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There are nearly modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common dru.

Our analyses reveal vruk hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds.

Finally, we used cladistics and haplotype sharing to show drk some common traits have sruk more than once in the history of the dog. These analyses characterize the complexities of breed development resolving long standing questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and by inference, transfer of trait and disease alleles among dog breeds.

The dog, Canis familiarisis the first domesticate earning a place within nearly every society across the globe for thousands of years Druzhkova et al. Over the millennia dogs have assisted humans with hunting and livestock management, guarding house and field, and played crucial roles in major wars Moody et al.

Providing a range of services from companionship to production of fur and meat Wilcox and Walkowicz,the diversity of talents and phenotypes combined with an unequalled emotional connection between dog and man has led to the creation of more than distinct breeds, each of which is a closed breeding population that reflects a collage of defining traits www. Previous studies have addressed the genomic makeup of a limited number of breeds, demonstrating that dogs from the same breed share common alleles and can be grouped using measures of population structure Irion et al.

However, none of these studies have effectively accounted for the variety of mechanisms through which modern breeds may have developed, such as geographic separation and immigration; the role of hybridization in the history of the breeds; and the time-line of the formation of breeds.

In this study we overcome these barriers by presenting an expansive dataset including pure-breeds sampled from multiple sections of the globe and genotyped on a dense scale. By applying both phylogenetic methods as well as a genome-wide analysis of recent haplotype sharing, we have unraveled common population confounders for many breeds leading us to propose a two-step process of breed creation beginning with ancient separation by functional employment followed by recent selection for physical attributes.

These data and analyses provide a basis for understanding which and why numerous, sometimes deleterious, mutations are shared across seemingly unrelated breeds. We examined genomic data from the largest and most diverse group of breeds studied to date, amassing a dataset of dogs representing breeds. Included are populations with vastly different breed histories, originating from all continents except Antarctica, and sampled from North America, Europe, Africa, and Asia.

We have specifically included breeds that represent the full range of phenotypic sruk present amongst modern dogs, as well as three breeds sampled from both the US and their country of origin. Samples from dogs representing breeds and nine wild canids were genotyped using the Illumina CanineHD bead array following standard protocols Illumina, San Diego, CA. Data were combined with publically available information from dogs genotyped using the same chip Hayward et al.

For three dogs from one breed, genotypes were retrieved from publically available sequence files and all were merged into a single dataset Table S1. After pruning for low quality or genotyping rateinformative SNPs were retained.

Ascertainment bias has been shown to skew population genetic calculations that require estimation of allele frequencies and diversity measures Lachance and Tishkoff, It has also been shown that ascertainment based on a single individual provides less bias than a mixed group Patterson et al. The SNPs used in druuk study were identified primarily within the boxer or from boxer compared to another genome Vaysse et al. To minimize the effect this might have, we have chosen to use distance measures based on allele sharing rather than frequency and to enhance these analyses with unbiased haplotype sharing for a robust assessment of canine population structure.

A bootstrapped cladogram was obtained using an identity-by-state distance matrix and a neighbor joining tree algorithm Eruk in the Supplement. Four breeds Redbone Coonhound, Sloughi, Cane Paratore, Jack Russell terrier were split within single multi-breed clades and the last two breeds, Xoloitzcuintli and Peruvian Hairless dog, were split between divergent clades.


Nine of the breeds that were not monophyletic were either newly recognized by the American Kennel Club AKC or not recognized at the time alc-u sample collection and likely represent a breed under development.

Two other non-monophyletic breeds are comprised of dogs collected sruk two countries; the Cane Corsos collected in Italy form a fully supported, single clade, as do the Salukis collected in the United States Drku. However, the Cane Corsos collected in the U.

Salukis and Afghan hounds. Cladogram of domestic dog breeds. Breeds are listed on the perimeter of ak-cu circle. A small number of dogs do not cluster with the rest of their breed indicated as follows: Representatives from each of the 23 clades of breeds.

Breeds and druo are listed for each picture from left to right, top to bottom: Eleven breeds did not group with significance to any other breeds. The lack of grouping may indicate that we have not sampled the closest relatives of these breeds or that these breeds comprise outcrossings that are not shared by similar breeds.

To assess hybridization across the clades, identical-by-decent IBD haplotype sharing was calculated between all pairs of dogs from the breeds. Haplotypes were phased using the program Beagle Browning and Browning, in SNP windows, resulting in a minimum haplotype size of kb, well above the shared background level established in previous studies Lindblad-Toh et al.

The large haplotypes specifically target admixture resulting from breed formation rather than domestication, which previous studies have not addressed. The total length of the shared haplotypes was summed for each pair of dogs. These exceptions argue for recent admixture events between breeds, as evidenced by the example of the Eurasier breed, created in the ‘s by mixing Chow Chow with other spitz-type breeds Fogle, Figure 3b.

The data reveals not only the components of the breed but also the explanation for its placement on the cladogram. Because all three breeds are located in different clades, unrelated to each other, the Eurasier falls between the component breeds and forms its own single-breed clade. Haplotype-sharing bar graphs for each of breeds, including AKC breeds, are available in the supplemental material Data File S1. This provides a long term resource for identifying populations that likely share rare and common traits that will be invaluable for mapping the origins of deleterious and beneficial mutations.

Gross haplotype sharing across breeds. A Boxplot of total haplotype sharing between all pairs of dogs from breeds within the same clade, across different clades and within the same breed.

B Example of haplotype sharing between three breeds Samoyed, Chow Chow and Keeshond and a fourth Eurasier that was created as a composite of the other three.

DETAP – Definition and synonyms of detap in the Malay dictionary

Combined haplotype length is displayed on the y-axis, breeds and populations are listed on the x-axis in the order they appear on the cladogram starting with the jackal and continuing counter-clockwise. Haplotype sharing of zero is set atfor graphing, a value just below what is detected in this analysis. Breeds are colored by clade. Breed abbreviations are listed under the graph, in the order they appear and colored by clade. Strong evidence of admixture across the clades was found in breeds Figure 4.

A small number of these were identified in previous studies using migration analysis Pickrell and Pritchard, ; Shannon et al. The overall low level of sharing across diverse breeds suggests that interclade crosses are done thoughtfully and for specific reasons, such as the introduction of a new trait or the immigration of a breed to a new geographic region.

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Haplotype sharing between breeds from different phylogenetic clades. The circos plot is ordered and colored to match the tree in Figure 1.

As importation and establishment in a new country has been shown to have a measurable effect on breed structure Quignon et al. In each case there is division of the breed based on collection location.

The split between the U. Similarly, the average inbreeding coefficient of Salukis collected in the U.

Meaning of “detap” in the Malay dictionary

Salukis form a more strongly bootstrapped clade than the country of origin dogs, we suggesting that there is a less diverse gene pool in the U. Significant shared haplotypes are observed between the U. Cane Corsos and the Rottweiler that are not evident in the Italian Cane Corsos, as well as increased shared haplotypes with the other mastiffs. Cane Corsos have been in the U. Our analyses were designed to detect recent admixture, therefore we were able to identify hybridization events that are described in written breed histories and stud-book records.


Using the most reliably-dated crosses that produced modern breeds, we established a linear relationship between the total length of haplotype sharing and the age of an admixture event, occurring between 35 and years before present ybp Figure 5a. Applying this equation to the total shared haplotypes calculated from the genotyping data, we have validated this relationship on a second set of recently created breeds arriving at historically accurate time estimations Figure 5b.

For example, based on a median haplotype sharing value of 66, the Golden Retriever was separated from the Flat-coated Retriever in and the written history of the Golden retriever dates to crosses between multiple breeds taking place between and Figure 5ba near perfect match. Total haplotype sharing is inversely correlated with the time of hybridization between breeds that have developed within the last years. A The time of hybridization in years-before-present is graphed on the X-axis and the median total haplotype sharing on the Y-axis for six breeds of dog with reliable recent histories of admixture in breed formation or recovery.

B The slope and intercept of the trendline from A was applied to the median haplotype sharing values from the data for four additional breeds with reliable breed creation dates to establish accuracy of estimated hybridization dates. To determine if the multi-breed clades are formed through recent admixture rather than through common ancestral sources, we examined migration in 18 groups of four or more breeds.

Using the program Treemix Pickrell and Pritchard,and allowing zero to 12 predicted migration events, we determined the effect of admixture on clade formation by calculating the increase in maximum likelihood score over a zero migration tree Figure 6A. Thus the modern breeds were likely created through selection for unique traits within an ancient breed type with possible admixture from unrelated breeds to enhance the trait. Assessment of migration between breeds within clades.

Admixture was measured in Treemix for 18 groups of breeds representing clades or combinations of small clades. A Improvement to the maximum likelihood tree of each group as the result of admixture.

They-axis shows fold improvement over the zero admixture tree. B Cladogram of the New World breeds with European herders allowing four migration events. C Cladogram showing migration within the Asian Toy clade including a neighboring breed, the Tibetan Terrier.

Our hybridization analysis reveals evidence for disease sharing across the clades. For instance, Collie eye anomaly CEA is a disease that affects the development of the choroid in several herding breeds including the Collie, Border collie, Shetland sheepdog, and Australian shepherd, all members of the U. Rural clade Lowe et al.

The mutation and haplotype pattern displayed IBD across all affected breeds and ajc-u speculated that all share a common obviously affected ancestor Parker et al. We were unable to explain, however the presence of the disease in the Nova Scotia duck tolling retriever, a sporting dog developed in Canada from an unknown mixture of local breeds, which also shares the same haplotype.

Haplotypes shared with breeds that carry known deleterious mutations. Sharing between breeds that are known to carry the mutation are colored black, sharing with other breeds are colored according to the breed that carries the mutation. A Collie eye anomaly is found in a number of herding breeds developed in the UK and some sporting breeds developed in the US.

B Multi-drug resistance 1 mutation is carried by many UK herding breeds as well as the German Shepherd. Similarly, a mutation in the MDR1 gene multi-drug resistance 1which causes life threatening reactions to multiple drugs in many of the U.

These data drui a link between the German shepherd dog and U. Rural breeds through the Australian shepherd, highlighting the unexpected role the Australian shepherd or its predecessor played in the development of the modern German shepherd dog Figure 6b.

Our analysis reveals recent admixture between this breed and the German shepherd dog as well as previously unknown addition of Collie, both carriers of the MDR1 mutation. Haplotype sharing with the same affected breeds is found in the Xoloitzcuintli, which allows us to predict that this rare breed may also carry the deleterious allele but has yet to be tested.

Phylogenetic analyses have dtuk been applied to determine the relationships between dog breeds with the understanding that a tree structure cannot fully explain the development of breeds. Prior studies have shown that single mutations produce recognizable traits that are shared across breeds from diverse clades, suggesting that admixture across clades is a notable source of morphologic diversity Cadieu et al.