, over the last century, many anthropogenic stressors have led to substantial declines in freshwater mussels of the families Unionidae and Margaritiferidae in North America. Conserving the remaining mussel fauna is a priority, as they play an integral role in freshwater ecosystems. The Little River in Arkansas is home to one of the last remaining populations of the federally endangered freshwater mussel, Arcidens wheeleri (Unionidae: Anodontini). Population dynamics information is lacking for A. wheeleri, and no population genetics study has been conducted on this species. A greater understanding of the genetic diversity within a population can serve as a benchmark for developing an effective management plan. We sampled A. wheeleri from three locations in the Little River. Genomic data were generated with a single-enzyme restriction-site-associated DNA sequencing approach to assess genetic diversity and structure of A. wheeleri in the Little River. Genetic structure analyses indicated one genetic population among the three locations, with limited, fine-scale subpopulation structure. Observed heterozygosity values were considerably lower than expected heterozygosity values, with Ho = 0.14 and He = 0.22, likely indicating a genetic bottleneck. Demographic analysis of the Little River population of A. wheeleri also suggests a historical bottleneck. Furthermore, a high inbreeding coefficient (FIS = 0.33) indicates A. wheeleri in the Little River is losing genetic diversity. Data generated indicate considerable risk of extirpation for A. wheeleri from the Little River and should serve as a baseline for future monitoring. Given its high risk of extinction, we recommend increased study of A. wheeleri across its range and on-the-ground conservation actions that include habitat protection and restoration, which are the only options until a successful host fish and protocols are identified for propagation.

Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats

Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e−05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100–150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex (B. liuyanii, B. longgangensis, B. masoniana and B. variegata) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between B. liuyanii and B. longgangensis occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of B. masoniana have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Range-wide genetic analysis of an endangered bumble bee (Bombus affinis, Hymenoptera: Apidae) reveals population structure, isolation by distance, and low colony abundance.

Declines in bumble bee species range and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumble bee (Bombus affinis) is the first federally listed bumble bee species in North America. We conducted a range-wide population genetics study of B. affinis from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted a site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range-wide male diploidy rate of ~15%. Our results suggest the Appalachians represent a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for B. affinis compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies, suggesting that B. affinis has undergone a recent decline and exhibit substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where B. affinis is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and help set clear recovery targets for this and other threatened bumble bee species.

Sex-specific effects of inbreeding in juvenile brown trout.

Inbreeding depression, that is, the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. It has therefore been predicted that sexual selection and the associated stress usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In some salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (Salmo trutta), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise full-factorial breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, sampled them 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We used whole-genome resequencing to calculate the kinship coefficients for each breeding pair and hence the expected average inbreeding coefficient per family. Juvenile growth could be predicted from these expected inbreeding coefficients and the genetic sex: Females reached lower body sizes with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females were on average smaller than males by the end of their first summer.

Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.

Describing geographical variation in morphology of organisms in combination with data on genetic differentiation and biogeography can provide important information on how natural selection shapes such variation. Here we study genetic structure using ddRAD seq and wing shape variation using geometric morphometrics in 14 populations of the damselfly Lestes sponsa along its latitudinal range in Europe. The genetic analysis showed a significant, yet relatively weak population structure with high genetic heterozygosity and low inbreeding coefficients, indicating that neutral processes contributed very little to the observed wing shape differences. The genetic analysis also showed that some regions of the genome (about 10%) are putatively shaped by selection. The phylogenetic analysis showed that the Spanish and French populations were the ancestral ones with northern Swedish and Finnish populations being the most derived ones. We found that wing shape differed significantly among populations and showed a significant quadratic (but weak) relationship with latitude. This latitudinal relationship was largely attributed to allometric effects of wing size, but non-allometric variation also explained a portion of this relationship. However, wing shape showed no phylogenetic signal suggesting that lineage-specific variation did not contribute to the variation along the latitudinal gradient. In contrast, wing size, which is correlated with body size in L. sponsa, had a strong negative correlation with latitude. Our results suggest a relatively weak population structure among the sampled populations across Europe, but a clear differentiation between south and north populations. The observed geographic phenotypic variation in wing shape may have been affected by different local selection pressures or environmental effects.

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data.

Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.

Restricted dispersal and inbreeding in a high‐elevation bird across the ‘sky islands’ of the European Alps

AbstractAimHigh‐elevation specialist species are threatened by climate change and habitat loss, and their distributions are becoming increasingly reduced and fragmented. In such a context, dispersal ability is crucial to maintain gene flow among patches of suitable habitat. However, information about dispersal is often lacking for these species, especially for those taxa that are usually considered as good dispersers such as birds. We adopted a landscape genomics approach to investigate dispersal in a climate‐sensitive high‐elevation specialist bird. Our aims were to assess the levels of gene flow within a wide mountain area, and to assess the effects of geographic distance and landscape characteristics on dispersal, by testing the isolation by distance (IBD) hypothesis against the isolation by resistance (IBR) hypothesis.LocationEuropean Alps.Taxon Montifringilla nivalis. MethodsWe sampled individuals from several breeding areas and obtained single nucleotide polymorphism (SNP) data by ddRAD sequencing. We then calculated site‐ and individual level genetic distances and individual inbreeding coefficients. To test IBD versus IBR, we related genetic distances to both geographic distances and different measures of landscape resistance by using maximum likelihood population effects models.ResultsGene flow among breeding areas was partly restricted, and we found support for IBD, indicating that geographic distance limits snowfinch dispersal. Spatial patterns of genetic distances suggested that philopatry strongly contributed to determine the observed IBD. High inbreeding coefficients in several individuals indicated frequent mating among relatives.Main ConclusionsRestricted dispersal and frequent inbreeding within ‘sky island’ systems can also occur in highly mobile species, because their potential ability to cover very large distances can be counteracted by high philopatry levels that are likely related to high dispersal costs. IBD and philopatry will increasingly hinder snowfinch dispersal among suitable areas within the future more restricted and fragmented breeding range, increasing the risks of local extinctions.

Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction.

Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations.

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR's ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease.

Genetic Variability and Kinship Analyses of Seized Red-Browed Amazon, Amazona rhodocorytha (Aves, Psittacidae)

Analyzing genetic variability and kinship relations is essential to guide conservation management plans for threatened species. The Red-browed Amazon (Amazona rhodocorytha) is one of the four Amazona parrots that are endemic to remnants of the Atlantic Forest, classified as Vulnerable (IUCN) owing to habitat loss and fragmentation and trapping for the illegal pet trade. At the end of 2021, 19 Red-browed Amazons were rescued from illegal trade in the Espírito Santo state, Brazil, including 14 nestlings reportedly captured in the Sooretama Biological Reserve, which provided the first opportunity to address the genetic parameters of a wild population of this threatened parrot. We used Single-Nucleotide Polymorphism (SNP) data to assess the genetic diversity and kinship relations between the rescued birds. We observed high heterozygosity levels and low inbreeding coefficients. Principal Component Analysis revealed the presence of at least two distinct genetic groups, suggesting past isolation followed by secondary contact. Our results suggest that the population from Sooretama is an important genetic and demographic repository of the Red-browed Amazon, and the presence of individuals from the two genetic lineages in the same area reduces concerns about potential inbreeding depression in rehabilitation and reintroduction plans and also inspires further investigations on historical and contemporary population structuring.

Elucidating genetic diversity and population structure of Alpine x Beetal goats using pedigree analysis

Pedigree analysis is essential for effective management of the breeding program and to keep the inbreeding under acceptable limits. Alpine x Beetal is a crossbred population of goats, bred at National Dairy Research Institute (NDRI) Karnal for last five decades. This germplasm is adapted to the tropical climate and has high milk potential as well as prolificacy. Objective of this study was to elucidate the genetic diversity and population structure in the flock of the Alpine x Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal for 5656 animals from the year 1971–2021. Animals born between 2014 and 2017 were 283, considered as reference cohort. Results revealed that the average generation interval was 3.40 years for the complete pedigree. The average inbreeding coefficient and the average relatedness for the whole population were 4.77% and 7.84%, respectively, and 9.65% and 11.98% respectively, for the reference population. High inbreeding coefficient and average relatedness in the reference cohort demonstrated the impact of closed gene pool and demands immediate intervention for management of genetic diversity in the closed nucleus under study. Ancestors contributing 50% of the gene pool were 8 for the complete pedigree which illustrates that few ancestors were responsible for genetic diversity in the flock. This resulted in the decline of effective population size (51.39). Effective number of founders (fe), ancestors (fa), and founder genomes equivalents (fg) were 24, 12, and 4.17, respectively. The (fe/fa) ratio in the reference population was 2 indicating the occurrence of the bottleneck effect in the flock. To lessen inbreeding and augment genetic diversity in the flock, the use of sires with lower average relatedness and the use of appropriate mating strategies are recommended.

Investigating the relationship between inbreeding and life expectancy in dogs: mongrels live longer than pure breeds.

This study aimed to investigate the establishment of relationship between inbreeding and life expectancy in dogs. A dataset of N=30,563 dogs sourced from the VetCompass™ Program, UK was made available by the Royal Veterinary College, University of London, containing information about breed and longevity and was subject to survival analysis. A Cox regression proportional hazards model was used to differentiate survivability in three groups of dogs (mongrel, cross-bred and pure breed). The model was found highly significant (p<0.001) and we found that mongrel dog had the highest life expectancy, followed by cross-bred dogs with only one purebred ancestor and purebred dogs had the lowest life expectancy. A second Cox regression was also found highly significant (p<0.001) differentiating the lifespan of different dog breed and correlating positively the hazard ratio and the Genetic Illness Severity Index for Dogs (GISID). The results show that survivability is higher in mongrel dogs followed by cross-bred with one of the ancestor only as a pure breed, and pure breed dog have the highest morbidity level. Higher morbidity is associated with higher GISID scores, and therefore, higher inbreeding coefficients. These findings have important implications for dog breeders, owners, and animal welfare organizations seeking to promote healthier, longer-lived dogs.

Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori

Clinch Dace (Chrosomus sp. cf. saylori) is a newly recognized and yet-undescribed species of minnow with a restricted and fragmented distribution in the upper Tennessee River basin in southwestern Virginia, USA. We collected Clinch Dace from seven streams and observed variations at nine selectively neutral microsatellite DNA loci to infer population genetic processes and identify units for conservation management. Bayesian cluster analysis showed that three of the seven surveyed populations were genetically distinct, while the other four populations showed signs of recent admixture. Estimated effective population sizes and m-ratios were low within most populations, suggesting loss of alleles due to recent genetic drift. Positive FIS values, high average individual inbreeding coefficients, and high degrees of inferred relatedness among individuals suggested that inbreeding is taking place in some populations. FST values were high, and analysis of molecular variance indicated genetic divergence among populations. These indicators suggest that Clinch Dace populations are subject to the genetic processes that are characteristic of small and isolated populations.

Analysis of genetic variability and population structure of the Mangalica pig breed using pedigree data

The maintenance of genetic diversity (GD) and low rate of inbreeding are two main goals for any conservation programs, especially in a small, closed population which is likely to violate these conservation targets in a long run. Among the conservation programs in Hungary probably the most characterizing is that of the Mangalica pigs, which is an autochthonous Hungarian pig breed group that has been preserved for biological diversity since 1973. The current study aimed to expose the evolution of population structure, GD and inbreeding coefficient with different approaches by analysing the pedigree of these breeds in the context of the conservation program. Genealogy analysis used the data of 12,808, 2393 and 3963 Blonde, Swallow-Belly and Red breeding animals born between 1980 and 2021, respectively. The reference populations (REF2021) were defined as breeding animals born between 2016 and 2021. Pedigree completeness was more than 90% in the fifth generation and the complete generation equivalent ranged from 4.29 to 7.08 and from 6.87 to 9.73 for the whole and the reference populations (REF2021), respectively. Generation interval on average was vary from 3.06 to 3.45 years with the longer pathways to the son. Most of different estimated inbreeding coefficient showed increased trends through pedigrees except for the Kalinowski new inbreeding coefficient (FNew) which decreased in all breeds in the last decade. The mean Wright inbreeding coefficient (Fw) was low, being 5.50%, 4.30% and 7.54% for the Blonde, Swallow-Belly, and Red reference populations (REF2021), respectively. Fw showed strong correlation with FNew but low correlation with FBal while the two types of ancestral inbreeding coefficients (FBal and FKal) were ranging from moderate strong to strong correlation in every breed. Effective population size of the reference populations (REF2021) was 85.57, 76.91, and 57.56, respectively. Based on the predicted future inbreeding for the next 25 years only the Red Mangalica breed was predicted to be “Transitional” in the endangerment categories. The GD loss in these three breeds was 5.6%, 5.7% and 8.7%, respectively, in which the loss due to genetic drift was decisive compared to the unequal founder contributions. In conclusion, the three populations at the present and in the next few generations are having optimistic perspective in terms of GD. These populations should be focused on reducing new inbreeding in mating plans and the Red population need to be monitored more carefully because of its current highest GD loss, smallest effective population size and highest inbreeding coefficient.

Gene flow drives genomic diversity in Asian Pikas distributed along the core and range-edge habitats in the Himalayas.

Studying the genetic variation among different species distributed across their core and range-edge habitats can provide valuable insights into how genetic variation changes across the species' distribution range. This information can be important for understanding local adaptation, as well as for conservation and management efforts. In this study, we have carried out genomic characterization of six species of Asian Pikas distributed along their core and range-edge habitats in the Himalayas. We utilized a population genomics approach using ~28,000 genome-wide SNP markers obtained from restriction-site associated DNA sequencing. We identified low nucleotide diversity and high inbreeding coefficients in all six species across their core and range-edge habitats. We also identified evidence of gene flow among genetically diverse species. Our results provide evidence of reduced genetic diversity in Asian pikas distributed across the Himalayas and the neighboring regions and indicate that recurrent gene flow is possibly a key mechanism for maintaining genetic diversity and adaptive potential in these pikas. However, full-scale genomics studies that utilize whole-genome sequencing approaches will be needed to quantify the direction and timing of gene flow and functional changes associated with introgressed regions in the genome. Our results represent an important step toward understanding the patterns and consequences of gene flow in species, sampled at the least studied, yet climatically vulnerable part of their habitat that can be further used to inform conservation strategies that promote connectivity and gene flow between populations.