Genetic adaptation to urban living: molecular DNA analyses of wild boar populations in Budapest and surrounding area

Studies of wild boar, Sus scrofa Linnaeus 1758, in urban and suburban areas of Budapest, Hungary, have indicated that these populations do not have continuous contact. Based on the assumption that the city has a discrete population, we hypothesized that the urban wild boar would differ genetically from those in suburban areas. Analysis of single-nucleotide polymorphism (SNP) data using the GeneSeek Genomic Profiler (GGP) Porcine 50 K system (Neogen, Scotland, UK) differentiated three populations: Buda (B) from the Western bank of the Danube; Buda Surrounding (BS); and Valkó (V) from the Eastern bank of the Danube. The coefficient of genetic differentiation (FST) for the B and BS populations was low. The inbreeding coefficients of the populations BS and V were close to zero, while population B had a high positive value reflecting the influence of founders and the inbreeding of the continuous urban population. The genome regions that were most differentiated between the B and BS populations were analyzed based on the FST values of the SNP markers using a mixed linear multi-locus model and BayeScan software. The most differentiated marker, WU_10.2_18_56278226, was found on chromosome 18. The surrounding region contained several candidate genes that could play important roles in adaptations related to human-induced stress. Two of these, encoding the adenylate cyclase 1 (ADCY1) and inhibin beta A chain precursor (INHBA) genes, were sequenced. While IHBA gene did not display variation, the allele distribution of the ADCY1 gene in the B population was significantly different from that of the BS population supporting the parapatric differentiation of wild boar.

Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data

Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (n = 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (Ne) were evaluated. The correlations between inbreeding based on the runs of homozygosity (FROH) and pedigree (FPED) were also calculated. The average FPED for all animals was 3.44%, while the FROH varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The Ne, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49–0.54) were observed between FPED and FROH. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

Rank-invariant estimation of inbreeding coefficients

The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.

Detecting inbreeding depression in a severely bottlenecked, recovering species: The little spotted kiwi (Apteryx owenii)

<p>Population bottlenecks reduce genetic variation and population size. Small populations are at greater risk of inbreeding, which further erodes genetic diversity and can lead to inbreeding depression. Inbreeding depression is known to increase extinction risk. Thus, detecting inbreeding depression is important for population viability assessment and conservation management. However, identifying inbreeding depression in wild populations is challenging due to the difficulty of obtaining long-term measures of fitness and error-free measures of individual inbreeding coefficients. I investigated inbreeding depression and our power to detect it in species that have very low genetic variation, using little spotted kiwi (Apteryx owenii) (LSK) as a case study. This endemic New Zealand ratite experienced a bottleneck of, at most, five individuals ~100 years ago and has since been subjected to secondary bottlenecks as a result of introductions to new predator-free locations. There is no behavioural pedigree data available for any LSK population and the status of the species is monitored almost exclusively via population growth. I conducted two seasons of field work to determine hatching success in the two LSK populations with the highest and lowest numbers of founders; Zealandia Sanctuary (40 founders) and Long Island (two founders). I also used simulation-based modelling to assess the feasibility of reconstructing pedigrees based on individual genotypes from LSK populations to calculate pedigree inbreeding coefficients. Finally, I used microsatellite genotypes to measure the genetic erosion in successive filial groupings of Long Island and Zealandia LSK as a result of their respective bottlenecks, and tested for inbreeding depression on Long Island. Hatching success was significantly lower on Long Island than in Zealandia in both years of the study despite significantly higher reproductive effort on Long Island. Although this was suggestive of inbreeding depression on Long Island, simulation results showed that constructing a pedigree for any LSK population based on the genetic markers and samples currently available would lead to inaccurate pedigrees and invalid estimates of individual inbreeding coefficients. Thus, an alternative method of detecting inbreeding and inbreeding depression was required. Microsatellite data showed continued loss of heterozygosity in both populations, but loss of allelic diversity on Long Island only. Individual genotypes indicated that the majority (74%) of the adult Long Island population is comprised of the founding pair (F) and their direct offspring (F1) rather than birds from subsequent generations (F2+). This is not what would be expected if survival was equal between these two filial classes. I suggest that the high levels of inbreeding (≥0.25) in F2+ birds is impacting on their survival, creating a demographic skew in the population and resulting in lower hatching success on average on Long Island when compared to the relatively outbred Zealandia birds. This inbreeding depression appears to have been masked, thus far, by positive population growth on Long Island resulting from the long life span of LSK (27-83 years) and continued reproductive success of the founding pair. Thus, it is likely that the Long Island population will go into decline when the founding pair cease to reproduce. This study highlights the challenges of measuring inbreeding depression in species with very low genetic variation and the importance of assessing the statistical power and reliability of the genetic tools available for those species. It also demonstrates that basic genetic techniques can offer valuable insight when more advanced tools prove error-prone. Monitoring vital rates such as hatching success in conjunction with genetic data is important for assessing the success of conservation translocations and detecting potentially cryptic genetic threats such as inbreeding depression. My results suggest that LSK are being affected by inbreeding depression and that careful genetic management will be required to ensure the long-term viability of this species.</p>

Detecting inbreeding depression in a severely bottlenecked, recovering species: The little spotted kiwi (Apteryx owenii)

<p>Population bottlenecks reduce genetic variation and population size. Small populations are at greater risk of inbreeding, which further erodes genetic diversity and can lead to inbreeding depression. Inbreeding depression is known to increase extinction risk. Thus, detecting inbreeding depression is important for population viability assessment and conservation management. However, identifying inbreeding depression in wild populations is challenging due to the difficulty of obtaining long-term measures of fitness and error-free measures of individual inbreeding coefficients. I investigated inbreeding depression and our power to detect it in species that have very low genetic variation, using little spotted kiwi (Apteryx owenii) (LSK) as a case study. This endemic New Zealand ratite experienced a bottleneck of, at most, five individuals ~100 years ago and has since been subjected to secondary bottlenecks as a result of introductions to new predator-free locations. There is no behavioural pedigree data available for any LSK population and the status of the species is monitored almost exclusively via population growth. I conducted two seasons of field work to determine hatching success in the two LSK populations with the highest and lowest numbers of founders; Zealandia Sanctuary (40 founders) and Long Island (two founders). I also used simulation-based modelling to assess the feasibility of reconstructing pedigrees based on individual genotypes from LSK populations to calculate pedigree inbreeding coefficients. Finally, I used microsatellite genotypes to measure the genetic erosion in successive filial groupings of Long Island and Zealandia LSK as a result of their respective bottlenecks, and tested for inbreeding depression on Long Island. Hatching success was significantly lower on Long Island than in Zealandia in both years of the study despite significantly higher reproductive effort on Long Island. Although this was suggestive of inbreeding depression on Long Island, simulation results showed that constructing a pedigree for any LSK population based on the genetic markers and samples currently available would lead to inaccurate pedigrees and invalid estimates of individual inbreeding coefficients. Thus, an alternative method of detecting inbreeding and inbreeding depression was required. Microsatellite data showed continued loss of heterozygosity in both populations, but loss of allelic diversity on Long Island only. Individual genotypes indicated that the majority (74%) of the adult Long Island population is comprised of the founding pair (F) and their direct offspring (F1) rather than birds from subsequent generations (F2+). This is not what would be expected if survival was equal between these two filial classes. I suggest that the high levels of inbreeding (≥0.25) in F2+ birds is impacting on their survival, creating a demographic skew in the population and resulting in lower hatching success on average on Long Island when compared to the relatively outbred Zealandia birds. This inbreeding depression appears to have been masked, thus far, by positive population growth on Long Island resulting from the long life span of LSK (27-83 years) and continued reproductive success of the founding pair. Thus, it is likely that the Long Island population will go into decline when the founding pair cease to reproduce. This study highlights the challenges of measuring inbreeding depression in species with very low genetic variation and the importance of assessing the statistical power and reliability of the genetic tools available for those species. It also demonstrates that basic genetic techniques can offer valuable insight when more advanced tools prove error-prone. Monitoring vital rates such as hatching success in conjunction with genetic data is important for assessing the success of conservation translocations and detecting potentially cryptic genetic threats such as inbreeding depression. My results suggest that LSK are being affected by inbreeding depression and that careful genetic management will be required to ensure the long-term viability of this species.</p>

Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.

Short Communication: A Within- and Across-country Assessment of the Genomic Diversity and Autozygosity of South African and Eswatini Nguni Cattle

In southern Africa, the Nguni cattle breed is classified as an indigenous and transboundary animal genetic resource that manifests unique adaptation abilities across distinct agroecological zones. The genetic integrity of various ecotypes is under potential threat due to both indiscriminate crossbreeding and uncontrolled inbreeding. The aim of this study was to assess the genetic diversity and autozygosity that exists both across countries (ES: eSwatini; SA: South Africa) and within-country (SA), between purebred stud animals (SA-S) and research herds (SA-R). Subsets of 96 ES, 96 SA-S and 96 SA-R genotyped for 40 930 common SNPs were used to study inbreeding, runs of homozygosity (ROH) and heterozygosity (ROHet) profiles as well as population structure. The highest proportion (0.513) of the 3 595 ROH was &lt;4Mb in length, while the majority (0.560) of the 4 409 ROHet segments fell within the 0.5-1Mb length category. Inbreeding coefficients indicated low inbreeding (FROH range: 0.025 for SA-S to 0.029 for SA-R). Principal component (PCA) and population structure (K=5) analyses illustrated genomic distinctiveness between SA and ES populations, greater admixture for SA-R (mean±standard deviation proportion shared=0.631±0.353) compared to SA-S (mean±standard deviation proportion shared=0.741±0.123), and three subpopulations for ES. Overall, results illustrated that genetic distinctiveness in the Nguni resulted from both geographic isolation and exposure to different production strategies. Although no impending threat to genetic diversity was observed, further loss should be monitored to prevent endangerment of unique and beneficial indigenous resources.

Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes’ ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.