Development and testing of a genetic marker-based pedigree reconstruction system 'PR-genie' incorporating size-class data

For wildlife populations, it is often difficult to determine biological parameters that indicate breeding patterns and population mixing, but knowledge of these parameters is essential for effective management. A pedigree encodes the relationship between individuals and can provide insight into the dynamics of a population over its recent history. Here, we present a method for the reconstruction of pedigrees for wild populations of animals that live long enough to breed multiple times over their lifetime and that have complex or unknown generational structures. Reconstruction was based on microsatellite genotype data along with ancillary biological information: sex and observed body size class as an indicator of relative age of individuals within the population. Using body size-class data to infer relative age has not been considered previously in wildlife genealogy and provides a marked improvement in accuracy of pedigree reconstruction. Body size-class data are particularly useful for wild populations because it is much easier to collect noninvasively than absolute age data. This new pedigree reconstruction system, PR-genie, performs reconstruction using maximum likelihood with optimization driven by the cross-entropy method. We demonstrated pedigree reconstruction performance on simulated populations (comparing reconstructed pedigrees to known true pedigrees) over a wide range of population parameters and under assortative and intergenerational mating schema. Reconstruction accuracy increased with the presence of size-class data and as the amount and quality of genetic data increased. We provide recommendations as to the amount and quality of data necessary to provide insight into detailed familial relationships in a wildlife population using this pedigree reconstruction technique.

Testing the regional genetic representativeness of captive koala populations in South-East Queensland

Context Captive breeding for release back to the wild is an important component of ex situ conservation but requires genetic diversity that is representative of the wild population and has the ultimate goal of producing ecologically sustainable and resilient populations. However, defining and testing for representativeness of captive populations is difficult. Koalas (Phascolarctos cinereus) are bred for educational and tourism purposes in zoos and wildlife parks in South-East Queensland, but there are drastic declines evident in some wild koala populations in this region. Aim We compared genetic diversity at microsatellite loci and mitochondrial DNA in two captive koala populations with that of the local, wild koalas of South-East Queensland, determining the degree to which genetic diversity of neutral loci had been preserved and was represented in the captive populations. Key results The expected heterozygosity and the allelic richness was significantly greater in one captive colony than one wild South-East Queensland population. There was low but significant differentiation of the captive from wild populations using FST, with greater differentiation described by Jost’s Dest. In contrast, a newly introduced Kullback–Leibler divergence measure, which assesses similarity of allele frequencies, showed no significant divergence of colony and wild populations. The captive koalas lacked many of the mitochondrial haplotypes identified from South-East Queensland koalas and possessed seven other haplotypes. Conclusions Captive colonies of koalas have maintained levels of overall neutral genetic diversity similar to wild populations at microsatellite loci and low but significant differentiation likely resulted from drift and founder effects in small captive colonies or declining wild populations. Mitochondrial DNA suggests that captive founders were from a wider geographic source or that haplotypes have been lost locally. Implications Overall, tested captive koalas maintain sufficient microsatellite diversity to act as an in situ reservoir for neutral genetic diversity of regional populations.

A genome-wide analysis of annexins from parasitic organisms and their vectors

In this study, we conduct an in-depth analysis of annexin proteins from a diverse range of invertebrate taxa, including the major groups that contain the parasites and vector organisms that are harmful to humans and domestic animals. Using structure-based amino acid sequence alignments and phylogenetic analyses, we present a classification for this protein group and assign names to sequences with ambiguous annotations in public databases. Our analyses reveal six distinct annexin clades, and the mapping of genes encoding annexins to the genome of the human blood fluke Schistosoma mansoni supports the hypothesis of gene duplication as a major evolutionary event in annexin genesis. This study illuminates annexin diversity from a novel perspective using contemporary phylogenetic hypotheses of eukaryote evolution, and will aid the consolidation of annexin protein identities in public databases and provide a foundation for future functional analysis and characterisation of these proteins in parasites of socioeconomic importance.

Monitoring dolphins in an urban marine system: total and effective population size estimates of Indo-Pacific bottlenose dolphins in Moreton Bay, Australia

Moreton Bay, Queensland, Australia is an area of high biodiversity and conservation value and home to two sympatric sub-populations of Indo-Pacific bottlenose dolphins (Tursiops aduncus). These dolphins live in close proximity to major urban developments. Successful management requires information regarding their abundance. Here, we estimate total and effective population sizes of bottlenose dolphins in Moreton Bay using photo-identification and genetic data collected during boat-based surveys in 2008–2010. Abundance (N) was estimated using open population mark-recapture models based on sighting histories of distinctive individuals. Effective population size (N_e) was estimated using the linkage disequilibrium method based on nuclear genetic data at 20 microsatellite markers in skin samples, and corrected for bias caused by overlapping generations (N_ec). A total of 174 sightings of dolphin groups were recorded and 365 different individuals identified. Over the whole of Moreton Bay, a population size N of 554±22.2 (SE) (95% CI: 510–598) was estimated. The southern bay sub-population was small at an estimated N = 193±6.4 (SE) (95% CI: 181–207), while the North sub-population was more numerous, with 446±56 (SE) (95% CI: 336–556) individuals. The small estimated effective population size of the southern sub-population (N_ec = 56, 95% CI: 33–128) raises conservation concerns. A power analysis suggested that to reliably detect small (5%) declines in size of this population would require substantial survey effort (>4 years of annual mark-recapture surveys) at the precision levels achieved here. To ensure that ecological as well as genetic diversity within this population of bottlenose dolphins is preserved, we consider that North and South sub-populations should be treated as separate management units. Systematic surveys over smaller areas holding locally-adapted sub-populations are suggested as an alternative method for increasing ability to detect abundance trends.

Prevalence of congenital hereditary sensorineural deafness in Australian Cattle Dogs and associations with coat characteristics and sex

Background

Congenital hereditary sensorineural deafness (CHSD) occurs in many dog breeds, including Australian Cattle Dogs. In some breeds, CHSD is associated with a lack of cochlear melanocytes in the stria vascularis, certain coat characteristics, and potentially, abnormalities in neuroepithelial pigment production. This study investigates phenotypic markers for CHSD in 899 Australian Cattle Dogs.

Results

Auditory function was tested in 899 Australian Cattle Dogs in family groups using brainstem auditory evoked response testing. Coat colour and patterns, facial and body markings, gender and parental hearing status were recorded.

Deafness prevalence among all 899 dogs was 10.8% with 7.5% unilaterally deaf, and 3.3% bilaterally deaf, and amongst pups from completely tested litters (n = 696) was 11.1%, with 7.5% unilaterally deaf, and 3.6% bilaterally deaf.

Univariable and multivariable analyses revealed a negative association between deafness and bilateral facial masks (odds ratio 0.2; P ≤ 0.001). Using multivariable logistic animal modelling, the risk of deafness was lower in dogs with pigmented body spots (odds ratio 0.4; P = 0.050).

No significant associations were found between deafness and coat colour.

Within unilaterally deaf dogs with unilateral facial masks, no association was observed between the side of deafness and side of mask. The side of unilateral deafness was not significantly clustered amongst unilaterally deaf dogs from the same litter. Females were at increased risk of deafness (odds ratio from a logistic animal model 1.9; P = 0.034) after adjusting for any confounding by mask type and pigmented body spots.

Conclusions

Australian Cattle Dogs suffer from CHSD, and this disease is more common in dogs with mask-free faces, and in those without pigmented body patches. In unilaterally deaf dogs with unilateral masks, the lack of observed association between side of deafness and side of mask suggests that if CHSD is due to defects in molecular pigment pathways, the molecular control of embryonic melanoblast migration from ectoderm to skin differs from control of migration from ectoderm to cochlea. In Australian Cattle Dogs, CHSD may be more common in females.

Species boundaries and possible hybridization between the black mongoose (Galerella nigrata) and the slender mongoose (Galerella sanguinea)

Major climatic oscillations since the mid-Miocene climatic optimum are known to have played a key role in promoting speciation events. In this study we use molecular data to elucidate the evolutionary history of Galerella nigrata and link its divergence to known major climatic events. A total of 51 samples from G. nigrata and 17 from Galerella sanguinea were used to provide the first molecular evidence that G. nigrata may be a species in its own right. Both mitochondrial cytochrome b and the nuclear ß-fibrinogen intron seven sequences of G. nigrata form distinct monophyletic clades, separate from its sister species G. sanguinea. We estimate the divergence of these two species to have occurred 3.85-4.27 million years ago, coinciding with a period of the Plio-Pleistocene that was characterised by cooling global temperatures and strong aridity in southern Africa. However, evidence for potential hybridization between the two species was documented for ten individuals using phenotypic (pelage colouration) and/or molecular (nuclear and mtDNA sequences and microsatellite loci) data. There appeared to be a bias towards unidirectional hybridization with all potential hybrids showing mtDNA haplotypes from G. nigrata. We suggest that as the desert expanded across Namibia, G. sanguinea likely retreated with the savanna, leaving some mongooses stranded on the granite inselbergs of north-western Namibia. Subsequent adaptation of these mongooses to local conditions on granite inselbergs could have led to ecological speciation. Secondary contact zones would have been re-established with subsequent global warming events. It appears that the two species have not yet undergone complete reproductive isolation.

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small-scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine-scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F(ST) = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite-based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ(ST) = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine-scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter-related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine-scale population structure among bottlenose dolphins in Moreton Bay.

Genetic diversity in natural and introduced island populations of koalas in Queensland

Island populations of animals are expected to show reduced genetic variation and increased incidence of inbreeding because of founder effects and the susceptibility of small populations to the effects of genetic drift. Koalas (Phascolarctos cinereus) occur naturally in a patchy distribution across much of the eastern Australian mainland and on a small number of islands near the Australian coast. We compared the genetic diversity of the naturally occurring population of koalas on North Stradbroke Island in south-east Queensland with other island populations including the introduced group on St Bees Island in central Queensland. The population on St Bees Island shows higher diversity (allelic richness 4.1, He = 0.67) than the North Stradbroke Island population (allelic richness 3.2, He = 0.55). Koalas on Brampton, Newry and Rabbit Islands possessed microsatellite alleles that were not identified from St Bees Island koalas, indicating that it is most unlikely that these populations were established by a sole secondary introduction from St Bees Island. Mitochondrial haplotypes on the central Queensland islands were more similar to a haplotype found at Springsure in central Queensland and the inland clades in south-east Queensland, rather than the coastal clade in south-east Queensland.

Congenital sensorineural deafness in Australian stumpy-tail cattle dogs is an autosomal recessive trait that maps to CFA10

Background

Congenital sensorineural deafness is an inherited condition found in many dog breeds, including Australian Stumpy-tail Cattle Dogs (ASCD). This deafness is evident in young pups and may affect one ear (unilateral) or both ears (bilateral). The genetic locus/loci involved is unknown for all dog breeds. The aims of this study were to determine incidence, inheritance mechanism, and possible association of congenital sensorineural deafness with coat colour in ASCD and to identify the genetic locus underpinning this disease.

Methodology/Principal Findings

A total of 315 ASCD were tested for sensorineural deafness using the brain stem auditory evoked response (BAER) test. Disease penetrance was estimated directly, using the ratio of unilaterally to bilaterally deaf dogs, and segregation analysis was performed using Mendel. A complete genome screen was undertaken using 325 microsatellites spread throughout the genome, on a pedigree of 50 BAER tested ASCD in which deafness was segregating. Fifty-six dogs (17.8%) were deaf, with 17 bilaterally and 39 unilaterally deaf. Unilaterally deaf dogs showed no significant left/right bias (p = 0.19) and no significant difference was observed in frequencies between the sexes (p = 0.18). Penetrance of deafness was estimated as 0.72. Testing the association of red/blue coat colour and deafness without accounting for pedigree structure showed that red dogs were 1.8 times more likely to be deaf (p = 0.045). The within family association between red/blue coat colour and deafness was strongly significant (p = 0.00036), with red coat colour segregating more frequently with deafness (COR = 0.48). The relationship between deafness and coat speckling approached significance (p = 0.07), with the lack of statistical significance possibly due to only four families co-segregating for both deafness and speckling. The deafness phenotype was mapped to CFA10 (maximum linkage peak on CFA10 −log10 p-value = 3.64), as was both coat colour and speckling. Fine mapping was then performed on 45 of these 50 dogs and a further 48 dogs (n = 93). Sequencing candidate gene Sox10 in 6 hearing ASCD, 2 unilaterally deaf ASCD and 2 bilaterally deaf ASCD did not reveal any disease-associated mutations.

Conclusions

Deafness in ASCD is an incompletely penetrant autosomal recessive inherited disease that maps to CFA10.

Multiple paternity in Rhipicephalus (Boophilus) microplus confirmed by microsatellite analysis

The aim of this study was to determine if individual ticks among the progeny of a single female Rhipicephalus (Boophilus) microplus tick removed from cattle under natural conditions are the result of mating with one or several males. To this end, simulations were run using an existing dataset of genotypes from 8 microsatellite loci to predict the number of samples required and the best locus. Subsequently, 14-22 progeny from each of 15 engorged female ticks removed from three cows, and the engorged females themselves, were genotyped for the BmM1 locus and the minimum number of potential male parents was determined for each progeny group. Of the 15 progeny groups, 10 must have been sired by more than one male, as indicated by the presence of five unique alleles among the progeny or three unique alleles that could not have been contributed by the female. This finding demonstrates multiple paternity in R. microplus.

Spectral domain optical coherence tomography for quantitative evaluation of drusen and associated structural changes in non-neovascular age-related macular degeneration

Background/aims:

To demonstrate how spectral domain optical coherence tomography (SDOCT) can better evaluate drusen and associated anatomical changes in eyes with non-neovascular age-related macular degeneration (AMD) compared with time domain optical coherence tomography (TDOCT).

Methods:

Images were obtained from three eyes of three patients with AMD using an experimental SDOCT system. Both a titanium–sapphire (Ti:sapphire) laser and a superluminescent diode (SLD) were used as a broadband light source to achieve cross-sectional images of the retina. A qualitative and quantitative analysis was performed for structural changes associated with non-neovascular AMD. An automated algorithm was developed to analyse drusen area and volume from SDOCT images. TDOCT was performed using the fast macular scan (StratusOCT, Carl Zeiss Meditec, Dublin, California).

Results:

SDOCT images can demonstrate structural changes associated with non-neovascular AMD. A new SDOCT algorithm can determine drusen area, drusen volume and proportion of drusen.

Conclusions:

With new algorithms to determine drusen area and volume and its unprecedented simultaneous ultra-high speed ultra-high resolution imaging, SDOCT can improve the evaluation of structural abnormalities in non-neovascular AMD.

Genetic heterogeneity of day blindness in Alaskan Malamutes

Day blindness is a progressive and specific degeneration of cone photoreceptors in the retina of young dogs. This disorder has been associated with a breed-specific non-synonymous substitution in exon 6 of the cyclic nucleotide gated channel beta3 (CNGB3) gene in German Shorthaired Pointer dogs and a genomic deletion removing the entire gene in Alaskan Malamute dogs from the USA. To further investigate this disorder, we characterized CNGB3 in a three-generation pedigree of Alaskan Malamute dogs from Australia segregating for day blindness. Fifteen of the dogs showed clinical signs of day blindness. Four of these were definitively diagnosed by standardized electroretinography. Polymerase chain reaction amplification of exon 6 of CNGB3 was attempted, and as expected, amplification was successful in the 18 unaffected or carrier dogs. However, a non-mutated exon 6 was also amplified and sequenced in six of the 15 affected dogs. On sequencing each exon and exon/intron boundary in two such affected individuals and two unaffected individuals, three exonic substitutions and 12 intronic changes were noted. These sequence variations in affected individuals were also present in one or both unaffected dogs and so appear to have no obvious effect on the protein's function. Hence, day blindness shows genetic heterogeneity within the Alaskan Malamute population of Australia, a result that is somewhat unexpected given the relatively small effective population size of this breed.

Inverse lyotropic phases of lipids and membrane curvature

In recent years it has become evident that many biological functions and processes are associated with the adoption by cellular membranes of complex geometries, at least locally. In this paper, we initially discuss the range of self-assembled structures that lipids, the building blocks of biological membranes, may form, focusing specifically on the inverse lyotropic phases of negative interfacial mean curvature. We describe the roles of curvature elasticity and packing frustration in controlling the stability of these inverse phases, and the experimental determination of the spontaneous curvature and the curvature elastic parameters. We discuss how the lyotropic phase behaviour can be tuned by the addition of compounds such as long-chain alkanes, which can relieve packing frustration. The latter section of the paper elaborates further on the structure, geometric properties, and stability of the inverse bicontinuous cubic phases.

Molecular subtyping of feline immunodeficiency virus from domestic cats in Australia

OBJECTIVE

To determine the prevalent subtypes of feline immunodeficiency virus (FIV) present in the domestic cat population of Australia.

METHOD

Blood samples were collected from 41 FIV antibody positive cats from four cities across Australia. Following DNA extraction, polymerase chain reaction (PCR) was performed to amplify the variable V3-V5 region of the envelope (env) gene. Genotypes were assessed by direct sequencing of PCR products and comparison with previously reported FIV sequences. Phylogenetic analysis allowed classification of the Australian sequences into the appropriate subtype.

RESULTS

Of the 41 FIV samples, 40 were found to cluster with previously reported subtype A isolates, whilst the remaining sample grouped within subtype B.

CONCLUSIONS

Subtype A was found to be the predominant FIV subtype present in Australia, although subtype B was also found. These results broaden our knowledge of the genetic diversity of FIV and the associated implications for preventative, diagnostic and therapeutic approaches.

Understanding the phylogeographic patterns of European hedgehogs, Erinaceus concolor and E. europaeus using the MHC

The genome of the European hedgehog, Erinaceus concolor and E. europaeus, shows a strong signal of cycles of restriction to glacial refugia and postglacial expansion. Patterns of expansion, however, differ for mitochondrial DNA (mtDNA) and preliminary analysis of nuclear markers. In this study, we determine phylogeographic patterns in the hedgehog using two loci of the major histocompatibility complex (MHC), isolated for the first time in hedgehogs. These genes show long persistence times and high polymorphism in many species because of the actions of balancing selection. Among 84 individuals screened for variation, only two DQA alleles were identified in each species, but 10 DQB alleles were found in E. concolor and six in E. europaeus. A strong effect of demography on patterns of DQB variability is observed, with only weak evidence of balancing selection. While data from mtDNA clearly subdivide both species into monophyletic subgroups, the MHC data delineate only E. concolor into distinct subgroups, supporting the preliminary findings of other nuclear markers. Together with differences in variability, this suggests that the refugia history and/or expansion patterns of E. concolor and E. europaeus differ.

Kinetics and mechanism of the interconversion of inverse bicontinuous cubic mesophases

This paper describes time-resolved x-ray diffraction data monitoring the transformation of one inverse bicontinuous cubic mesophase into another, in a hydrated lipid system. The first section of the paper describes a mechanism for the transformation that conserves the topology of the bilayer, based on the work of Charvolin and Sadoc, Fogden and Hyde, and Benedicto and O'Brien in this area. We show a pictorial representation of this mechanism, in terms of both the water channels and the lipid bilayer. The second section describes the experimental results obtained. The system under investigation was 2:1 lauric acid: dilauroylphosphatidylcholine at a hydration of 50% water by weight. A pressure-jump was used to induce a phase transition from the gyroid (Q(G)(II)) to the diamond (Q(D)(II)) bicontinuous cubic mesophase, which was monitored by time-resolved x-ray diffraction. The lattice parameter of both mesophases was found to decrease slightly throughout the transformation, but at the stage where the Q (D)(II) phase first appeared, the ratio of lattice parameters of the two phases was found to be approximately constant for all pressure-jump experiments. The value is consistent with a topology-preserving mechanism. However, the polydomain nature of our sample prevents us from confirming that the specific pathway is that described in the first section of the paper. Our data also reveal signals from two different intermediate structures, one of which we have identified as the inverse hexagonal (H(II)) mesophase. We suggest that it plays a role in the transfer of water during the transformation. The rate of the phase transition was found to increase with both temperature and pressure-jump amplitude, and its time scale varied from the order of seconds to minutes, depending on the conditions employed.

SNPs in ecological and conservation studies: a test in the Scandinavian wolf population

Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.

MHC promoter polymorphism in grey wolves and domestic dogs

A functional immune system requires a tight control over major histocompatibility complex (MHC) gene transcription, as the abnormal MHC expression patterns of severe immunodeficiency and autoimmune diseases demonstrate. Although the regulation of MHC expression has been well documented in humans and mice, little is known in other species. In this study, we detail the level of polymorphism in wolf and dog MHC gene promoters. The promoter regions of the DRB, DQA and DQB locus were sequenced in 90 wolves and 90 dogs. The level of polymorphism was high in the DQB promoters, with variation found within functionally relevant regions, including binding sites for transcription factors. Clear associations between DQB promoters and exon 2 alleles were noted in wolves, indicating strong linkage disequilibrium in this region. Low levels of polymorphism were found within the DRB and DQA promoter regions. However, a variable site was identified within the T box, a TNF-alpha response element, of the DQA promoter. Furthermore, we identified a previously unrecognised 18-base-pair deletion within exon 1 of the DQB locus.

A temporal analysis shows major histocompatibility complex loci in the Scandinavian wolf population are consistent with neutral evolution

The major histocompatibility complex (MHC) has an integral role in the immune system, and hence diversity at its genes may be of particular importance for the health of populations. In large populations, balancing selection maintains diversity in MHC genes, but theoretical expectations indicate that this form of selection is absent or inefficient in small populations. We examine the level of diversity at three MHC class II loci in the wolf population of Scandinavia, a population naturally recolonized with a genetic contribution from as few as three founders, and in four neighbouring wolf populations. In the Scandinavian wolf population, two alleles were found for each locus and the distribution of alleles is compatible with their linkage into two haplotypes. Changes in the level of heterozygosity over time since recolonization demonstrate the effects of the proposed arrival of an immigrant wolf. The maintenance of diversity is shown to be compatible with a neutral, random allocation of alleles, in conjunction with crossing between packs. A total of 15 DRB1, seven DQA and 10 DQB1 alleles are found in four neighbouring wolf populations, with substantial sharing across populations. Even in these larger populations, bottlenecks and fragmentation with consequent genetic drift are likely to have resulted in few indicators for balancing selection and significant differentiation of populations.