Challenges in inbreeding estimation of large populations based on Polish Holstein-Friesian cattle pedigree

The aim of this study was to evaluate observed and future inbreeding level in Polish Holstein-Friesian cattle population. In total, over 9.8 mln animals were used in the analysis coming from the pedigree of Polish Federation of Cattle Breeders and Dairy Farmers. Inbreeding level, as an average per birth year, was estimated with the method accounting for missing parent information with the assumption of year 1950 as the base year of the population. If an animal had no ancestral records, an average inbreeding level from its birth year was assigned. Twice the average inbreeding level served as relatedness of the animal to the population, which enabled estimation of inbreeding in its offspring. The future inbreeding of potential offspring was estimated as an average of animals (bulls and cows) available for mating in a certain year. It was observed that 30–50% of animals born between 1985 and 2015 had no relevant ancestral information, which is caused by a high number of new animals and/or entire farms entering the national milk recordings. For the year 2015, the observed inbreeding level was 3.30%, which was more than twice the inbreeding with the classical approach (without missing parent information) and higher by 0.4% than the future inbreeding. The average increase of inbreeding in years 2010–2015 was 0.10%, which is similar to other countries monitored by World Holstein-Friesian Federation. However, the values might be underestimated due to low pedigree completeness. The estimates of future inbreeding suggested that observed inbreeding could be even lower and also increase slower, which indicates a constant need to monitor rate of increase in inbreeding over time. The most important aspect of presented results is the necessity to advise individual farmers to keep precise recordings of the matings on their farm in order to improve the pedigree completeness of Polish Holstein-Friesian and to use suitable mating programs to avoid too rapid growth of inbreeding.     

Sex-biased natal dispersal and inbreeding avoidance in American black bears as revealed by spatial genetic analyses

We tested the hypothesis that sex-biased natal dispersal reduces close inbreeding in American black bears, a solitary species that exhibits nearly complete male dispersal and female philopatry. Using microsatellite DNA and spatial data from reproductively mature bears (>or= 4 years old), we examined the spatial genetic structure of two distinct populations in New Mexico from 1993 to 2000. As predicted, relatedness (r) and the frequency of close relationships (parent-offspring or full siblings) decreased with distance among female dyads, but little change was observed among male or opposite-sex dyads. Neighbouring females were more closely related than neighbouring males. The potential for inbreeding was low. Most opposite-sex pairs that lived sufficiently close to facilitate mating were unrelated, and few were close relatives. We found no evidence that bears actively avoided inbreeding in their selection of mates from this nearby pool, as mean r and relationship frequencies did not differ between potential and actual mating pairs (determined by parentage analysis). These basic patterns were apparent in both study areas despite a nearly two-fold difference in density. However, the sex bias in dispersal was less pronounced in the lower-density area, based on proportions of bears with male and female relatives residing nearby. This result suggests that male bears may respond to reduced competition by decreasing their rate or distance of dispersal. Evidence supports the hypothesis that inbreeding avoidance is achieved by means of male-biased dispersal but also indicates that competition (for mates or resources) modifies dispersal patterns.     

Selection, load and inbreeding depression in a large metapopulation

The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient F(ST) and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.     

Spatial and temporal patterns of problem polar bears in Churchill,Manitoba

Human–bear interactions near the town of Churchill, Manitoba occur annually because the Western Hudson Bay polar bear population spends 4–5 months on-land each year when the sea ice melts completely. Significant changes have occurred in the Hudson Bay ecosystem and in the bear population as a result of climate warming; however, how these changes may have influenced human–bear interactions near Churchill is unclear. This study examined the temporal and spatial patterns of 1,487 problem bears captured in the Churchill area from 1970 to 2004. We also examined the relationship between problem bears and environmental variables as well as the Nunavut harvest. The number of individual problem bears caught near Churchill varied from 10 to 90 individuals per year and increased over time. Subadult males comprised 39%, subadult females 23%, adult males 18%, females with young 14%, and solitary females 6% of captures. Bears that became problem individuals were in closer proximity to the Churchill area. Nutritional stress and a northward shift in the distribution of the bears that spend the summer on-land in northeastern Manitoba may account for the increase in problem bear numbers. The date of sea ice freeze-up, which is getting progressively later, was the best predictor explaining the annual variation in the occurrence of problem bears. These results provide an understanding of how a warming climate may directly impact polar bear behaviour. This information may allow wildlife managers to predict relative levels of human–bear interactions and thereby implement effective management strategies to improve human safety and the conservation of polar bears.     

Occurrence and prevalence of Clostridium perfringens in polar bears from Svalbard, Norway

To obtain insight into the occurrence and prevalence of Clostridium perfringens and its major toxins in polar bears (Ursus maritimus), we took fecal samples for bacteriologic analysis from live-captured bears in the Svalbard Archipelago, Norway, in 2001. Clostridium perfringens was isolated from 40 of 92 samples (44%). Thirty strains were further characterized by determining toxin type and were classified to be type A, while one was also positive for the gene encoding beta2-toxin. Despite the fact that C. perfringens type A has been associated with fatal diseases in several animal species as well as in humans, our data indicate that C. perfringens type A is an normal inhabitant of the gastrointestinal tract of polar bears.     

The genetic consequences of fluctuating inbreeding depression and the evolution of plant selfing rates

The magnitude of inbreeding depression, a central parameter in the evolution of plant mating systems, can vary depending on environmental conditions. However, the underlying genetic mechanisms causing environmental fluctuations in inbreeding depression, and the consequences of this variation for the evolution of self‐fertilization, have been little studied. Here, we consider temporal fluctuations of the selection coefficient in an explicit genetic model of inbreeding depression. We show that substantial variance in inbreeding depression can be generated at equilibrium by fluctuating selection, although the simulated variance tends to be lower than has been measured in experimental studies. Our simulations also reveal that purging of deleterious mutations does not depend on the variance in their selection coefficient. Finally, an evolutionary analysis shows that, in contrast to previous theoretical approaches, intermediate selfing rates are never evolutionarily stable when the variation in inbreeding depression is due to fluctuations in the selection coefficient on deleterious mutations.     

Pharmacokinetics and tissue residues of Telazol in free-ranging polar bears

A pharmacokinetic and tissue residue study was conducted to assess the risks associated with human consumption of polar bears in arctic Canada that have been exposed to the immobilizing drug Telazol, a mixture of tiletamine hydrochloride and zolazepam hydrochloride. Twenty-two bears were remotely injected with about 10 mg/kg of Telazol. Following immobilization, serum samples were collected serially at regular intervals until the bears awakened. Sixteen of the bears were relocated and killed under permit by local hunters at various times from 0.5 to 11 days after dosing. Serum, kidney, muscle and adipose tissue samples were collected immediately after death. All samples were stored at -70 C until analysis by HPLC. The concentration-time data of tiletamine and zolazepam in serum during the immobilization period were fitted to curves by computer and the pharmacokinetic parameters assessed. In addition, the serum and tissue samples collected at the time of death were analyzed for both parent drugs, for one metabolite of tiletamine (CI-398), and for three metabolites of zolazepam (metabolites 1, 2 and 4). A one-compartment model with first-order absorption and elimination best fit the time-series data for the drugs in serum during the immobilization period. This model gave half-lives (mean +/- SE) for tiletamine and zolazepam of 1.8+/-0.2 h and 1.2+/-0.08 h, respectively, clearance values of 2.1+/-0.3 l x h(-1) x kg(-1) and 1.1+/-0.1 l x h(-1) x kg(-1), and volumes of distribution of 5.2+/-0.6 l/kg and 1.8+/-0.2 l/kg. The concentrations of both drugs and their metabolites declined rapidly to trace levels by 24 h post-dosing, although extremely low concentrations of some metabolites were encountered sporadically over the entire sampling period. In particular, zolazepam metabolite 2, remained detectable in fat and muscle tissue at the end of the study, 11 days after dosing. It was concluded that during immobilization, both tiletamine and zolazepam levels decline rapidly in a monoexponential fashion, and their pharmacokinetic parameters in polar bears are similar to those observed in other species. Tissue levels of the drugs and their metabolites declined sufficiently rapidly that individuals eating meat from exposed bears would be unlikely to experience pharmacological effects from the drugs. Nevertheless, slight exposure to the drugs and/or their metabolites might be possible for an indeterminate time after dosing.     

Correlated pedigree and molecular estimates of inbreeding and their ability to detect inbreeding depression in the Icelandic sheepdog, a recently bottlenecked population of domestic dogs

We examine the relationship of the inbreeding coefficient (f) and molecular estimates of inbreeding (IR, sMLH) in the Icelandic sheepdog. The breed experienced a severe genetic bottleneck and near extinction in the last century. Molecular estimates and the inbreeding coefficient are significantly correlated despite the moderate number of markers and individuals used in this study. This is most likely an effect of the extreme relatedness and relatively high variance in individual inbreeding coefficients in the population. There is a significant relationship between inbreeding (f) and the occurrence of hip dysplasia. However, the molecular measures did not detect hip dysplasia as an inbreeding effect.     

Evidence of inbreeding depression but not inbreeding avoidance in a natural house sparrow population

Inbreeding is common in small and threatened populations and often has a negative effect on individual fitness and genetic diversity. Thus, inbreeding can be an important factor affecting the persistence of small populations. In this study, we investigated the effects of inbreeding on fitness in a small, wild population of house sparrows (Passer domesticus) on the island of Aldra, Norway. The population was founded in 1998 by four individuals (one female and three males). After the founder event, the adult population rapidly increased to about 30 individuals in 2001. At the same time, the mean inbreeding coefficient among adults increased from 0 to 0.04 by 2001 and thereafter fluctuated between 0.06 and 0.10, indicating a highly inbred population. We found a negative effect of inbreeding on lifetime reproductive success, which seemed to be mainly due to an effect of inbreeding on annual reproductive success. This resulted in selection against inbred females. However, the negative effect of inbreeding was less strong in males, suggesting that selection against inbred individuals is at least partly sex specific. To examine whether individuals avoided breeding with close relatives, we compared observed inbreeding and kinship coefficients in the population with those obtained from simulations of random mating. We found no significant differences between the two, indicating weak or absent inbreeding avoidance. We conclude that there was inbreeding depression in our population. Despite this, birds did not seem to actively avoid mating with close relatives, perhaps as a consequence of constraints on mating possibilities in such a small population.     

Disease-mediated inbreeding depression in a large,open population of cooperative crows

Disease-mediated inbreeding depression is a potential cost of living in groups with kin, but its general magnitude in wild populations is unclear. We examined the relationships between inbreeding, survival and disease for 312 offspring, produced by 35 parental pairs, in a large, open population of cooperatively breeding American crows (Corvus brachyrhynchos). Genetic analyses of parentage, parental relatedness coefficients and pedigree information suggested that 23 per cent of parental dyads were first- or second-order kin. Heterozygosity–heterozygosity correlations suggested that a microsatellite-based index of individual heterozygosity predicted individual genome-wide heterozygosity in this population. After excluding birds that died traumatically, survival probability was lower for relatively inbred birds during the 2–50 months after banding: the hazard rate for the most inbred birds was 170 per cent higher than that for the least inbred birds across the range of inbreeding index values. Birds that died with disease symptoms had higher inbreeding indices than birds with other fates. Our results suggest that avoidance of close inbreeding and the absence of inbreeding depression in large, open populations should not be assumed in taxa with kin-based social systems, and that microsatellite-based indices of individual heterozygosity can be an appropriate tool for examining the inbreeding depression in populations where incest and close inbreeding occur.     

A study of the occurrence of monochorionic and monozygotic twinning in the pig

In humans as well as in most farm animals, monozygotic twins have been described. Nevertheless, only a few reports of twinning in the pig have been published. It has been suggested that monozygotic twins are formed during the first 14 days of pregnancy. This monozygotic twin study includes the investigation of porcine monochorionic embryos from 76 sows at days 26–29 post-insemination (p.i.), as well as an examination of 10 whole litters at days 21–22 p.i. In the former group, 29% of the sows carried monochorionic embryos. Based on DNA profiling using microsatellite markers, one monozygotic twin pair was found among these embryos. In the latter group, three monozygotic twin pairs were identified. Thus, it can be concluded that although the occurrence of monozygotic twins in pigs is a sporadic event, the fusion of extra-embryonic membranes is relatively common.     

Evidence for linkage on chromosome 3q25-27 in a large autism extended pedigree

Though autism shows strong evidence for genetic etiology, specific genes have not yet been found. We tested for linkage in a candidate region on chromosome 3q25-27 first identified in Finnish autism families [1]. The peak in this previous study was at D3S3037 (183.9 cM). We tested this region in seven affected family members and 24 of their relatives from a single large extended Utah pedigree of Northern European ancestry. A total of 70 single nucleotide polymorphisms (SNPs) were analyzed from 165 to 204 cM. The maximum NPL-all nonparametric score using SimWalk2snp was 3.53 (empirical p val ue = 0.0003) at 185.2 cM (SNP rs1402229), close to the Finnish peak. A secondary analysis using MCLINK supported this result, with a maximum of 3.92 at 184.6 cM (SNP rs1362645). We tested for alterations in a candidate gene in this region, the fragile X autosomal homolog, FXR1. No variants likely to contribute to autism were found in the coding sequence, exon-intron boundaries, or the promoter region of this gene.     

Identification of genetic loci for basal cell nevus syndrome and inflammatory bowel disease in a single large pedigree

Basal Cell Nevus Syndrome (BCNS) is an autosomal dominant disease. PTCH1 gene mutations have been found responsible in many but not all pedigrees. Inflammatory Bowel Disease (IBD) is a complex genetic disorder, disproportionate in Ashkenazim, and characterized by chronic intestinal inflammation. We revisited a large Ashkenazim pedigree, first reported in 1968, with multiple diagnoses of BCNS and IBD, and with a common genetic cause for both disorders proposed. We expanded the pedigree to four generations and performed a genome-wide linkage study for BCNS and IBD traits. Twelve members with BCNS, seven with IBD, five with both diagnoses and eight unaffected were genotyped. Both non-parametric (GENEHUNTER 2.1) and parametric (FASTLINK) linkage analyses were performed and a validation through simulation was performed. BCNS linked to chromosome 9q22 (D9S1120) just proximal to the PTCH1 gene (NPL=3.26, P=0.003; parametric two-point LOD=2.4, parametric multipoint LOD=3.7). Novel IBD linkage evidence was observed at chromosome 1p13 (D1S420, NPL 3.92, P=0.0047; parametric two-point LOD=1.9). Linkage evidence was also observed to previously reported IBD loci on 4q, (D4S2623, NPL 3.02, P=0.012; parametric two-point LOD=2.15), 10q23 (D10S1225 near DLG5, NPL 3.33, P=0.0085; parametric two-point LOD=1.3), 12 overlapping the IBD2 locus (D12S313, NPL 2.6, P=0.018; parametric two-point LOD=1.52), and 7q (D7S510 and D7S3046, NPL 4.06, P=0.0035; parametric two-point LOD=2.18). In this pedigree affected by both BCNS and IBD, the two traits and their respective candidate genetic loci segregate independently; BCNS maps to the PTCH1 gene and IBD maps to several candidate regions, mostly overlapping previously observed IBD loci.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.Carolien I. Panhuysen and Amir Karban contributed equally to this work     

Evidence for genetic control of nematode egg-shedding rates in calves

Differences in nematode fecal egg counts from 167 purebred Angus calves born in 1986 and 133 born in 1987 that had been naturally exposed to infection on pasture were analyzed for sire effects. The calves were sired by 26 different bulls, all of which were related. Differences among fecal egg counts were attributable to sires (P less than 0.0002), to age of the calf (P less than 0.0007), to age of dam (P less than 0.05), and to collection year (P less than 0.0001). No variation in fecal egg count was attributable to calf sex (P greater than 0.23). After accounting for the effects of year, age of calf, and age of dam, heritability was estimated to be 29% (SE = 18%). It was concluded that a paternal contribution to the genome of each calf played an important role in determining average fecal egg output of the sire group. With heritability at 29%, selection against higher fecal egg counts or selection for lower fecal egg counts would be expected to produce measurable genetic change in a population.     

Trends in the twinning rate in Johannesburg, South Africa, 1969-1989 and estimated twinning rates for 1990.

Birth statistics for the Johannesburg Metropolitan Region were collected for 757 151 confinements from 1969 to 1989 (467513 Black, 194375 White, 67250 Coloured and 28013 Indian confinements). From 1969 to 1978 data on the sexes of twins were also collected for 375 203 of the confinements (203 504 Black, 129 631 White, 28 253 Coloured and 13 815 Indian confinements). A twin confinement was defined as two deliveries during one confinement. Twinning rates (TRs), defined as the number of twin confinements per 1000 total confinements, were calculated per year for each population group and from 1969-1978 estimates of the relative proportions of dizygotic (DZ) and monozygotic (MZ) twins were calculated and thus the relative DZTRs and MZTRs. A significant decline in Black and Coloured TRs was observed between 1969 and 1989. A significant decline in Black DZTR but not Black MZTR was observed between 1969 and 1978, the Coloured twin sample was too small to show significant trends over this period. It is probable that the overall decline in Black twinning may be explained by a decline in the DZTR. An analysis of birth statistics for 159 748 confinements (134 504 Black and 25 244 White confinements) collected as part of a prospective study of TRs in the Johannesburg Metropolitan Region from 1988 to 1990, indicated that the Black TR continued to decline at least until the end of 1990. TRs in the Johannesburg Metropolitan Region calculated from City Health Department birth statistics collected from 1988 to 1990 were: 13.8 and 10.77 for the Black and White populations, respectively. TRs for this period calculated from the combined birth statistics of 14 hospitals, nursing homes and maternity clinics across the region were: 12.4 and 10.88 for the Black and White populations, respectively.     

The effect on net photosynthesis of pedigree selection for low and high rates of photorespiration in tobacco

A normal appearing plant with a low rate of photorespiration (ratio of ¹⁴CO₂ released light/dark = 1.6) was found in an unselected tobacco (Nicotiana tabacum) cultivar. The plant was self-pollinated, and further selections were made on several successive generations. Excised leaves from the progeny of the selections were examined for photorespiration and net CO₂ assimilation in normal air during photosynthesis. Similar measurements were made of plants derived from selfed parents with high rates of photorespiration (ratio of ¹⁴CO₂ released light/dark = 3.0 or greater). Efficient photosynthetic plants (greater than 22.0 mg of CO₂ dm⁻² hr⁻¹) with low rates of photorespiration produced a larger proportion of efficient progeny (about 25%) than did selfing inefficient plants (about 6%), but this proportion did not increase in successive generations.     

A comparison of inbreeding rates in India, Japan, Europe and China.

This is a report on an application of a new method for estimating inbreeding rates in large, semi-isolated populations over time. This study is intended to further show the versatility of the method. In a previous study, the method was shown to be useful in analysing the effect of details in a single population curve on inbreeding. In this study, the method is applied to the population curves of India, Japan, Europe and China over the past two millennia, to allow inter-comparisons of the inbreeding within those populations. Anthropologists traditionally concentrate on small isolates within a country for the estimation of inbreeding. Those isolates, however, might not be representative of the country as a whole. The method used in this study attempts to estimate inbreeding over large regions over an extended period of time. The method models the genealogical 'paradox' and yields estimates of the average inbreeding in terms of Pearl's coefficient Z, as a function of time. It is first assumed that the whole population of each country is the adult (breeding) population, corresponding to minimum inbreeding. It is found that the more complex the population curve examined, the greater the precision of the Z curves obtained. The effect of incorporating a single known value of inbreeding into the analyses is also investigated. This procedure produces a more realistic situation where the adult (breeding) population is considerably less than the entire population. It is shown, that if it is assumed that the whole population of the country is the adult (breeding) population, then a present day person from one of the four regions/countries studied is descended from between 72% and 97% of the early medieval population of the particular country. On the other hand, if a known value of inbreeding for Britain is incorporated into the analysis, these values become of the order of 1% for the older-settled regions/countries, and about 16% for Japan. However, that value for Japan is reduced to about 1% when a known value of inbreeding for this country is used. Although some uncertainty in these results remains, the versatility of the method demonstrated here will provide more accurate results, as better input-data become available.     

Diet composition of polar bears in Svalbard and the western Barents Sea

We estimated both the numerical and biomass composition of the prey of polar bears (Ursus maritimus) from 135 opportunistic observations of kills in Svalbard and the western Barents Sea collected from March to October 1984-2001. By number, the prey composition was dominated by ringed seals (Phoca hispida) (63%), followed by bearded seals (Erignathus barbatus) (13%), harp seals (P. groenlandica) (8%) and unknown species (16%). However, when known prey were converted to biomass, the composition was dominated by bearded seals (55%), followed by ringed seals (30%) and harp seals (15%). Results indicated that bearded seals are an important dietary item for polar bears in the western Barents Sea. We believe that different patterns of space use by different bears may result in geographic variation of diet within the same population.