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Dog genome sequence and analysis published in "Nature"
EurekAlert (AAAS) ^ | 07 December 2005 | Staff

Posted on 12/08/2005 4:23:38 AM PST by PatrickHenry

Analysis unlocks genetic variation among dog breeds; evolutionary conservation with human reveals regulatory controls of key genes.

An international research team led by scientists at the Broad Institute of MIT and Harvard announced today the completion of a high-quality genome sequence of the domestic dog, together with a catalog of 2.5 million specific genetic differences across several dog breeds. Published in the December 8 issue of Nature, the dog research sheds light on both the genetic similarities between dogs and humans and the genetic differences between dog breeds. Comparison of the dog and human DNA reveals key secrets about the regulation of the master genes that control embryonic development. Comparison among dogs also reveals the structure of genetic variation among breeds, which can now be used to unlock the basis of physical and behavioral differences, as well the genetic underpinnings of diseases common to domestic dogs and their human companions.

"Of the more than 5,500 mammals living today, dogs are arguably the most remarkable," said senior author Eric Lander, director of the Broad Institute, professor of biology at MIT and systems biology at Harvard Medical School, and a member of the Whitehead Institute for Biomedical Research. "The incredible physical and behavioral diversity of dogs -- from Chihuahuas to Great Danes – is encoded in their genomes. It can uniquely help us understand embryonic development, neurobiology, human disease and the basis of evolution."

Similarities to humans

Dogs not only occupy a special place in human hearts, they also sit at a key branch point in the evolutionary tree relative to humans. By tracking evolution's genetic footprints through the dog, human and mouse genomes, the scientists found that humans share more of their ancestral DNA with dogs than with mice, confirming the utility of dog genetics for understanding human disease.

Most importantly, the comparison revealed the regions of the human genome that are most highly preserved across mammals. Roughly 5% of the human genome has been well preserved by evolution over the past 100 million years and must encode important biological functions. The researchers discovered that the most highly conserved of these sequences are not randomly distributed throughout the genome. Instead, they are crowded around just a tiny fraction (about 1%) of the genes that encode crucial regulatory proteins involved in development (such as transcription factors or axon guidance receptors). "The clustering of regulatory sequences is incredibly interesting," said Kerstin Lindblad-Toh, first author of the Nature paper and co-director of the genome sequencing and analysis program at Broad. "It means that a small subset of crucial human genes is under much more elaborate control than we had ever imagined."

Differences between dog breeds

Dogs were domesticated from gray wolves as long as 100,000 years ago, but selective breeding over the past few centuries has made modern dog breeds a testament to biological diversity. Obvious examples include the contrasting body sizes of 6-pound Chihuahuas and 120-pound Great Danes, the hyperactivity of Jack Russell terriers relative to mild-mannered basset hounds, and the herding instincts of Shetland sheepdogs compared with the protective proclivity of dalmatians.

Efforts to create the genetic tools needed to map important genes in dogs have gained momentum over the last 15 years, and already include a partial survey of the poodle genome. More than two years ago, Lindblad-Toh, Lander, and their colleagues embarked on a two-part project to assemble a complete map of the dog genome. First, they acquired high-quality DNA sequence from a female boxer named "Tasha," covering nearly 99% of the dog's genome. Using this information as a genetic 'compass,' they then sampled the genomes of 10 different dog breeds and other related canine species, including the gray wolf and coyote. By comparing these dogs, they pinpointed ~2.5 million individual genetic differences among breeds, called single nucleotide polymorphisms (SNPs), which serve as recognizable signposts that can be used to locate the genetic contributions to physical and behavioral traits, as well as disease.

Finally, the scientists used the SNP map to reconstruct how intense dog breeding has shaped the genome. They discovered that selective breeding carried large genomic regions of several million bases of DNA into breeds, creating 'haplotype blocks' that are ~100 times larger than seen in the human population. "The huge genomic regions should make it much easier to find the genes responsible for differences in body size, behavior and disease," said Lander. "Such studies will need many fewer markers than for human studies. It should be like hitting the side of a barn."

Mapping human disease-related genes in dogs

Breeding programs not only selected for desired traits, they also had the unintended consequence of predisposing many dog breeds to genetic diseases, including heart disease, cancer, blindness, cataracts, epilepsy, hip dysplasia and deafness. With the dog genome sequence and the SNP map, scientists around the world now have the tools to identify these disease genes.

Humans suffer from many of the same illnesses as their four-legged friends and even show similar symptoms, but the genetic underpinnings have proved difficult to trace. "The genetic contributions to many common diseases appear to be easier to uncover in dogs," said Lindblad-Toh. "If so, it is a significant step forward in understanding the roots of genetic disease in both dogs and humans."

For this work, the dog-owner community is an essential collaborator. "We deeply appreciate the generous cooperation of individual dog owners and breeders, breed clubs and veterinary schools in providing blood samples for genetic analysis and disease gene mapping," said Lindblad-Toh. "Without their interest and help we could not be doing this work."

Funding and data access

Sequencing of the dog genome began in June 2003, funded in large part by the National Human Genome Research Institute (NHGRI). The Broad Institute is part of NHGRI's Large-Scale Sequencing Research Network. NHGRI is one of 27 institutes and centers at the National Institutes of Health (NIH), an agency of the Department of Health and Human Services. The NHGRI Division of Extramural Research supports grants for research and for training and career development at sites nationwide. Information about NHGRI, including the dog genome initiative, can be found at: www.genome.gov.

[The original article has contact info that I've omitted.]


TOPICS: Culture/Society; Philosophy
KEYWORDS: agriculture; animalhusbandry; crevolist; dogs; godsgravesglyphs; grandmaster; helixmakemineadouble
Someone has another thread on this topic, using an article from the NYT. I thought this article was worth starting a new thread. If you must clutter up a thread with pics of your own dogs, do it in the other thread: Researchers Decode Dog Genome.
1 posted on 12/08/2005 4:23:39 AM PST by PatrickHenry
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To: VadeRetro; Junior; longshadow; RadioAstronomer; Doctor Stochastic; js1138; Shryke; RightWhale; ...
Evolution Ping

The List-O-Links
A conservative, pro-evolution science list, now with over 320 names.
See the list's explanation, then FReepmail to be added or dropped.
To assist beginners: But it's "just a theory", Evo-Troll's Toolkit,
and How to argue against a scientific theory.

2 posted on 12/08/2005 4:24:47 AM PST by PatrickHenry (Virtual Ignore for trolls, lunatics, dotards, common scolds, & incurable ignoramuses.)
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To: PatrickHenry

Well, I won't clutter up this thread with pics of my wonderful dogs, but as the article states, dogs are remarkable. Yes, indeed.


3 posted on 12/08/2005 4:29:02 AM PST by hershey
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To: PatrickHenry
""Efforts to create the genetic tools needed to map important genes in dogs have gained momentum over the last 15 years, and already include a partial survey of the poodle genome.""

They find there is a direct DNA link to the French poodle and the French people - Threaten them and they run around peeing on the carpet and find the safest place to hide.

4 posted on 12/08/2005 4:36:53 AM PST by Abathar (Proudly catching hell for posting without reading since 2004)
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To: Abathar

LOL!!!!


5 posted on 12/08/2005 4:50:29 AM PST by Recovering Ex-hippie (If Iran has nukes, to hell with my diet!)
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To: Abathar

The problem with that is the poodle breed was imported from Russia to France in the early 18th century.


6 posted on 12/08/2005 4:52:59 AM PST by doc30 (Democrats are to morals what and Etch-A-Sketch is to Art.)
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To: PatrickHenry

Thanks for the ping!


7 posted on 12/08/2005 5:08:14 AM PST by Alamo-Girl
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To: PatrickHenry

This could be potentially interesting for the crevo debate in regards to the ability of mutation.

The unique case here is that most anti-evos accept that different dog breeds share a common ancestor. I think we are near to finding out the exact nature of the genetic changes which were necessary to produce such different breeds of dogs. It will be interesting to see the differences due to mutation. I expect that a lot of the variation in physical structure between breeds will be due to mutation of some key genes.

Dog breeds might end up being a good demonstration of the ability of mutation, just as the peppered moth is a good demonstration of the ability of natural selection.


8 posted on 12/08/2005 5:29:59 AM PST by bobdsmith
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To: doc30; Abathar

The toy poodle is really a hyper lap dog, but my experience with actual poodles (80 lb. dogs) is that they are fine guard and livestock dogs.


9 posted on 12/08/2005 5:43:52 AM PST by SampleMan
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To: PatrickHenry

Bump.


10 posted on 12/08/2005 5:49:19 AM PST by aculeus
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To: PatrickHenry; HairOfTheDog

HairOfTheDogGenomePing.


11 posted on 12/08/2005 5:55:28 AM PST by martin_fierro (< |:)~)
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To: PatrickHenry
Today's Wall Street Journal also had a version of the story.

Thanks for posting.

12 posted on 12/08/2005 6:05:27 AM PST by Gumlegs
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To: martin_fierro
lol - this was also posted here... and I just DoggiePinged the other thread...

Researchers Decode Dog Genome

13 posted on 12/08/2005 6:07:42 AM PST by HairOfTheDog (Join the Hobbit Hole Troop Support - http://freeper.the-hobbit-hole.net/ 1,000 knives and counting!)
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To: PatrickHenry

Barking up the canine Tree Of Life?

Cave Cane!


14 posted on 12/08/2005 6:43:48 AM PST by Doctor Stochastic (Vegetabilisch = chaotisch ist der Charakter der Modernen. - Friedrich Schlegel)
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To: PatrickHenry
Obvious examples include the contrasting body sizes of 6-pound Chihuahuas and 120-pound Great Danes...

Chihuahuas are descended from rats not wolves... Right?

15 posted on 12/08/2005 6:51:35 AM PST by GOPJ ("Protests at a funerals are a new low for the left. I am sickened by this" FormerMilitaryChick)
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To: Doctor Stochastic

16 posted on 12/08/2005 6:54:14 AM PST by js1138 (Great is the power of steady misrepresentation.)
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To: PatrickHenry
This is terrific news.

As a Dobe owner, I've lost FIVE dogs to DCM. The Dobermans are poster child for this genetic heart disease whose first symptom is often death. Sixty per cent of males and forty per cent of the bitches have DCM.

How wonderful it will be when they finally find the marker for this horrible affliction.

17 posted on 12/08/2005 6:56:30 AM PST by doberville
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To: Doctor Stochastic; js1138
Cave Cane!

Veni, vidi, voidi. (I came, I saw, I soiled my trousers.)

18 posted on 12/08/2005 7:39:05 AM PST by PatrickHenry (Virtual Ignore for trolls, lunatics, dotards, common scolds, & incurable ignoramuses.)
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To: PatrickHenry
These tile murals were all the rage in Pompeii.
19 posted on 12/08/2005 7:46:39 AM PST by js1138 (Great is the power of steady misrepresentation.)
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To: PatrickHenry

" "The clustering of regulatory sequences is incredibly interesting," said Kerstin Lindblad-Toh, first author of the Nature paper and co-director of the genome sequencing and analysis program at Broad."

I have been saying for awhile that this a key component in evolution. I think the more critters that get sequenced, the more profound these "non-coding" differences will be. I am looking forward, eagerly.


20 posted on 12/08/2005 7:55:29 AM PST by furball4paws (The new elixir of life - dehydrated toad urine.)
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To: furball4paws
I think the more critters that get sequenced, the more profound these "non-coding" differences will be. I am looking forward, eagerly.

We had a thread a while back on very conserved areas of the genome. One idea tossed around is that the more vital a particular sequence is, the more likely it is to remain conserved, simply because if it varies (which it may) the consequences are catastrophic, so only the conserved versions survive to participate in the biosphere.

21 posted on 12/08/2005 8:12:27 AM PST by PatrickHenry (Virtual Ignore for trolls, lunatics, dotards, common scolds, & incurable ignoramuses.)
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To: PatrickHenry

22 posted on 12/08/2005 8:21:11 AM PST by Paleo Conservative (Hey hey ho ho Andy Heyward's got to go!)
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To: longshadow
Dog of a thread, placemarker.
23 posted on 12/08/2005 1:29:39 PM PST by PatrickHenry (Virtual Ignore for trolls, lunatics, dotards, common scolds, & incurable ignoramuses.)
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To: bobdsmith
...Dog breeds might end up being a good demonstration of the ability of mutation...

I've often used dogs as an example of a ring species, since, say, chihuahuas and great Danes cannot (AFAIK) mate, but there is a continuum of other breeds of intermediate size.

Remember that Darwin used pigeon breeding as one of his main examples.

24 posted on 12/08/2005 5:07:36 PM PST by Virginia-American
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To: Paleo Conservative

You should be ashamed of yourself!! Posting such a cute little dog together with that bitch (it's okay to say that when talking about dogs, right?) ;P


25 posted on 12/08/2005 6:22:02 PM PST by anguish (while science catches up.... mysticism!)
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 GGG managers are SunkenCiv, StayAt HomeMother & Ernest_at_the_Beach
Note: this topic is dated 7 December 2005.

Blast from the Past.

Thanks PatrickHenry.

Just adding to the catalog, not sending a general distribution.

To all -- please ping me to other topics which are appropriate for the GGG list.


26 posted on 03/03/2013 8:47:15 PM PST by SunkenCiv (Romney would have been worse, if you're a dumb ass.)
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