Wesley R. Elsberry posted Entry 223 on May 25, 2004 07:44 AM.
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Dog Genome Yields Information That May Benefit Human Health

A new genetic analysis of man’s best friend could help scientists explain why a border collie has knack for herding or why poodles sport a curly coat. In the May 21 issue of Science, researchers at Fred Hutchinson Cancer Research Center report the first extensive genetic comparison of domestic dog breeds.

The study, led by Fred Hutchinson researchers Drs. Elaine Ostrander, Leonid Krugylak and graduate student Heidi Parker, revealed distinct DNA blueprints for each of the 85 varieties of purebreds that were analyzed as well as similarities between certain breeds. The researchers expect that understanding these genetic relationships will help them uncover the genes responsible for the physical features and behaviors unique to each breed as well as the diseases to which they are commonly susceptible, such as cancer, deafness, blindness, heart disease and hip dysplasia.

The findings also have generated excitement among those who study diseases of the human animal. Because at least half of the more than 300 inherited canine disorders-including a number of cancers-resemble specific diseases of man, many scientists believe that the dog genome holds a wealth of information that will benefit human health.

There are a number of things claimed for this study, most of which confirm things that we already knew or suspected.

  • The nearest relatives of dogs are wolves.

  • Dog breeds are genetically distinct.

  • Dog breeds cluster into four large groups. One is more closely related to wolves, and includes the Alaskan Malamute and Siberian Husky. Another includes mastiff-like breeds. The third includes herding dogs. The fourth comprises hunting dogs.

  • The analysis is being used to find genetic bases for various canine diseases.

The clustering noted above is shaking up some notions of the history of certain breeds:

Noticeably absent from this ancient cluster were several breeds long
regarded as the most ancient by breeders, including the Pharaoh Hound and the
Ibizan Hound — depicted on Egyptian tomb walls. The researchers said their
analysis indicated that the modern representatives of these breeds were
recreated in more recent times from combinations of other breeds. The
researchers also found genetic evidence for a recent origin of the Norwegian
Elkhound, believed to be of ancient Scandinavian origin.

(PR Newswire)

I think that it is important to note that this study is based on microsatellite analysis, not whole-genome data. The claim of the headline and press release that this study “may benefit human health” appears to be a long way from turning possibility into performance. It seems certain that the canine study will be useful in helping track down genetic diseases in dogs, but to have that carry over to humans we would have to know that many of the same microsatellite markers exist in both species, and that has not yet been established as far as I can tell. (As an organismal biologist skimming bioinformatics, though, I could easily be wrong on this. I would be grateful to anyone who can point to work where this has been accomplished.) Some microsatellite studies show useful cross-species comparisons are possible, and other studies show that they don’t work so well, depending upon the particular species under consideration. By contrast, comparative genomics has already identified the genetic basis of a human disease, Bardet-Biedl Syndrome (BBS).

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Comment #2783

Posted by ~DS~ on May 25, 2004 7:28 AM (e)

I think it would be most interesting to see a cladogram for familiar breeds of dogs.

Comment #2784

Posted by ~DS~ on May 25, 2004 7:29 AM (e)

I think it would be most interesting to see a cladogram for familiar breeds of dogs.

Comment #2854

Posted by Navy Davy on May 25, 2004 6:55 PM (e)

My uncle Jethro is a dog-breeder in Louisville. Been breedin’ for years, knows that big dogs tend to give birth to big dogs, and fast dogs tend to give birth to fast dogs.

But, he wants to know, How many more years of dog-breeding will it take before he gets a wolf:)

Comment #2856

Posted by Sean on May 25, 2004 7:07 PM (e)

How many more years of dog-breeding will it take before he gets a wolf?

Ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ha ah ha ha ha ha ha ha ha ha.

Good one. Are those the kind of jokes you share with your “zillions of experts”, Navy Davy? If so, I can see why they charge you so much to talk with them.

Comment #2888

Posted by Bob Maurus on May 26, 2004 6:43 AM (e)

My wife caught Neal Boortz (libertatian talk radio host) this morning on her commute. He was talking about the study, and she says he insisted that it provided genetic research that proved that Chihuahuas were, in fact, not dogs but rats - but then Boortz can be pretty outageous. I guess a couple of listeners bit.

Comment #2889

Posted by Bob Maurus on May 26, 2004 6:58 AM (e)

That’s cute Navy Davy, but I don’t think it’s possible. I think, though, he might could do a backbreeding experiment using Malemutes and Siberians as his basic stock and stringently selecting for resemblance, and eventually arrive at something that looked like a wolf. I believe that was done to recreate the appaloosa. I also think I read somewhere that Predzawalzki’s (sp?) Horse was recreated from existing offspring from Predz/domestic matings. You might want to pass that on to Uncle Jethro.

Cheers,
Bob

Comment #2905

Posted by tafga on May 26, 2004 12:11 PM (e)

A great study to support a conclusion understood intuitively by most. What is sad is that no-one would dare apply the same kind of analysis to human populations because of the fear of being labelled a racist and of providing fodder to racist people who would use the findings to support incorrect and jaundiced conclusions.

As human populations mix with increasing frequency, we are pregressively losing the opportunity to understand the earliest stages in population divergences which occurred in the past. We are justifiably afraid to apply the principle that “population divergence is the beginning of incipient speciation” to our own species. Rather, a lot of intellectual horsepower is focused on confirming the obvious -that we are all one species - just to counter racist idiocy. What a pity.

It is gratifying to know that canine characteristics that “breed true” are genetically based and unique, and that identification of such a genetic basis of consistent variation between breeds does not automatically consign the breeds to different species. What a shame we can not do the same for ourselves. I for one would like to understand some of the genetic basis for the variation of characteristics between the different populations of our own single species. We are nearly as diverse as domestic dogs, except no-one DID it to us - it happened naturally. What a wonderful natural experiment - and we are virtually ignoring the implications for studying and understanding evolutionary processes. Moreover, looking at canine variations and the manner in which characteristics are inherited in mixed-breed dogs, the genetic basis, just like ours, does not appear to be simple single-gene Mendellian inheritance.

Racism is not only damaging to the targets of its own xenophobia, but to science as well.

tafga

Comment #2907

Posted by Marmaduke on May 26, 2004 1:04 PM (e)

We are nearly as diverse as domestic dogs

I disagree with this admittedly vague statement.

For example, does any adult human race weigh more than ten times any other adult human race, on average?

My opinion is that dogs are quite a bit more diverse than humans, as we might expect them to be (given their artificial manipulation by humans).

Comment #2909

Posted by Reed A. Cartwright on May 26, 2004 1:31 PM (e)

Actually the study found that dogs weren’t that diverse. Most of the 200+ breeds examined fell into one large grouping with no descernible evolutionary structure. Note that they didn’t look at all dogs, but at the purebred ones. These purebreeds are highly imbred and totally isolated from other breeds. Because of this isolation they were able to use a large set of microsattlite markers to detect detect with 99% accuracy an individuals breed.

Such a study would not work on humans or mongrels.

Comment #2910

Posted by Marmaduke on May 26, 2004 1:41 PM (e)

Reed -

I believe that tafga was not referring to the similarity of DNA sequences when he/she used the term “diverse.” Rather, I think tafga understood “diverse” to mean “variation of characteristics,” i.e., phenotypes, between dog breeds.

It’s obviously somewhat subjective but as I scan through my mind the phenotypic characteristics which are used to describe the various races of humans, the amount of variation isn’t as extreme as the difference between, say, a miniature chihuahua and an Irish Wolfhand. Or a bulldog and a greyhound. Or a dachsund and a St. Bernard. Etc.

Comment #2920

Posted by Navy Davy on May 26, 2004 3:39 PM (e)

Can I ask a stupid question to the dog pound?

Assuming macroevolution is the best explanation of what happened in the past, then it logically follows that: (a) it is happening right now and (b) it will continue to happen in the future.

Granted, it might be happening at imperceptably slow speed.

But my questions are:

1. Are there any species right now (sea urchins?bacteria? bugs?) that are undergoing natural speciation as we speak?

2. And if so, What changes in DNA do we observe of any particular organism of a species, undergoing such speciation?

Much obliged,

Navy Davy

Comment #2923

Posted by Bob Maurus on May 26, 2004 4:22 PM (e)

Navy Davy,
Depending on your definition of species, I would suggest for starters: sticklebacks, lions, tigers, horses, asses, possibly zebras, wolves, jackals, foxes, a couple of monkey species I can’t remember at the moment, and Darwin’s assorted finches.

As to DNA changes, potentially not much, judging by the differences between chimps and humans?

Cheers,
Bob

Comment #2925

Posted by Navy Davy on May 26, 2004 4:31 PM (e)

Bob Maurus,

Thanks … I think:)

1. How can jackals (for example) be undergoing speciation, without corresponding changes in their DNA?

2. How does one differentiate between observed normal variations within the species and actual speciation?

Comment #2927

Posted by Wesley R. Elsberry on May 26, 2004 4:42 PM (e)

Navy Davy,

Re: (1) The key phrase you are looking for is “incipient speciation”, and there is a voluminous literature on this. Visit the library and be prepared for a lot of hits on a search.

There is a FAQ on observed speciation at the TalkOrigins Archive.

Re: (2) Quite a lot of the speciation events that have been observed have some form of chromosomal rearrangement or some duplication of karyotype (various forms of polyploidy). Some speciation, though, seems to require little in the way of change in genetics or morphology, as in some neotropical pseudoscorpions.

Comment #2928

Posted by Wesley R. Elsberry on May 26, 2004 4:50 PM (e)

Navy Davy,

The FAQ on observed speciation discusses a number of current species concepts. Distinguishing intraspecific variation from speciation woud depend upon which species concept is appropriate.

For most of the animals that laymen are familiar with, though, obligate reproductive isolation is a sufficient criterion. The pseudoscorpions mentioned in my last comment show post-zygotic reproductive isolation, for example, even though the daughter species do not have distinct morphological differences.

Comment #2931

Posted by Navy Davy on May 26, 2004 5:08 PM (e)

Wesley,

Appreciate your informed comments and the cited material. In the process of reviewing. Memo to self: Brush up on “post-zygotic reproductive isolation”:)

Cheers, Navy Davy

Comment #2932

Posted by Navy Davy on May 26, 2004 5:10 PM (e)

Wesley,

Appreciate your informed comments and cited materials. Will review and digest.

Much obliged,

Navy Davy

Comment #2934

Posted by RBH on May 26, 2004 5:44 PM (e)

Navy Davy wrote

Assuming macroevolution is the best explanation of what happened in the past, then it logically follows that: (a) it is happening right now and (b) it will continue to happen in the future.

Um, “macroevolution” is not an explanation; it’s a phenomenon that requires explanation.

Navy Davy asked

1. Are there any species right now (sea urchins?bacteria? bugs?) that are undergoing natural speciation as we speak?

2. And if so, What changes in DNA do we observe of any particular organism of a species, undergoing such speciation?

Try this paper for an instance of what appears to be speciation in progress with some analyses of the genetics associated with the phenomenon.

RBH

Comment #2935

Posted by Bob Maurus on May 26, 2004 6:27 PM (e)

Navy Davy,
As I said, depending on your definition of species.

Lions and tigers are cross-fertile. Horses and asses are cross-fertile. Wolves, coyotes, jackals, foxes, and domestic dogs are cross-fertile. Darwin’s Finches are all one species, but with such drastically different physical attributes and habits that they don’t recognizde each other, and consequently don’t interbreed.

All of these examples are, if not separate species, well on their way to becoming separate species - if we don’t drive them into extinction first.

The Galapagos Tortoises are another example, and also the Galapagos marine iguana.

Concerning your (1), I didn’t say there was no change. I suggested looking at the degree of DNA difference between humans and chimps (our closest relatives) to get an idea of how little there might be.

Concerning your (2), that’s where your operative definition of species comes into play. There are some in-depth posts on the Speciation thread that reference this question.

Most of the examples I listed are considered species by one criteria, but not necessarily by another. At the least, they’re species in the making.

With the exception of wolves and coyotes, and possibly domestic dogs, I’m not aware of any of the others interbreeding in the wild - obviously I’m talking about the different same family types here, not suggesting that lions and foxes can interbreed - which is one potential criteria. Lions and tigers have been crossed in captivity, and mules have been bred for hundreds or thousands of years.

Happy research - there’s lots of things that are still slippery. Thanks to Rich and others for some of this.

Bob

Comment #2965

Posted by Gwangi on May 27, 2004 7:13 AM (e)

To get back to the original topic here, I find it a bit sad that we have to justify basic research by saying that it could potentially lead to new ideas about human diseases. I work with the brains of songbirds, looking at areas that are in no way connected to anything that we even come close to having. Whenever new people find out what I do, they invariably ask how it relates to humans. When they find out it doesn’t, they give me looks like I’m throwing my life away. Whatever happened to people doing research for research’s own sake?

Comment #2975

Posted by tafga on May 27, 2004 8:31 AM (e)

I agree with the commentors, above. We are not morphologically as diverse as canids, but there are few other cosmopolitan species in the world that match the diversity of either us or dogs. In that respect we are similarly divergent within our respective species definitions.

My lamentation is that the natural divergence of the varieties of the human species, vs the conscious manipulation of the divergence of the varieties of dogs, is being mostly ignored - and those researches who tread into that territory are pilloried as racist.

Looking at us dispassionately, what are we? A cosmopolitan species with definite, albeit in some instances subtle, variation in heritable phenotypic characteristics between populations which are regionalized in a manner not unlike ring species, although not as systematically arranged. I was expressing a wish that we could have some basic research into this most intriguing of puzzles in human evolution in the manner being applied to dogs.

tafga

Comment #3209

Posted by Russell on May 30, 2004 7:13 PM (e)

Tafga’s questions remind me to ask - if there are any anthropology buffs reading this - what is the current thinking as to whether pre-modern human populations (e.g. those that came out of Africa prior to the migration around 200K years ago, e.g. Neanderthals in Europe) contributed anything to the genes of you and me? Last I checked, the question still seemed open.

Comment #3226

Posted by Bob Maurus on May 31, 2004 5:13 AM (e)

Also referencing tafqa’s last post - I would venture to assume that even, say, 100 years ago, the surface/”cosmetic” differences between various european etnic groups was more distinct than now, as xenophilia has steadily replaced xenophobia, or as the globe has shrunk.

A personal anecdote - we spent a couple of years in Okinawa during the 60s (USAF). My wife and I were in a bar in Kadena city one night, and a “hostess” sat down at our table, thinking she recognized Ginger. When corrected, she replied, “Sorry, all you round-eyes look alike to me.” We were understandably amused at the twist of the cliche.