Methods to estimate effective population size using pedigree data: Examples in dog,sheep, cattle and horse

Background

Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.

Results

Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusions

When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.     

msABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis

With the availability of whole-genome sequence data biologists are able to test hypotheses regarding the demography of populations. Furthermore, the advancement of the Approximate Bayesian Computation (ABC) methodology allows the demographic inference to be performed in a simple framework using summary statistics. We present here msABC, a coalescent-based software that facilitates the simulation of multi-locus data, suitable for an ABC analysis. msABC is based on Hudson's ms algorithm, which is used extensively for simulating neutral demographic histories of populations. The flexibility of the original algorithm has been extended so that sample size may vary among loci, missing data can be incorporated in simulations and calculations, and a multitude of summary statistics for single or multiple populations is generated. The source code of msABC is available at http://bio.lmu.de/~pavlidis/msabc or upon request from the authors.     

Random amplified polymorphic DNA in cattle and sheep: application for detecting genetic variation

The present study investigated the use of the random amplified polymorphic DNA (RAPD) method to detect genetic variation in cattle and sheep. The animals studied consisted of samples from five Finnish cattle breeds: native Eastern (18 animals), Northern (24), Western Finncattle (24), Finnish Ayrshire (24), and Finnish Friesian (18); as well as a white (6 animals) and a grey (9) colour type of Finnsheep. The cattle and sheep populations were analysed with 11 and 13 RAPD primers demonstrating the most repeatable amplification pattern. Two out of ten RAPD fragments tested by cross hybridization showed homology between the two species. The RAPD method did not prove efficient for finding new polymorphisms in either species, because we found only three polymorphic RAPD markers for cattle and seven markers for sheep with different allele frequencies between the breeds. Although there is a greater presence of polymorphic RAPD markers in sheep, according to the similarity indices the sheep populations showed a higher degree of homogeneity than the cattle breeds. However, the interbreed and intrabreed similarity indices for cattle did not suggest any significant differentiation of the Finnish breeds, contrary to earlier results based on blood group and protein polymorphism.     

Number of females in cattle, sheep, pig, goat and horse breeds predicted from a single year's registration data

An objective and accountable method is needed for deducing the number of registered animals in a breed from registration data. By following the principle that individual breeders register sufficient young females to be certain of having enough replacements for their current breeding stock, the ratios were calculated of the number of adult females in a breed to the number of female registrations, in a given year. Number of breeds considered were 8 cattle, 16 sheep, 8 pigs, 1 goat and 2 equines, all in the United Kingdom or Ireland. This yielded multipliers (4.4 for cattle, 3.3 for sheep, 3.1 for pigs, with confidence limits; and a point estimate of 5.2 for goats) enabling total adult female population to be predicted from a single year's registration data. There was considerable variation between breeds in values of the multiplier, apparently for reasons of breed history and function. This was particularly evident for equines where the two breeds yielded multipliers of 3.8 and 13.9. Multipliers, using registration data that are already in the public domain, can provide an estimate of breed numerical size, which a breed society can either accept or replace with an audited census.     

A polymorphic antigen displaying different molecular weights in sheep and cattle sera

The polymorphic antigen Bl is present, exhibiting different molecular weights, in both sheep and cattle sera. The molecular weight of the antigen, purified from both sera by a specific immunoabsorbent, was analysed by SDS polyacrylamide gel electrophoresis and calibrated gel filtration. Results indicate that only one subunit, 35 000 MW, forms cattle Bl while a further subunit, 60 000 MW, is present in sheep Bl. The antigen activity is localized on the 35 000 MW subunit, which appears to be the same in both species.     

Marker-assisted conservation of European cattle breeds: An evaluation

Two methods have been developed for the assessment of conservation priorities on the basis of molecular markers. According to the Weitzman approach, contributions to genetic diversity are derived from genetic distances between populations. Alternatively, diversity within and across populations is optimized by minimizing marker-estimated kinships. We have applied, for the first time, both methods to a comprehensive data set of 69 European cattle breeds, including all cosmopolitan breeds and several local breeds, for which genotypes of 30 microsatellite markers in 25–50 animals per breed have been obtained. Both methods were used to calculate the gain in diversity if a breed was added to a set of nine non-endangered breeds. Weitzman-derived diversities were confounded by genetic drift in isolated populations, which dominates the genetic distances but does not necessarily increase the conservation value of a breed. Marker-estimated kinships across populations were less disturbed by genetic drift than the Weitzman diversities and assigned high conservation values to Mediterranean breeds, which indeed have genetic histories that differ from the non-endangered breeds. Prospects and limitations of marker-assisted decisions on conservation priorities are discussed.     

Sequence diversity and rates of molecular evolution between sheep and cattle genes

Experiments that aim to identify genes of importance in sheep are currently inhibited by a paucity of genomic resources. One approach, therefore, is to exploit the wealth of data and associated capabilities becoming available for the bovine genome. Cross-species application of microarrays and comparative sequencing to identify single nucleotide polymorphisms are two possibilities; however, both are dependant on the level of nucleotide sequence similarity between the two species. This study used 120 gene orthologues consisting of over 60 kb of aligned sequence to estimate the gene diversity between cattle and sheep. Less than 3% of protein-coding nucleotide positions were found to be different, indicating that the prospect for successfully using cross-species strategies is high. Substitution at synonymous sites ranged between 6.9 and 7.7% (+/- 0.3%), and was higher than at non-synonymous sites (1.4-1.7 +/- 0.1%). The relative rate test was used to determine whether the observed mutation rates were constant between the two lineages. While the rate at synonymous sites appeared constant, the rate at non-synonymous sites was significantly higher within the caprinae lineage (sheep) when compared with bovinae (cattle; chi2 = 10.03; d.f. = 1, P < 0.01). This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.     

Prevalence and strain diversity of thermophilic campylobacters in cattle, sheep and swine farms

AIMS: To determine prevalence and strain diversity of thermophilic campylobacters in healthy ruminants and swine. METHODS AND RESULTS: Faecal samples collected from 343 herds (120 sheep, 124 beef cattle, 82 dairy cattle and 17 swine) in the Basque Country were screened in pools for thermophilic campylobacters. Two hundred and three herds were positive (67.1% dairy cattle, 58.9% beef cattle, 55.0% sheep and 52.9% pig), and species-specific PCR identified Campylobacter jejuni in 20.7% of the herds and Campylobacter coli in 6.4%. Campylobacter coli was isolated from the four production systems and was the most prevalent species in swine, where C. jejuni was not found. Other thermophilic campylobacters were found in all production systems. Four hundred and ninety-three animals from 11 positive herds were individually analysed, detecting significantly higher within-herd prevalences in dairy cattle (66.7%) and swine (57.8%) than in sheep (8.8%) or beef cattle (5.4%). flaA PCR-RFLP and pulsed-field gel electrophoresis analysis of a selection of isolates showed high genetic diversity. CONCLUSIONS: Healthy swine, cattle and sheep are important reservoirs of thermophilic campylobacters of different species and high genetic diversity. SIGNIFICANCE AND IMPACT OF THE STUDY: Efficient farm-based intervention measures are needed to reduce risk of infection. Non-C. jejuni/C. coli species should be monitored to investigate their significance for infection.     

Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches

Genetic relationships between 61 dog breeds were investigated, using a sampling of 1514 animals and a panel of 21 microsatellite markers. Based on the results from distance-based and Bayesian methods, breed constituted the main genetic structure, while groups including genetically close breeds showed a very weak structure. Depending on the method used, between 85.7% and 98.3% of dogs could be assigned to their breed, with large variations according to the breed. However, breed heterozygosity influenced assignment results differently according to the method used. Within-breed and between-breed diversity variations when breeds were removed were highly negatively correlated ( r  = −0.963, P  <   0.0001), because of the genetic structure of the breed set.     

Somatic cell mapping of the bovine prion protein gene and restriction fragment length polymorphism studies in cattle and sheep

Brains affected by the progressive neurological disease bovine spongiform encephalopathy (BSE) contain scrapie-associated fibrils and the protease-resistant isoform of prion protein. The gene encoding the normal host prion protein (PRNP) has been mapped to human chromosome 20 and mouse chromosome 2 with the hamster cDNA probe pEA974. Using this probe and a panel of bovine-rodent hybrid somatic cells, we have mapped PRNP to bovine syntenic group U11 (100% concordancy). PRNP restriction fragment length polymorphisms (RFLPs) were detected with five of six enzymes (BglII, EcoRI, HindIII, MspI and TaqI) in sheep, in contrast to one of 16 enzymes (HincII) in cattle. Codominant segregation of the bovine HincII RFLP was demonstrated in six backcross pedigrees. While PRNP RFLPs are tightly linked to scrapie incubation period, and consequently susceptibility or resistance to disease in rodents and sheep, the relationship between the PRNP RFLPs and BSE incubation period has not been determined.     

The Quetzal Coalescence template library: A C++ programmers resource for integrating distributional,demographic and coalescent models

Genetic samples can be used to understand and predict the behaviour of species living in a fragmented and temporally changing environment. In this regard, models of coalescence conditioned to an environment through an explicit modelling of population growth and migration have been developed in recent years, and simulators implementing these models have been developed, enabling biologists to estimate parameters of interest with Approximate Bayesian Computation techniques. However, model choice remains limited, and developing new coalescence simulators is extremely time consuming because code re‐use is limited. We present Quetzal, a C++ library composed of re‐usable components, which is sufficiently general to efficiently implement a wide range of spatially explicit coalescence‐based environmental models of population genetics and to embed the simulation in an Approximate Bayesian Computation framework. Quetzal is not a simulation program, but a toolbox for programming simulators aimed at the community of scientific coders and research software engineers in molecular ecology and phylogeography. This new code resource is open‐source and available at https://becheler.github.io/pages/quetzal.html along with other documentation resources.     

Localization of the ß-subunit of follicle stimulating hormone in cattle and sheep by in situ hybridization

The locus for the beta-subunit of the follicle stimulating hormone gene (FSHB) has been determined in both cattle and sheep by in situ hybridization of a bovine and an ovine cDNA probe, respectively, to metaphase chromosomes. Our results show that the FSHB locus is on cattle chromosome 15 in the region of bands q24-qter and in sheep on the cytogenetically homologous chromosome 15, also in the region q24-qter. The mapping of the FSHB gene in cattle together with the location of other genes (CAT, HBB and PTH) previously found to be syntenic in cattle and on human chromosome 11p, defines an evolutionarily conserved synteny. The localization of the FSHB gene to a cytogenetically homologous region in cattle and sheep is consistent with the hypothesis of extensively conserved chromosome structure in these two species.     

National survey for Salmonella in pigs, cattle and sheep at slaughter in Great Britain (1999-2000)

AIMS: The objective of these surveys was to estimate the prevalence of faecal carriage of Salmonella in healthy pigs, cattle and sheep at slaughter, and of pig carcase contamination with Salmonella. These data can be used as a baseline against which future change in Salmonella prevalence in these species at slaughter can be monitored. METHODS AND RESULTS: In this first randomized National Survey for faecal carriage of Salmonella in slaughter pigs, cattle and sheep in Great Britain, 2509 pigs, 891 cattle and 973 sheep were sampled in 34 pig abattoirs and 117 red meat abattoirs in England, Scotland and Wales. Carriage of Salmonella in 25 g caecal contents was identified in 578 (23.0% pigs) but in only 134 (5.3%) of carcase swabs. The predominant Salmonella serovars found in both types of sample were S. Typhimurium (11.1% caeca, 2.1% carcases) and S. Derby (6.3% caeca, 1.6% carcases). The main definitive phage types (DT) of S. Typhimurium found were DT104 (21.9% of caecal S. Typhimurium isolates), DT193 (18.7%), untypable strains (17.6%), DT208 (13.3%) and U302 (13.3%). Three isolates of S. Enteritidis (PTs 13A and 4) and one enrofloxacin-resistant S. Choleraesuis were also isolated. A positive 'meat-juice ELISA' was obtained from 15.2% of pigs at 40% optical density (O.D.) cut-off level and 35.7% at 10% cut-off. There was poor correlation between positive ELISA results or carcase contamination and the caecal carriage of Salmonella. The ratio of carcase contamination to caecal carriage rates was highest in abattoirs from the midland region of England and in smaller abattoirs. In cattle and sheep 1 g samples of rectal faeces were tested. Two isolates (i.e. 0.2%) were recovered from cattle, one each of S. Typhimurium, DT193 and DT12. One sheep sample (0.1%) contained a Salmonella, S. Typhimurium DT41. In a small subsidiary validation exercise using 25 g of rectal faeces from 174 cattle samples, three (1.7%) isolates of Salmonella (S. Typhimurium DT104, S. Agama, S. Derby) were found. CONCLUSIONS: The carriage rate of Salmonella in prime slaughter cattle and sheep in Great Britain was very low compared with pigs. This suggests that future control measures should be focused on reduction of Salmonella infection on pig farms and minimizing contamination of carcases at slaughter. SIGNIFICANCE AND IMPACT OF THE STUDY: This work has set baseline figures for Salmonella carriage in these species slaughtered for human consumption in Great Britain. These figures were collected in a representative way, which enables them to be used for monitoring trends and setting control targets.     

An assessment of Walk-over-Weighing to estimate short-term individual forage intake in sheep

The main limitation for determining feed efficiency of freely grazing ruminants is measurement of daily individual feed intake. This paper describes an investigation that assessed a method for estimating intake of forage based on changes in BW of ewes. A total of 24 dry and non-pregnant Romane ewes (12 hoggets, HOG; mean±SD 51.8±2.8 kg BW; body condition score (BCS) 2.6±0.2; and 12 adults, ADU; 60.4±8.5 kg BW; BCS 2.7±0.8) were selected for the study and moved from their rangeland system to a confined pen with controlled conditions and equipped with individual automatic feeders. The experiment lasted for 28 days (21 days adaptation and 7 days feed intake measurement). Ewes were fed hay and trained to use the electronic feeders (one feeding station per ewe) in which actual daily intake (H_intake24) was measured. The pens were designed to maximize movement of trained ewes through an automated Walk-over-Weighing device, by using water and mineral salts as attractants. Total individual intake of hay measured in the automatic feeder at each meal (H_intake) was compared with indirect estimates of feed intake determined using differences in the BW of the ewes (∆BW) before and 1 h following morning and afternoon feeding at fixed times. The BW, BCS, H_intake, H_intake24, as well as plasma non-esterified fatty acids (NEFA), glucose and insulin profiles were determined. The BW was higher in ADU v. HOG but BCS was not affected by parity. The H_intake24 was affected by day of experiment as a consequence of reduced availability and intake of water on one day. Plasma glucose, NEFA and insulin were not affected by parity or day of experiment. The H_Intake was and ∆BW tended to be higher in the morning in HOG, whereas H_intake was and ∆BW tended to be higher in ADU at the afternoon meal. Irrespective of parity or feeding time, there was very strong correlation (r²=0.93) between H_intake and ∆BW. This relationship confirms that our indirect method of estimating individual forage intake was reliable within the strictly controlled conditions of the present experiment. The method appears suitable for use in short-term intensive group feeding situations, and has potential to be further developed for longer-term forage intake studies, with a view to developing a method for freely grazing ruminants.     

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

The identification of individuals’ breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. The results using independent analysis, such as admixture, F_st, principal component analysis and random forest, confirmed the ability of these methods in selecting distinctive markers. The identified SNPs may constitute a starting point for the development of a SNP based identification test as a tool for breed assignment and traceability of animal products.     

Frequencies of genes for coat colour and horns in Nordic cattle breeds

Gene frequencies of coat colour and horn types were assessed in 22 Nordic cattle breeds in a project aimed at establishing genetic profiles of the breeds under study. The coat colour loci yielding information on genetic variation were: extension, agouti, spotting, brindle, dun dilution and colour sided. The polled locus was assessed for two alleles. A profound variation between breeds was observed in the frequencies of both colour and horn alleles, with the older breeds generally showing greater variation in observed colour, horn types and segregating alleles than the modern breeds. The correspondence between the present genetic distance matrix and previous molecular marker distance matrices was low (r = 0.08 – 0.12). The branching pattern of a neighbour-joining tree disagreed to some extent with the molecular data structure. The current data indicates that 70% of the total genetic variation could be explained by differences between the breeds, suggesting a much greater breed differentiation than typically found at protein and microsatellite loci. The marked differentiation of the cattle breeds and observed disagreements with the results from the previous molecular data in the topology of the phylogenetic trees are most likely a result of selection on phenotypic characters analysed in this study.     

Comparative mapping of sheep inhibin subunit βb to chromosome 2 in sheep and cattle by fluorescence in situ hybridization

A cosmid clone containing the complete sheep inhibin subunit β_B gene (INHBB) was assigned to sheep and cattle homologous chromosome bands 2q31-q33 by fluorescence in situ hybridization. The assignment of INHBB in sheep excludes another candidate gene as the site of the Fec^B mutation.     

Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data

The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37–0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator ( r  =   0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.     

Comparison of initial wetting pattern,nutrient concentrations in soil solution and the fate of15N-labelled urine in sheep and cattle urine patch areas of pasture soil

Three field experiments were carried out to compare cattle and sheep urine patches in relation to (i) initial wetting pattern and volume of soil affected, (ii) soil solution ionic composition and (iii) the fate of¹⁵N-labelled urine in the soil over the winter period. The distribution of Br^– (used as a urine tracer) across the soil surface and down the profile was irregular in all the patches. The pasture area covered by Br^– in the sheep patches was 0.04–0.06 m² and Br^– was detected to a depth of 150 mm. Cattle patches were significantly larger covering a surface area of 0.38–0.42 m² and penetrating to a depth of 400 mm. The rapid downward movement of urine occurred through macropore flow but even so, over half of the applied Br^– was detected in the 0–50 mm soil layer in both sheep and cattle patches. Due to the larger volume of urine added to the cattle patches (2000 mL for cattle and 200 mL for sheep) the effective application rate was about 5 L m^–2 compared with 4 L m^–2 for sheep. Concentrations of extractable mineral N and ionic concentrations in soil solution were higher in cattle than sheep patches particularly near the soil surface. In both sheep and cattle patches, urea was rapidly hydrolysed to NH ₄ ⁺ and nitrification occurred between 14 and 29 days after urine application. Initially the major anions and cations in the soil solution were HCO ₃ ^– , SO ₄ ⁼ , Cl^–, NH ₄ ⁺ , Mg⁺⁺, K⁺ and Na⁺, which were derived from the urine application. Ionic concentrations in the soil solution decreased appreciably over time due to plant uptake and possibly some leaching. As nitrification proceeded, NO ₃ ^– became the dominant anion in soil solution and the major accompanying cation was Ca⁺⁺. The fate of¹⁵N-labelled urine-urea was followed during a 5 month period beginning in late autumn. Greater leaching losses of NO ₃ ^– occurred below cattle patches (equivalent to 60 kg N ha^–1 below 300 mm and 37 kg N ha^–1 below 600 mm) compared with sheep patches (10 kg N ha^–1 below 300 mm and 1 kg N ha^– below 600 mm). While 6% of the applied¹⁵N was leached the amount of N leached was equivalent to 11% of the applied urine-N in cattle patches. This suggests that there was significant immobilsation-mineralisation turnover in urine patch soil with the release of mineral N from native soil organic matter. In both sheep and cattle patches 60% of the¹⁵N was accounted for in plant uptake, remaining in the soil and leaching. About 40% of the applied N was therefore lost through gaseous emission.