Tuesday, November 4, 2014

DOMESTIC DOG (Canis lupus familiaris) BREED DNA TEST?!

DISCLAIMER
Source: dogfoster.blogspot.com
I was about the neighborhood the other day and  couldn’t help but notice the plethora of dog breeds of passersby. It is universal canines — no matter the breed — always want to check each other out, good or bad ( and at the discretion of their owners of course). This made me think about the  American Kennel Club and so-called “pure breed” pedigrees. And the pounds and pet adoption  "agencies." We humans judge and assign value to them on breed purity and phenotypical features, while dogs judge us on more intrinsic values. I then wondered how it would if dog-breed DNA tests were more widely available and affordable to pet owners. If I know us, it would probably be analogous to how we get so rabid about “racial purity” and ethnicity when discussing our own ethnic make-up tofay. LOL. Still I daydreamed about how a canine’s “ethnic” composition might look as well as change notions of breed purity. The dogs REALLY don’t care, but I can imagine the Kennel Club would be turned on its head. So I decided to take it a step further and do a sort of dog-breed composition parody using ethnicity admixture tools by gedmatch.com and 23andme.com, including haplogroup assignments and “Neanderthal” percentage. My examples are purely fictional and fun, but you get the idea. However if you want to discuss the dogs and bones here, feel free to leave a comment. And by the way, if you seriously wanted to give your “best friend” companion a DNA test, please visit (at your own risk): 
And if you need some inspiration:
http://pets.webmd.com/dogs/features/dog-dna-testin

HERE ARE MY DOG BREED ADMIXTURE EXAMPLES:


(1) PURE BREED
Scrubby, GREAT DANE
Source: www.petfinder.com

German Mastiff … 97%
English Mastiff … 0.6%
Irish Wolfhound … 0.4%
Gray Wolf (Canis lupus pallipes) ... 2%
Great Dane …100%

(2) AMERICAN MIXED BREED
Chi-Chi, AMERICAN PIT BULL TERRIER
Source: animalsadda.com

Old English Terrier ........ 46.2%
Old English Bulldog ….. 45.7%
White English Terrier … 3%
French Bulldog ……...... 2%
Scottish Terrier ……...... 0.6%
Welsh Terrier ………..... 0.5%
Gray Wolf (Canis lupus pallipes) ..... 1%
American Pit Bull Terrier …............. 100%

(3) MONGREL @ 23andme.com parody
Max, MUTT
Source: Google Images
MAX'S ANCESTRY COMPOSITION

46.1%  Sub-Saharan African
40.5% West African Basenji
1.9%  Central & South African Africanis
0.2% East African Azawakh
3.5% Broadly Sub-Saharan African
45.0% European
Northern European
3.4% British Sheep & Irish Setter
3.6% French Great Pyrenees & German Shepherd
0.5% Scandinavian Spitz
0.2% Finnish Lapphund
11.6% Broadly Northern European
Southern European
1.0% Sardinian Pastore Fonnese
1.0% Italian Greyhound
5.1% Iberian Andalusian Hound
0.4% Balkan Romanian Raven Shepherd
0.5% Broadly Southern European
Ashkenazi
0.2% Ashkenazi Ovcharka
Eastern European
0.6% Eastern European Polish Pound
2.3% Broadly European
6.8% East Asian & Native American
5.0% Native American Inca Orchid
1.2% Southeast Asian Telomian
East Asian
0.0% Japanese Sanshu
0.0% Korean Jingo
0.5% Yakut - East Siberian Laika
0.5% Mongolian Tibetan Mastiff
0.0% Chinese Shar pei
0.1% Broadly East Asian 
0.5% Broadly East Asian & Native American
0.3% Middle Eastern & North African
0.1% Middle Eastern Canaan
0.1% North African Sloughi
0.1% Broadly Middle Eastern & North African
South Asian
0.1% South Asian Alungu Mastiff
Oceania
0.0%Oceanian Dingo
0.7% Unassigned
100% Max
Source: www.mnn.com
MAX'S MATERNAL HAPLOGROUP ASSIGNMENT
MT-DNA:  d1 (found in Scandinavian Spitzes)

*The domestic dog mitochondrial DNA (mtDNA)-gene pool consists of a homogenous mix of haplogroups shared among all populations worldwide, indicating that the dog originated at a single time and place. However, one small haplogroup, subclade d1, found among North Scandinavian/Finnish spitz breeds at frequencies above 30%, has a clearly separate origin. We studied the genetic and geographical diversity for this phylogenetic group to investigate where and when it originated and whether through independent domestication of wolf or dog-wolf crossbreeding. We analysed 582 bp of the mtDNA control region for 514 dogs of breeds earlier shown to harbour d1 and possibly related northern spitz breeds. Subclade d1 occurred almost exclusively among Swedish/Finnish Sami reindeer-herding spitzes and some Swedish/Norwegian hunting spitzes, at a frequency of mostly 60-100%. Genetic diversity was low, with only four haplotypes: a central, most frequent, one surrounded by two haplotypes differing by an indel and one differing by a substitution. The substitution was found in a single lineage, as a heteroplasmic mix with the central haplotype. The data indicate that subclade d1 originated in northern Scandinavia, at most 480-3000 years ago and through dog-wolf crossbreeding rather than a separate domestication event. The high frequency of d1 suggests that the dog-wolf hybrid phenotype had a selective advantage. *[Source: excerpted from  http://www.ncbi.nlm.nih.gov/pubmed/20497152]

MAX'S PATERNAL HAPLGROUP ASSIGNMENT
Y-DNA: H23  (found almost exclusive to East Asia)

**The dog Y-chromosome gene pool was to a large degree shared among the populations across the world (Figures 1b and c). Two of the five haplogroups (HG1 and HG23) were virtually universally represented and carried by 62% of all dogs in the study. The three central haplotypes within these haplogroups, H1, H1* and H23*, were carried by almost half (46%) of the dogs and shared by dogs in Europe, SW Asia and China, by 75%, 44% and 32% of the individuals, respectively. However, there were also distinct differences in the geographical representation and distribution of haplogroups and haplotypes. The other three haplogroups were also distributed across relatively large distances but not universally spread. HG3 was found in East Asia (including Siberia) and America, and at lower frequency in SW Asia, Scandinavia and Britain, but not in samples from the European continent and Africa. HG6 was found in East Asia and at low frequency in SW Asia, but was absent elsewhere. Finally, HG9 was found in only totally four individuals, but as far apart as East Siberia (one individual) and Central Africa (three individuals). As the sample sizes were relatively limited, haplogroups with low frequency, for example, HG9 may have remained undetected in some populations. However, the general pattern was that the four main haplogroups were relatively equally represented in the eastern part of the world, whereas west of the Himalayas and the Urals haplogroups HG1 and HG23 were represented by 89% of the individuals, and HG6 and HG3 rare or absent. Thus, HG1 and HG23 were universally represented, whereas HG3 and HG6 had restricted distributions. Only in East Asia and SW Asia all four major haplogroups were represented. **[Source: excerpted from http://www.nature.com/hdy/journal/v108/n5/full/hdy2011114a.html]

MAX'S ARCHAIC DOG 
Ancient Canis lupus pallipes (or Iranian wolf, Southern-East Asian Wolf and Asian Wolf) …2.3%

[Wiki excerpt ] Indian wolf as a separate species from the grey wolf and distinguished Canis pallipes from Canis laniger (the Himalayan wolf) by its smaller size, much shorter and thinner winter coat, and smaller skull and teeth.

In 1941, the British taxonomist Pocock subordinated both to Canis lupus under the trinomials Canis lupus pallipes and Canis lupus laniger, respectively.[6] Today, the Himalayan wolf initially described by Hodgson in 1847 (C. lupus laniger) is generally considered to be part of the Eurasian wolf subspecies, C. lupus lupus, whereas the Indian wolf (C. lupus pallipes) is considered to be a subspecies, or a species in its own right.

Indian wolves are likely of a much older lineage than northern wolves. Morphologically, Indian wolves greatly resemble primitive European wolves from 500,000 years ago. Recent DNA research suggests the Indian wolf populations in lowland peninsular India have not interbred significantly with any other wolf population for nearly 400,000 years, which could possibly make them an altogether separate species from the grey wolf.

Indian wolves, along with Arabian and Tibetan wolves, are among the wolf subspecies generally suspected to have been the main ancestors of domestic dogs.[9] The basis for this is that Indian wolves share several characteristics with dogs which are absent in northern wolves: their brains are proportionately smaller than northern wolves, their carnassials weaker, and their eyes are larger and rounder. Their vocalisations also include a higher proportion of short, sharp barking. Their small size and less aggressive demeanor in captivity than northern wolves would have made them much easier to tame. They seldom howl, unlike northern wolves.

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