No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Genetic variability of seven dog breeds based on microsatellite markers
Abstract
The present study, compared the genetic variability of seven dog breeds and a test sample from Switzerland by means of 26 microsatellite markers. Five loci were excluded from further analyses because one was monomorphic, one not in Hardy-Weinberg equilibrium in all breeds and three in linkage disequilibrium with linked loci. The proportion of shared alleles at the individual level of the remaining 21 microsatellite markers combined with the neighbour-joining method allowed for the clustering of the large majority of the individuals in accordance to their breed. The results were confirmed by analyses using a Bayesian approach for clustering and a Monte Carlo re-sampling method for individual assignment or exclusion to a given population.
... Evolutionary analyzes based on the comparison of mitochondrial DNA suggest that the dog diverged from the wolf (Canis lupus) more than 15,000 years ago [6], although the establishment as a domestic dog is a result of a small number of individuals domesticated [7,8] and despite this, from an intense selection, especially in the last 300 years, it was observed the creation of more than 400 distinct breeds, being dog, the most morphologicaly variable between the domestic species [6,9]. Although initially canine breeds have been developed from a specific aptitude (hunting, guarding, grazing, etc.), they are currently being selected, mainly due to esthetic parameters, from extremely endogenous genetic selection [10]. ...
... Evolutionary analyzes based on the comparison of mitochondrial DNA suggest that the dog diverged from the wolf (Canis lupus) more than 15,000 years ago [6], although the establishment as a domestic dog is a result of a small number of individuals domesticated [7,8] and despite this, from an intense selection, especially in the last 300 years, it was observed the creation of more than 400 distinct breeds, being dog, the most morphologicaly variable between the domestic species [6,9]. Although initially canine breeds have been developed from a specific aptitude (hunting, guarding, grazing, etc.), they are currently being selected, mainly due to esthetic parameters, from extremely endogenous genetic selection [10]. ...
... Although all canine breeds have common ancestors, during their development and even today, extremely endogenous genetic selections are performed in order to fix desirable phenotypic or behavioral characteristics [6,10,11]. Thus, the genetic proximity and the degree of inbreeding observed among dogs of the same breed may influence the in vitro quality of the thawed semen through the fixation of individual characteristics associated to increase or decrease of the survival of the spermatozoa to the freezing process. The genetics of a breed is generally determined by the genetics of its actual founders, who are individuals belonging to the total population of founders but who have made the greatest contribution to the formation of the present population through a large number of descendants [11]. ...
The present work aims to report the individual and racial difference found in the freezing of canine semen, as well as to analyze the correlation of the parameters of in vitro evaluation of semen before and after freezing. For this, 36 ejaculates were collected of 12 dogs of the Beagle, schnauzer, Doberman and Boxer breeds, by the digital manipulation method and frozen in Tris-Citrate medium containing 6% of glycerol. Semen was evaluated, before and after freezing, on sperm movement through vigor, motility and spermatic index, and on the integrity and viability of the spermatic membrane by hypoosmotic and supravital staining tests. Sperm longevity was estimated in the thawed semen through the thermoresistance test. Individual variation was observed on spermatic index in the thawed semen, but not in the fresh. The parameters of spermatic membrane integrity and viability presented individual variation in both. When the breed variable is considered was not observed significant differences on parameters in the fresh semen, but in the thawed semen significant variations in the integrity and viability of the sperm membrane were observed. Schnauzers had the lowest sperm longevity after thawing. As Doberman and Boxer breeds presented the best freezing results in the in vitro evaluation. Except for the supravital staining test, the parameters studied showed significant correlations between the data collected in the fresh semen and those observed in the thawed semen.
... Furthermore, separate lineages within a breed can be formed by selection for different sizes, coat colours or for performance vs. show features. This disruptive selection can lead to distinct genetic clustering within a breed, as recently shown for poodle (Björnerfeldt et al. 2008) and dachshund (Schelling et al. 2005). ...
... Although phenotypic similarities in morphology and behaviour are good predictors of the affiliation of individual purebred dogs to their specific breed, we demonstrate, in accordance with other studies (e.g. Schelling et al. 2005;Quignon et al. 2007;Björnerfeldt et al. 2008;Chang et al. 2009), that the number of genetic clusters of dogs may be considerably larger than the number of recognized breeds. ...
As a result of strong artificial selection, the domesticated dog has arguably become one of the most morphologically diverse vertebrate species, which is mirrored in the classification of around 400 different breeds. To test the influence of breeding history on the genetic structure and variability of today's dog breeds, we investigated 12 dog breeds using a set of 19 microsatellite markers from a total of 597 individuals with about 50 individuals analysed per breed. High genetic diversity was noted over all breeds, with the ancient Asian breeds (Akita, Chow Chow, Shar Pei) exhibiting the highest variability, as was indicated chiefly by an extraordinarily high number of rare and private alleles. Using a Bayesian clustering method, we detected significant genetic stratification within the closely related Schnauzer breeds. The individuals of these three recently differentiated breeds (Miniature, Standard and Giant Schnauzer) could not be assigned to a single cluster each. This hidden genetic structure was probably caused by assortative mating owing to breeders' preferences regarding coat colour types and the underlying practice of breeding in separate lineages. Such processes of strong artificial disruptive selection for different morphological traits in isolated and relatively small lineages can result in the rapid creation of new dog types and potentially new breeds and represent a unique opportunity to study the evolution of genetic and morphological differences in recently diverged populations.
... A Bayesian approach developed by Pritchard et al. (2000) constitutes another method, which assigns populations and animals to some clusters. It has already been used in some studies on dog (Parker et al. 2004Parker et al. , 2007 Schelling et al. 2005; VeitKensch et al. 2007). Some other methods have also been proposed to assess whether breeds constitute genetically differentiated structures, by testing assignation of animals to their own breed (Piry et al. 2004). ...
... In this case, for each animal, assignment can be compared to simulations, which allows excluding the animal from a breed if it is found to be more ÔdistantÕ from the breed than a chosen proportion of simulated individuals (type I error). These methods have already been used in the dog (Koskinen 2003; Parker et al. 2004; Schelling et al. 2005). To study conservation priorities across breeds, following the Weitzman (1992) approach, it is possible to estimate the contribution of a given breed to the diversity of a whole set of breeds (Caballero & Toro 2002; Simianer et al. 2003). ...
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.
... This process results in a rapid random genetic drift and unique allele frequencies. Consequently, attempts to reconstruct the relationship between breeds based on their allelic composition34528,29] are likely to have been heavily influenced by such random effects (Figure 3) and may not necessarily reflect true breed history. For example, our results suggest that, for neutral genetic markers , standard poodles are as differentiated from black and brown medium sized poodles as from giant schnauzers or Siberian huskies (Table 2 ). ...
... The situation observed in this study for the poodles, intra-breed structure , may be present in other breeds as well, as suggested by the large inbreeding coefficient in some of the breeds (Table 3), consistent with population fragmentation [30]. Similarly, Schelling, Gaillard and Dolf [29] observed that while longhaired and smooth dachshunds were genetically similar, wirehaired dachshunds clustered separately in a phylogenetic tree. For some breeds such as German shepherds, Siberian huskies and Labrador retrievers, two different lines of selection are maintained within the breed, separating animals intended for competition in dog shows for their appearance, and animals selected for work. ...
There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds.
Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds.
The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds.
... Often, the practice of restrictive breeding has led to a decrease in effective population size and increased genetic drift, leading to a loss of genetic diversity within breeds (Parker et al. 2004). Various studies have shown that the analysis of nuclear microsatellite loci can be of great benefit for studying the origin and phylogenetic relationships of domestic dog breeds, given their high variability that allows insight into allele frequency divergence through drift (Zajc et al. 1997;Koskinen and Bredbacka 2000;Kim et al. 2001;Irion et al. 2005;Schelling et al. 2005;Parra et al. 2008 (Katica et al. 2004Softić et al. 2006), reproductive capacity Salkić et al. 2006), and genetic diversity (Softić et al. 2016) of this autochthonous breed. ...
Fédération Cynologique Internationale (FCI) classifies a group of hound dogs in the sixth FCI group divided into three sections and three subsections that include 76 dog breeds. With the Istrian wire-haired hound, the Bosnian broken-haired hound—Barak is one of the two internationally recognized and standardized broken-haired hound breeds from the Balkans. However, genotyping of this breed has not been the subject of study so far. A total of 30 dogs (22 males and eight females) from different breeders from 17 locations in Bosnia and Herzegovina were selected for genotyping. All selected individuals had a valid pedigree issued by the Kennel Club in Bosnia and Herzegovina to ensure dogs were unrelated. Hairs with follicles were used for DNA extraction. Ten microsatellite loci from the commercial StockMarks® for Canine Genotyping Kit were amplified. Estimated genetic indices showed that Bosnian broken-haired hound—Barak harbors a high genetic variability. Phylogenetic relationships between Barak and the other 15 dog breeds, including Tornjak, another indigenous breed from Bosnia and Herzegovina, were assessed. An analysis showed clear differentiation of Barak, with Tornjak as the closest one among analyzed breeds. The results suggest that Barak, as we know it today, was developed during the formation of most modern breeds. Although Barak cannot yet be considered an endangered breed thanks to enthusiasts and hunters, the declining population trends impose the urgent need to establish an animal gene bank and programs for in situ conservation to protect and preserve this autochthonous breed of hound dog for future generations.
... Short tandem repeats panels involving breed traits rather than parentage panels exist but have not been standardised according to the recommendations of the IFSG, ISAG, or SWGWILD. Previous studies have used either quite a broad dog demographic representing all groups of the predominating kennel club of the region under study when assigning individuals to their breed or have tailored their studies to specific dog breeds (Koskinen, 2003;Leroy et al., 2009;Parra et al., 2008;Pires et al., 2009;Schelling et al., 2005;Sundqvist et al., 2008;Veit-Kensch et al., 2007). STRs may not be suitable for use when prosecuting individuals without further standardisation of the pipeline used. ...
This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost‐effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost‐effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.
... Yet, some of these undesirable traits may have resulted from rapid phenotypic selection wherein each breed was generated from multiple origins with a historical gene flow (Bigi et al., 2015;Boldura et al., 2017;Koskinen & Bredbacka, 2000;Parra et al., 2008;Shinkarenko et al., 2010). Likewise, genetic diversity, differentiation and the genetic structure of different dog breeds have routinely been evaluated based on mitochondrial DNA (Suarez et al., 2012), single nucleotide polymorphism (SNPs) (Boyko et al., 2010;Shannon et al., 2015) and nuclear microsatellites (Bigi et al., 2018;Bigi et al., 2015;Irion et al., 2003;Irion et al., 2005;Kim et al., 2001;Lee, Choi & Cho, 2014;Mellanby et al., 2013;Parker et al., 2004;Pedersen et al., 2013;Schelling, Gaillard & Dolf, 2005;Shinkarenko et al., 2010). ...
The identification of differing physical characteristics of dogs is an uncomplicated and straightforward way to categorize dog breeds. However, many dog owners and veterinarians still struggle to distinguish between pure breed and mixed variations in certain breeds of dogs. Presently, the absence of the tools and methods needed to confirm a pure breed dog is a significant problem since the only method available to validate pure or mongrel breeds is the official pedigree system. Inter-simple sequence repeat markers have been successfully used to assess genetic variations and differentiations. Notably, inter-simple sequence repeat markers coupled with high resolution melting analysis were effectively used for the breed identification of 43 breeds of dogs (total 463 dogs). The 10 primers chosen for analysis resulted in a range of 31-78.6% of breed discrimination when using one primer, while a combination of two primers was able to successfully discriminate between all of the 43 dog breeds (100%). Shannon's index information (I = 2.586 ± 0.034) and expected heterozygosity (H
e
= 0.908 ± 0.003) indicated a high level of genetic diversity among breeds. The fixation index (F
st
) revealed a value of 10.4%, demonstrating that there was a high level of genetic subdivision between populations. This study showed that inter-simple sequence repeat marker analysis was effective in demonstrating high genetic diversity among varying breeds of dogs, while a combination of Inter-simple sequence repeat marker analysis and high resolution melting analysis could provide an optional technique for researchers to effectively identify breeds through genetic variations.
... Currently, to assess genetic variability in dogs' populations, analysis based on nuclear or mitochondrial DNA (mtD--NA) are used. These analyzes include i.a.: polymorphism analysis of the mitochondrial control region of DNA (Okumura et al. 1996, 1998, 1999, Webb et al. 2009, Sindičić et al. 2011, Sugiyama et al. 2013, microsatellite length polymorphism analyzes (Koskinen and Bred-backa 2000, Kim et al. 2001, Irion et al. 2003, Schelling et al. 2004, Cho 2005, Ye et al. 2009, Phavaphutanon and Laop 2011, and analysis of coding sequences (Niimi et al. 2001). ...
In the following paper the genetic distance among selected Japanese dog breeds (Akita, Ki-shu, Kai, Shiba, Shikoku, Hokkaido) was estimated. In order to determine genetic differentiation we analyzed a fragment of the mitochondrial control region and 10 micro-satellite loci. We found that variation of the nuclear DNA was larger than that at the level of mitochondrial DNA. Within a fragment of 614 bp of control region, 13 haplotypes were identified. The highest diversity of mitochondrial DNA was found in Akita. Based on mitochondrial DNA analysis, genetic distance between breeds ranged from 0.003 to 0.018. The lowest genetic distance was observed between Shikoku and Kai (0.003), and the highest between Shiba and Akita (0.018). After the analysis of nuclear DNA, 65 alleles were identified. The mean percentage of polymorphic alleles in the applied microsatellite markers was 94.4% ±2.5%. The analysis showed that, the highest distance estimated on the frequency of microsatellite markers was found between Kai and Hokkaido (1.066), and the lowest between Shiba and Kai (0.212). Hokkaido and Shikoku were the only clearly distinguishing breeds.
... Yet for populations to maintain good health, they need genetic diversity. A number of studies have evaluated diversity and the structure of dog populations (Koskinen and Bredbacka 2000;Irion et al. 2003;Parker et al. 2004;Lupke and Distl 2005;Schelling, Gaillard and Dolf 2005). A common recommendation from these studies is to ensure adequate effective population sizes and prevent further loss of diversity. ...
Influential parts of the veterinary profession, and notably the American Veterinary Medicine Association, are promoting the routine neutering of cats and dogs that will not be used for breeding purposes. However , this view is not universally held, even among representatives of the veterinary profession. In particular, some veterinary associations in Europe defend the view that when reproduction is not an issue, then neutering, particularly of dogs, should be decided on a case-by-case basis. However, even in Europe the American view is gaining ground. In light of this situation, this paper considers whether or not routine neutering of cats and dogs, in cases where uncontrolled reproduction is not an issue, can be ethically defended. The starting point of this consideration is a review of the veterinary literature on the effects of neutering on companion animals. The focus is both on the welfare of neutered animals themselves, and on behavioral and other effects that may not directly affect the animals' welfare, but that may be motivating factors for owners to neuter their companion animals. Here it becomes clear that justification for routine neutering, particularly of confined male dogs, does not follow from claims about the dogs' own welfare. The costs of neutering male dogs, in terms of the increased risk of very serious diseases, may well outweigh the benefits. Then, building on this veterinary material, but including some other, additional considerations, the paper goes through some possible ethical approaches to routine animal neutering. These ethical approaches offer different degrees of concern about, or opposition to, routine neutering. Finally, based on this ethical exploration, it is argued that routine neutering, at least in the case of non-free-ranging companion animals, raises significant ethical questions, and from some ethical perspectives, looks highly problematic.
... Many methods of assignment testing have been developed using a variety of both genetic markers and statistical methods (Paetkau et al. 1995;Rannala & Mountain 1997;Pritchard et al. 2000;Baudouin & Lebrun 2001). These techniques have been applied to various breeding populations including pigs, cattle and dogs (Schelling et al. 2005;Negrini et al. 2009;Boitard et al. 2010). In cattle, Negrini et al. (2009) used 90 SNPs to both allocate and then assign 24 breeds under both the Bayesian methods of Pritchard et al. (2000), Rannala & Mountain (1997) and Baudouin & Lebrun (2001), and the likelihood method of Paetkau et al. (1995). ...
Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also in the historical origins of common household cats. The cat fancy is a relatively new institution with over 85% of its 40-50 breeds arising only in the past 75 years, primarily through selection on single-gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker-based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, that is, race.
... Cluster and principal component scatter plot analysis structure software is regarded as an ideal analytical tool for studying population genetic structure with many successes (Collins-Schramm et al. 2004;Heidi et al. 2004;Ibeagha-Awemu & Erhardt 2005;Schelling et al. 2005). The analysis presumes that every individual in any group has the same ancestor and estimates the probability of individuals in the group. ...
The genetic diversity and phylogenetic survey of native sheep breeds in the eastern and southern Central Asia were assessed in the present study. The clustering, principal components, structure and F statistics all demonstrate that the native sheep breeds in these regions be classified into two genetic groups: Mongolia-Tibetan sheep group and South-Southeast Asia sheep group. The Mongolia sheep group and the Tibetan sheep group had a certain degree of gene communication from the ancient times. In the present study we demonstrated that the Chinese native sheep populations belonged to Mongolia-Tibetan sheep group. However, the relationships among the sheep populations in Mongolia sheep group in China were not closely related to the geographical distance among sheep populations.
Genetic structure and breeding practices in dog species were investigated in order to develop some management tools for dog breeds in France. Three approaches were therefore used: surveys, genealogical analysis, and polymorphism of microsatellite markers. Nine-hundred eighty-five breeders, either hobby or professional, answered a questionnaire about their breeding practices. It showed some differences according to the breed raised or the status of the breeder. Pedigree analysis results realised on 61 breeds were in agreement with these results, practices and situations dealing with genetic diversity, with some results being quite different depending on the breeds. According to genealogical data, a low genetic diversity was found in some breeds. The results using molecular markers based on a sampling of 1514 dogs of the same breeds were sometimes in contradiction with pedigree analysis, which can be explained by the inherent specificities of both approaches. However, at the individual scale, correlations between genealogical kinship and molecular similarities were always significant. The analysis of genetic breed relationships confirmed the fact that breeds constitute homogeneous genetic groups, with 98.3% of dogs being correctly assigned in their breed. From this last result, some practical applications could be developed to establish policies for the management of genetic variability within breeds.
Genetic structure and breeding practices in dog species were investigated in order to develop some management tools for dog breeds in France. Three approaches were therefore used: surveys, genealogical analysis, and polymorphism of microsatellite markers. Nine-hundred eighty-five breeders, either hobby or professional, answered a questionnaire about their breeding practices. It showed some differences according to the breed raised or the status of the breeder. Pedigree analysis results realised on 61 breeds were in agreement with these results, practices and situations dealing with genetic diversity, with some results being quite different depending on the breeds. According to genealogical data, a low genetic diversity was found in some breeds. The results using molecular markers based on a sampling of 1514 dogs of the same breeds were sometimes in contradiction with pedigree analysis, which can be explained by the inherent specificities of both approaches. However, at the individual scale, correlations between genealogical kinship and molecular similarities were always significant. The analysis of genetic breed relationships confirmed the fact that breeds constitute homogeneous genetic groups, with 98.3% of dogs being correctly assigned in their breed. From this last result, some practical applications could be developed to establish policies for the management of genetic variability within breeds.
Pedigree data of nine French dog breeds, namely Barbet (BAR), Basset fauve de Bretagne (BAF), Beauceron (BEN), Berger des Pyrénées (BRP), Bouledogue Français (BUF), Braque Saint-Germain (BQG), Dogue de Bordeaux (DOB), Epagneul Breton (EPB) and Montagne des Pyrénées (MOP), were analysed. The effective numbers of ancestors of dogs born from 1997 to 2001 were equal to 6.7 (BAR), 40.2 (BAF), 36.5 (BEN), 16.0 (BRP), 37.0 (BUF), 13.1 (BQG), 28.9 (DOB), 33.3 (EPB) and 34.0 (MOP). The expected contributions of the major ancestors were found to be highly unbalanced in the EPB and BRP. The average coefficient of inbreeding of dogs born from 1997 to 2001 with both parents known was equal to 12.4% (BAR), 3.9% (BAF), 5.4% (BEN), 7.2% (BRP), 3.3% (BUF), 6.0% (BQG), 4.1% (DOB), 4.5% (EPB) and 4.0% (MOP). These values were found to be significantly higher than the average coefficient of kinship between the male and the female parents of these animals, except in the BAR and BQG, revealing an usual practice of mating between related animals. The results are discussed in relation with the demographic situation and the use of each breed. The method used to class an endangered breed and the ways to preserve the genetic variability, when necessary, are evoked.
Abstract The Italian wolf is in the process of regaining the Alpine region which comes into conflict with the extensive sheep keeping practiced in Switzerland during the summer. As in Switzerland, the wolf is a protected species, the government reimburses losses caused by wolves. Therefore we wanted to know whether the Italian wolf could be distinguished from the domestic dog by microsatellite analysis if DNA samples of the predators could be secured. The evaluation of combined genotypes for the microsatellites CanBern6, CPH4, CPH7, CPH9, CPH12, CPH22 and ZuBeCa1 made it possible to identify an individual as either a domestic dog or an Italian wolf. The assignment of an individual to either one of the two populations is based on the logarithm of the likelihood ratio of an individual being an Italian wolf rather than a domestic dog, given a specific combined genotype. The distribution of the Italian wolf combined genotypes (n = 42) is clearly distinct from the distribution of the domestic dog combined genotypes (n = 90). The likelihood ratio for the "worst" Italian wolf combined genotype was 2.3 E+5 and for the "worst" domestic dog combined genotype was 3.8 E-5.
Genetic variation at hypervariable loci is being used extensively for linkage analysis and individual identification, and may be useful for inter-population studies. Here we show that polymorphic microsatellites (primarily CA repeats) allow trees of human individuals to be constructed that reflect their geographic origin with remarkable accuracy. This is achieved by the analysis of a large number of loci for each individual, in spite of the small variations in allele frequencies existing between populations. Reliable evolutionary relationships could also be established in comparisons among human populations but not among great ape species, probably because of constraints on allele length variation. Among human populations, diversity of microsatellites is highest in Africa, which is in contrast to other nuclear markers and supports the hypothesis of an African origin for humans.
Mitochondrial DNA control region sequences were analyzed from 162 wolves at 27 localities worldwide and from 140 domestic
dogs representing 67 breeds. Sequences from both dogs and wolves showed considerable diversity and supported the hypothesis
that wolves were the ancestors of dogs. Most dog sequences belonged to a divergent monophyletic clade sharing no sequences
with wolves. The sequence divergence within this clade suggested that dogs originated more than 100,000 years before the present.
Associations of dog haplotypes with other wolf lineages indicated episodes of admixture between wolves and dogs. Repeated
genetic exchange between dog and wolf populations may have been an important source of variation for artificial selection.
We present a practical and efficient parentage analysis test for dogs. The method makes use of ten polymorphic microsatellite markers combined in three multiplex-PCR reactions. All three multiplexes can be performed under the same cycling conditions and using a multiple-dye detection system the PCR-products can be pooled for electrophoresis. Amplifications in four different thermal cyclers produced easily interpretable results throughout demonstrating the repeatability of the assay. In order to evaluate the method's efficiency a total of 100 dogs from four different breeds were typed. Assuming one known parent, exclusion probabilities ranging from 99.34% to 99.93% were attained.
The origin of the domestic dog from wolves has been established, but the number of founding events, as well as where and when
these occurred, is not known. To address these questions, we examined the mitochondrial DNA (mtDNA) sequence variation among
654 domestic dogs representing all major dog populations worldwide. Although our data indicate several maternal origins from
wolf, >95% of all sequences belonged to three phylogenetic groups universally represented at similar frequencies, suggesting
a common origin from a single gene pool for all dog populations. A larger genetic variation in East Asia than in other regions
and the pattern of phylogeographic variation suggest an East Asian origin for the domestic dog, ∼15,000 years ago.
The Italian wolf is in the process of regaining the Alpine region which comes into conflict with the extensive sheep keeping practiced in Switzerland during the summer. As in Switzerland, the wolf is a protected species, the government reimburses losses caused by wolves. Therefore we wanted to know whether the Italian wolf could be distinguished from the domestic dog by microsatellite analysis if DNA samples of the predators could be secured. The evaluation of combined genotypes for the microsatellites CanBern6, CPH4, CPH7, CPH9, CPH12, CPH22 and ZuBeCa1 made it possible to identify an individual as either a domestic dog or an Italian wolf. The assignment of an individual to either one of the two populations is based on the logarithm of the likelihood ratio of an individual being an Italian wolf rather than a domestic dog, given a specific combined genotype. The distribution of the Italian wolf combined genotypes (n=42) is clearly distinct from the distribution of the domestic dog combined genotypes (n=90). The likelihood ratio for the "worst" Italian wolf combined genotype was 2.3 E+5 and for the "worst" domestic dog combined genotype was 3.8 E-5.
We used molecular markers to study genetic relationships in a diverse collection of 85 domestic dog breeds. Differences among breeds accounted for approximately 30% of genetic variation. Microsatellite genotypes were used to correctly assign 99% of individual dogs to breeds. Phylogenetic analysis separated several breeds with ancient origins from the remaining breeds with modern European origins. We identified four genetic clusters, which predominantly contained breeds with similar geographic origin, morphology, or role in human activities. These results provide a genetic classification of dog breeds and will aid studies of the genetics of phenotypic breed differences.
GENECLASS2 is a software that computes various genetic assignment criteria to assign or exclude reference populations as the origin of diploid or haploid individuals, as well as of groups of individuals, on the basis of multilocus genotype data. In addition to traditional assignment aims, the program allows the specific task of first-generation migrant detection. It includes several Monte Carlo resampling algorithms that compute for each individual its probability of belonging to each reference population or to be a resident (i.e., not a first-generation migrant) in the population where it was sampled. A user-friendly interface facilitates the treatment of large datasets.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
Parentage control has been performed for 15 litters from 12 different dog breeds by amplification of microsatellites. As it was possible to include all putative parents in all cases, they were solved by exclusion. Discrimination between parents/non-parents was made after genotyping of 6-9 microsatellite loci. In 12 of the cases all but one of the alleged fathers were excluded while in three cases it was unambiguously shown that superfecundation had taken place. Furthermore, one inclusion case concerning disputed maternity has been investigated. Maternity indices were calculated for 12 loci and probability of maternity was estimated to be 99.99%. These results testify that microsatellites can be applied very efficiently for resolution of parentage in dogs.
Polymorphic animal microsatellites have proved valuable genetic markers. For this project, the variability of 19 canine microsatellite loci was examined within and between three pure breeds of dog: Greyhounds, Labradors, and German Shepherds. The number of alleles, absolute and relative frequencies, and the statistics that express polymorphism within a breed were determined. The evolutionary relationships among these closely related dog breeds were estimated by genetic distance measures developed for use with microsatellite loci. According to the pairwise genetic distances, Greyhounds and German Shepherds had longer diverse evolutionary histories than Greyhounds and Labradors or Labradors and German Shepherds. Although a few breed-specific alleles were observed, the significant differences between breeds are in their relative frequencies and distribution of the alleles across a locus. None of the three pure dog breeds corresponds to Hardy-Weinberg equilibrium. A considerable reduction in intrapopulation variation was observed within three pure breeds, compared with the population of individuals belonging to 15 dog breeds. This reduction was especially pronounced in the Greyhound breed, which expressed the lowest degree of variation. Intrapopulation variations of Labradors and German Shepherds did not differ significantly, that of Labradors being only slightly higher. The intra-species variation of dogs is lower than in humans, mouse, or rat, but similar to that in domestic animals, probably reflecting similarly high inbreeding coefficients. However, some highly informative loci were common to all dog breeds tested so far. Such population data are necessary for mapping studies and linkage analysis in dogs.
Pairwise analysis of HinfI/33.6 DNA fingerprints from a total of one hundred and fifty-three Irish greyhounds of known pedigree were used to determine band-share estimates of unrelated, first-degree and second-degree relationships. Forty-eight unrelated Irish greyhounds were used to determine allele frequencies for three single-locus minisatellites, and following a preliminary screen, eight of the most polymorphic tetra-nucleotide microsatellites from a panel of 15. The results indicated that both band-share estimates by DNA fingerprinting and microsatellite allele frequencies are highly effective in resolving parentage in this greyhound population, while single-locus minisatellites showed limited polymorphism and could not be used alone for routine parentage testing in this breed. The present study also demonstrated that, to obtain optimal resolution of parentage, sample sets of known pedigree status are required to determine the band-share distribution and/or microsatellite allele frequencies.
We present chromosomal fluorescence in situ hybridization (FISH) results that both extend the HSA20/BTA13 comparative map as well as cytogenetically anchor two microsatellite markers. A bovine bacterial artificial chromosome (BAC) library was screened for conserved genes (type 1 loci) previously assigned to HSA10 or HSA20 and BTA13, and for microsatellites selected from two published BTA13 linkage maps. Clones from six out of nine comparative loci and both microsatellites were found represented in the BAC library. These BAC clones were used as probes in single colour FISH to determine the chromosome band position of each locus. As predicted by the human/bovine comparative map, all type 1 loci mapped to BTA13. Because single colour FISH analysis revealed that the loci were clustered within the distal half of BTA13, dual colour FISH was used to confirm the locus order. Established order was centromere-PRNP-(SOD1L/AVP/OXT)-(BL42/GNAS1)- HCK-CSSM30. The findings confirm the presence of a conserved HSA20 homologous synteny group on BTA13 distal of a HSA10 homologous segment.
In total, 463 canine gene markers were identified and characterized to serve as reagents in canine genome map projects. These markers are distributed over 221 canine gene markers, 139 TOASTs (Traced Orthologous Sequence Tags), 27 canine TOASTs, and 76 huESTs (human Expressed Sequence Tags). Out of 310 canine gene markers, 59%-84% were successfully amplified on dog DNA, the highest rates of success being observed when the exon/intron structure is known. Concerning TOASTs and human ESTs, of the 225 and 300 markers analyzed, 62% and 25% respectively were able to produce a dog positive amplification. As part of an ongoing project to map the canine genome using a dog/hamster radiation hybrid panel, these markers were tested for their specificity on dog versus hamster DNA. Thus 61%, 21%, and 12% of dog gene markers, TOASTs, and huESTs met the criteria required for radiation hybrid mapping, respectively. All of these 463 canine gene markers, however, are available and will be of value to any other mapping strategies.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
A breeding programme to eradicate copper toxicosis in Danish Bedlington terriers has been established based on a DNA marker test. Genotyping of both parents is compulsory and after 1 January 2000, only homozygous non-carriers are used for breeding. In this study, two groups of Bedlington terriers were genotyped at 18 microsatellite loci. One group represented the original population of Bedlington terriers before introducing the breeding programme (n = 23); the other represented a group of homozygous non-carriers (n = 24) available for breeding after year 2000. Allele numbers, allele frequencies, observed heterozygosities (Ho), expected heterozygosities (He), locus-specific coefficients of inbreeding (Fl) and Nei's genetic distance (D) was calculated. Individual coefficients of inbreeding (Fi) were calculated from the pedigrees and an assignment test was performed. Four rare alleles were lost in the group of homozygous non-carriers. No significant differences were observed between the mean values of allele numbers, Ho, He, Fl and Fi of the two populations of dogs. Nei's genetic distance between the two populations was 0.06 and 88% of the homozygous non-carriers were assigned correctly in the assignment test. The overall diversity of the breed was low (Ho = 0.41) and the breeders were advised to include the heterozygous carriers again.
Modern individual clustering methods utilising hypervariable nuclear microsatellite DNA polymorphisms are being increasingly applied in the field of population genetics. This study explores the efficiency of the clustering methods in identifying the breeds of origin of 250 domestic dog (Canis familiaris) individuals based on 10 microsatellite loci. An allele sharing distance (DAS) matrix and the corresponding neighbour-joining tree of individuals revealed monophyletic assemblages that corresponded perfectly with the breeds of origin of the dogs. Individual assignment tests using a Bayesian statistical approach, an allele frequency based method, and a DCE genetic distance based method were all extremely powerful. Most strikingly, the Bayesian method provided 100% assignment success of individuals into their correct breeds of origin and 100% exclusion success of individuals from all alternate reference populations with a high level of statistical confidence (P < 0.0001). A Bayesian Markov Chain Monte Carlo clustering approach revealed clear distinction of individuals into groups according to their breeds of origin, with a near-zero level of 'genetic admixture' among breeds. The results demonstrate that an FST of 0.18, mean expected gene diversity of 0.6 across 10 loci, and approximately 50 individuals per reference population suffice to provide maximum individual assignment success in C. familiaris. This refutes the traditional view that DNA based dog breed identification is not feasible at the individual level of resolution.
As natural selection must act on underlying genetic variation, discovering the number and location of loci under the influence of selection is imperative towards understanding adaptive divergence in evolving populations. Studies employing genome scans have hypothesized that the action of divergent selection should reduce gene flow at the genomic locations implicated in adaptation and speciation among natural populations, yet once 'outlier' patterns of variation have been identified the function and role of such loci needs to be confirmed. We integrated adaptive QTL mapping and genomic scans among diverging sympatric pairs of the lake whitefish (Coregonus clupeaformis) species complex in order to test the hypothesis that differentiation between dwarf and normal ecotypes at growth-associated QTL was maintained by directional selection. We found evidence of significantly high levels of molecular divergence among eight growth QTL where two of the strongest candidate loci under the influence of directional selection exhibited parallel reductions of gene flow over multiple populations.
Microsat (version 1.5): A Com-puter Program for Calculating Various Statistics on Microsat-ellite Allele Data
- E Minch
- A Ruiz-Linares
- D Goldstein
- M Feldmann
Minch E., Ruiz-Linares A., Goldstein D., Feldmann M., Cavalli-Sforza L.L. (1996) Microsat (version 1.5): A Com-puter Program for Calculating Various Statistics on Microsat-ellite Allele Data (http://lotka.stanford.edu/microsat/ microsat.html).
- Sutton M.D.