Tag: Mitochondrial DNA

The book! Chapter Six.

Where Philip truly embraces the history, the very long history of man and dog.

I left Chapter Five with the lead character, Philip, having been given a detailed introduction into the social order of dogs, especially the roles and attributes of the three teaching dogs: Mentor, Minder and Nannie and realising that his German Shepherd dog, Pharaoh, was a Minder teaching dog (as he is in real life!).

One of our friends from our Payson days, dear MaryA, has been reading the chapters as they have been published in this place.  Her comment in a subsequent telephone conversation was that she found it a bit too intricate, a bit too drawn-out.  That accorded with Jeannie’s view.

It’s clear that much of the so-called fictional writing is highly auto-biographical.  I have no idea whether or not the ‘novel’ gets rejected because of that, or even if rejection is even part of what follows when the 50,000 words are achieved.

But anyone who knows my real life story will not have too much trouble reading between the lines of the fictional account of Philip’s life.

The consequence of this is that, at times, the words flow very easily because it’s very real in my own mind.  Thus too much detail, too much minutia, is a valid criticism.  Then again, the pressure of writing an average of 1,667 words a day, day in and day out, makes ‘dumping’ lots of detail feel rewarding because one is keeping up.  Just as an aside, at the time of writing this post, 3:30pm yesterday, Pacific Time, the NaNoWriMo counter shows that 21,720 words have been written against a requirement by the end of today, Day 13, for 21,677!  I have written for about three hours today. I’m 43 words ahead!

OK, enough of that. Here’s Chapter Six.

oooOOOooo

Learning from Dogs

Chapter Six

Yet again his return to Harberton had him describing to Maggie outcomes so very different to what he had been expecting when he had left the house. It was starting to be an expectation.  That, try as hard as he could to predict what he and Pharaoh were off to do, within a few hours of leaving home he would be returning with a report of events totally unanticipated.

However, these serendipitous and surprising events shared one common journey.  That journey of Philip better understanding the reality of his relationship with dogs in general, and with Pharaoh in particular. The visit to Angela earlier in the morning being outstanding in this regard; he would forever look at Pharaoh with different eyes.

He spent the afternoon pottering about the house and after supper settled down in front of the fire and picked up the article that Angela had given him as he and Pharaoh left her place.

Twenty minutes later, having read the article, he looked across to Maggie, who had settled down in an easy chair just opposite him, the fire creating a mood of comfort and contentment all around, and said, “Wow, Maggie, I had absolutely no idea that the relationship of humans with dogs went so far back in time.  This article is mind-blowing. It’s by a Dr. George Johnson who, according to his bio, is Professor Emeritus of Biology at Washington University in St. Louis.”

Philip went on to say, a smile across his face, in a more-or-less throwaway manner, “You know some day I must really understand what an emeritus professor means. Ah well!”

“Why don’t you read the article to me,” came Maggie’s reply.

“Alright, that would be nice.  Let me skip the opening paragraph and go straight to the heart of what Johnson writes.”

He ran his eye down the page.

“Apparently, the author had a dog called Boswell who died from choking on a chicken bone, which sort of raises some questions, but anyway then  Johnson writes in his second paragraph.

This week I found myself wondering about Boswell’s origins. From what creature did the domestic dog arise? Darwin suggested that wolves, coyotes, and jackals — all of which can interbreed and produce fertile offspring — may all have played a role, producing a complex dog ancestry that would be impossible to unravel. In the 1950s, Nobel Prize-winning behaviourist Konrad Lorenz suggested some dog breeds derive from jackals, others from wolves.

Based on anatomy, most biologists have put their money on the wolf, but until recently there was little hard evidence, and, as you might expect if you know scientists, lots of opinions.”

Philip looked up. “Is this OK for you? Am I reading clearly?”

“Yes, of course,” Maggie replied.

Philip again looked down at the paper, continuing, “The issue was finally settled in 1997 by an international team of scientists led by Robert Wayne of the University of California, Los Angeles. To sort out the evolutionary origin of the family dog, Wayne and his colleagues used the techniques of molecular biology to compare the genes of dogs with those of wolves, coyotes and jackals.

Wayne’s team collected blood, tissue, or hair from 140 dogs of sixty-seven breeds, and 162 wolves from North America, Europe, Asia, and Arabia. From each sample they extracted DNA from the tiny organelles within cells called mitochondria.”

Philip paused, took a couple of breaths, and carried on.

“While the chromosome DNA of an animal cell derives from both parents, the mitochondrial DNA comes entirely from the mother. Biologists love to study mitochondrial DNA because of this simple line of descent, female-to-female-to-female. As changes called mutations occur due to copying mistakes or DNA damage, the mitochondrial DNA of two diverging lines becomes more and more different. Ancestors can be clearly identified when you are studying mitochondrial DNA, because clusters of mutations are not shuffled into new combinations like the genes on chromosomes are. They remain together as a particular sequence, a signature of that line of descent.”

Philip again paused, looked up at Maggie. “Have to say I’m not completely clear just what the author is explaining here but, as you will hear, the crux of the findings is unmistakable.”

Turning back to the article, he continued, “When Wayne looked at his canine mitochondrial DNA samples, he found that wolves and coyotes differ by about 6% in their mitochondrial DNA, while wolves and dogs differ by only 1%. Already it smelled like the wolf was the ancestor.

Wayne’s team then focused their attention on one small portion of the mitochondrial DNA called the control region, because it was known to vary a lot among mammals. Among the sixty seven breeds of dogs, Wayne’s team found a total of 26 different sequences in the control region, each differing from the others at one or a few sites. No one breed had a characteristic sequence — rather, the breeds of dogs share a common pool of genetic diversity.”

Philip again looked up at Maggie.

“This is where it gets fascinating,” and looking back down, went on to read, “Wolves had 27 different sequences in the control region, none of them exactly the same as any dog sequence, but all very similar to the dog sequences, differing from them at most at 12 sites along the DNA, and usually fewer.

Coyote and jackal were a lot more different from dogs than wolves were. Every coyote and jackal sequence differed from any dog sequence by at least 20 sites, and many by far more.

That settled it. Dogs are domesticated wolves.”

The dog’s origin is the wolf. Philip paused, wanting the significance of this to settle over the two of them.  Or, perhaps, better said, settle over the three of them, for Pharaoh was laying prone on his tummy with his head resting between both outstretched front paws.  He was far from sleeping.  One could almost imagine that he was as engrossed in the findings of Dr. George Johnson as Maggie appeared to be.

Philip continued, “Using statistical methods to compare the relative similarity of the sequences, Wayne found that all the dog sequences fell into four distinct groups. The largest, containing 19 of the 26 sequences and representing 3/4 of modern dogs, resulted from a single female wolf lineage. The three smaller groups seem to represent later events when other wolves mated with the now-domesticated dogs. Domestication, it seems, didn’t happen very often, and perhaps only once.”

Again, Philip looked up, “Maggie, just listen to this last paragraph.

The large number of different dog sequences, and the fact that no wolf sequences are found among them, suggests that dogs must have been separated from wolves for a long time. The oldest clear fossil evidence for dogs is 12,000 – 14,000 years ago, about when farming arose. But that’s not enough time to accumulate such a large amount of mitochondrial DNA difference. Perhaps dogs before then just didn’t look much different from wolves, and so didn’t leave dog-like fossils. Our species first developed speech and left Africa about 50,000 years ago. I bet that’s when dogs came aboard, when our hunter-gatherer ancestors first encountered them. They would have been great hunting companions.”

Philip put the article down on the low wooden table in front of the settee. Pharaoh rolled over on to his side and closed his eyes.

“Just think, Maggie, humans have had a relationship with dogs for fifty thousand years. It really does feel that we humans were only able to evolve from the life-style of hunter-gatherer to that of farmer because of dogs.  By that I mean that dogs helped us to be such successful hunters; that we became so well nourished that we weren’t living hand-to-mouth, as it were.  Plus that dogs could protect us as we cleared the lands and became farmers of nature’s bounty.”

There was a silence in the living room.  A silence that flowed from both Maggie and Philip letting the enormity of these findings work their way into their consciousnesses. Fifty thousand years. It was almost beyond grasp.  Surely no other animal has been so bound to the fortunes of humans as the dog.  Philip had no intellectual or educational background, no objective means, to embrace this finding in anything other than a deeply subjective, emotional way.  He couldn’t articulate what it surely had to mean for the animal species, dog, to have been living, and dying, in such close association to the human species, man, for fifty thousand years.  “Phew!” was the only sound to escape his lips.

“Just going to step outside, Maggie.”

“OK,” she replied.  “Oh, looks as though Pharaoh’s coming out with you.”

Philip and Pharaoh stood on that gravelly front level just down from the front door.  It was a crystal clear night.  In the cul-de-sac where they lived, the glow of room-lights from many other homes was shining out through drawn curtains in numerous windows.

Overhead, the scale of the night sky spoke to him.  Those twinkling stars seemed to offer the same feelings of time and distance as those years of the relationship between man and dog.  That distant starlight that had been journeying for inconceivable amounts of time arriving here, at this very moment, this very instance, shining down on man and dog that, likewise, had been on an incredible journey; shining down on Philip and Pharaoh.

1,580 words. Copyright © 2013 Paul Handover

From wolf to dog!

The science behind our fabulous dogs.

I was doing some research for another writing project about the history of the domestication of the dog and came across a peer-reviewed article on The National Center for Biotechnology Information website, here in the USA.  The article was entitled: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. The website link is here.  (As an aside, if you drop in here and look at the NCBI sitemap it may well serve as an excellent resource.)

Anyway, the dog domestication article is, of necessity, highly scientific but nonetheless worth the read.  Here’s a taste from the Abstract.

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication 1,2. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data 3

But what really caught my eye was Figure 1, a wonderful illustration of the links between all the breeds of dogs and the grey wolf.

Neighbour-joining trees of domestic dogs and grey wolves.
Neighbour-joining trees of domestic dogs and grey wolves.

From:Nature. Author manuscript; available in PMC 2012 November 9.
Published in final edited form as: Nature. 2010 April 8; 464(7290): 898–902.
Published online 2010 March 17. doi: 10.1038/nature08837

Copyright/License ►Request permission to reuse

Branch colour indicates the phenotypic/functional designation used by dog breeders 8,9. A dot indicates ≥95% bootstrap support from 1,000 replicates. a, Haplotype-sharing cladogram for 10-SNP windows (n = 6 for each breed and wolf population). b, Allele-sharing cladogram of individuals based on individual SNP loci. c, Haplotype-sharing phylogram based on 10-SNP windows of breeds and wolf populations. d, Allele-sharing phylogram of individual SNPs for breeds and wolf populations. For c and d, we note breeds where genetic assignments conflict with phenotypic/functional designations as follows: 1, Brussels griffon; 2, Pekingese; 3, pug; 4, Shih-tzu; 5, miniature pinscher; 6, Doberman pinscher; 7, Kuvasz; 8, Ibizian hound; 9, chihuahua; 10, Pomeranian; 11, papillon; 12, Glen of Imaal; 13, German shepherd; 14, Briard; 15, Jack Russell; 16, dachshund; 17, great schnauzer; and 18, standard schnauzer. Gt, great; mtn, mountain; PBGV, petit basset griffon vendeen; pin., pinscher; ptr, pointer; ret., retriever; shep., shepherd; sp., spaniel; Staf., Staffordshire; std, standard; terr., terrier. Canine images not drawn to scale. Wolf image adapted from ref. 31; dog images from the American Kennel Club (http://www.akc.org).

The diagram on its own was a bit of a struggle but looked at in conjunction with the research paper was much better understood.  Another reason for going to the original article on the NCBI website is the interesting range of links to other scientific papers that may be seen to the right-hand side of the screen. For example:

Coat variation in the domestic dog is governed by variants in three genes.

mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves.

that included this in the Abstract:

The mean sequence distance to ancestral haplotypes indicates an origin 5,400-16,300 years ago (ya) from at least 51 female wolf founders. These results indicate that the domestic dog originated in southern China less than 16,300 ya, from several hundred wolves. The place and time coincide approximately with the origin of rice agriculture, suggesting that the dogs may have originated among sedentary hunter-gatherers or early farmers, and the numerous founders indicate that wolf taming was an important culture trait.

Ancient DNA evidence for Old World origin of New World dogs.

Abstract

Mitochondrial DNA sequences isolated from ancient dog remains from Latin America and Alaska showed that native American dogs originated from multiple Old World lineages of dogs that accompanied late Pleistocene humans across the Bering Strait. One clade of dog sequences was unique to the New World, which is consistent with a period of geographic isolation. This unique clade was absent from a large sample of modern dogs, which implies that European colonists systematically discouraged the breeding of native American dogs.

If you needed a reminder of the Pleistocene period, as I did, there’s a helpful Wikipedia entry here.

The final link that I wanted to highlight was this one, for all dog owners who worry about the health of our dogs.

The legacy of domestication: accumulation of deleterious mutations in the dog genome.

Abstract

Dogs exhibit more phenotypic variation than any other mammal and are affected by a wide variety of genetic diseases. However, the origin and genetic basis of this variation is still poorly understood. We examined the effect of domestication on the dog genome by comparison with its wild ancestor, the gray wolf. We compared variation in dog and wolf genes using whole-genome single nucleotide polymorphism (SNP) data. The d(N)/d(S) ratio (omega) was around 50% greater for SNPs found in dogs than in wolves, indicating that a higher proportion of nonsynonymous alleles segregate in dogs compared with nonfunctional genetic variation. We suggest that the majority of these alleles are slightly deleterious and that two main factors may have contributed to their increase. The first is a relaxation of selective constraint due to a population bottleneck and altered breeding patterns accompanying domestication. The second is a reduction of effective population size at loci linked to those under positive selection due to Hill-Robertson interference. An increase in slightly deleterious genetic variation could contribute to the prevalence of disease in modern dog breeds.

Have to say that there are some fabulous learning opportunities from the enormous range of websites available nowadays.

What is the dog?

Time to attempt an answer to this fundamental, well for this Blog, question!

 

Like wolves, the Dingo is smarter than pet dogs.

(The above photograph comes from an article on ImpactLab – see foot of Post for more details.)

When putting together the Blog ahead of the publication of the very first Post on July 15th, 2009, some 820 Posts ago, I prepared some additional material that set out to justify the Raison d’être for the venture.  Included was a piece regarding Dogs and integrity.  There I wrote:

Dogs are part of the Canidae, a family including wolves, coyotes and foxes, thought to have evolved 60 million years ago.  There is no hard evidence about when dogs and man came together but dogs were certainly around when man developed speech and set out from Africa, about 50,000 years ago.  See an interesting article by Dr. George Johnson.

Anyway, I revisited the article written by Dr Johnson and thought it worthy of being published in full, as a separate article in Learning from Dogs.  I requested permission to reproduce the article in full and Dr. George Johnson was very gracious in quickly coming back to me giving his agreement.  Thank you.  The original article can be read here, the ONSCIENCE home page is here and Dr. Johnson’s details are here.

Evolution of the family dog

I first suspected that Boswell would have a short life when he bit my wife on our nuptial bed.

Boswell was my dog, a feisty Toto-like terrier who shared my bachelor bed and resented the intrusion of a woman where he felt a dog — Boswell — ought to be. As it turns out, my suspicion was correct, and he did not live out the year, which was 1982. Staying with others while I and my bride were overseas, Boswell resented being denied chicken bones, ate them anyway, and died of the consequences. To this day I miss him.

This week I found myself wondering about Boswell’s origins. From what creature did the domestic dog arise? Darwin suggested that wolves, coyotes, and jackals — all of which can interbreed and produce fertile offspring– may all have played a role, producing a complex dog ancestry that would be impossible to unravel. In the 1950s, Nobel Prize-winning behaviorist Konrad Lorenz suggested some dog breeds derive from jackals, others from wolves.

Based on anatomy, most biologists have put their money on the wolf, but until recently there was little hard evidence, and, as you might expect if you know scientists, lots of opinions.

The issue was finally settled in 1997 by an international team of scientists led by Robert Wayne of the University of California, Los Angeles. To sort out the evolutionary origin of the family dog, Wayne and his colleagues used the techniques of molecular biology to compare the genes of dogs with those of wolves, coyotes and jackals.

Wayne’s team collected blood, tissue, or hair from 140 dogs of sixty-seven breeds, and 162 wolves from North America, Europe, Asia, and Arabia. From each sample they extracted DNA from the tiny organelles within cells called mitochondria.

While the chromosome DNA of an animal cell derives from both parents, the mitochondrial DNA comes entirely from the mother. Biologists love to study mitochondrial DNA because of this simple line of descent, female-to-female-to-female. As changes called mutations occur due to copying mistakes or DNA damage, the mitochondrial DNA of two diverging lines becomes more and more different. Ancestors can be clearly identified when you are studying mitochondrial DNA, because clusters of mutations are not shuffled into new combinations like the genes on chromosomes are. They remain together as a particular sequence, a signature of that line of descent.

When Wayne looked at his canine mitochondrial DNA samples, he found that wolves and coyotes differ by about 6% in their mitochondrial DNA, while wolves and dogs differ by only 1%. Already it smelled like the wolf was the ancestor.

Wayne’s team then focused their attention on one small portion of the mitochondrial DNA called the control region, because it was known to vary a lot among mammals. Among the sixty seven breeds of dogs, Wayne’s team found a total of 26 different sequences in the control region, each differing from the others at one or a few sites. No one breed had a characteristic sequence — rather, the breeds of dogs share a common pool of genetic diversity.Wolves had 27 different sequences in the control region, none of them exactly the same as any dog sequence, but all very similar to the dog sequences, differing from them at most at 12 sites along the DNA, and usually fewer.

Coyote and jackal were a lot more different from dogs than wolves were. Every coyote and jackal sequence differed from any dog sequence by at least 20 sites, and many by far more.

That settled it. Dogs are domesticated wolves.

Using statistical methods to compare the relative similarity of the sequences, Wayne found that all the dog sequences fell into four distinct groups. The largest, containing 19 of the 26 sequences and representing 3/4 of modern dogs, resulted from a single female wolf lineage. The three smaller groups seem to represent later events when other wolves mated with the now-domesticated dogs. Domestication, it seems, didn’t happen very often, and perhaps only once.

The large number of different dog sequences, and the fact that no wolf sequences are found among them, suggests that dogs must have been separated from wolves for a long time. The oldest clear fossil evidence for dogs is 12,000 – 14,000 years ago, about when farming arose. But that’s not enough time to accumulate such a large amount of mitochondrial DNA difference. Perhaps dogs before then just didn’t look much different from wolves, and so didn’t leave dog-like fossils. Our species first developed speech and left Africa about 50,000 years ago. I bet that’s when dogs came aboard, when our hunter-gatherer ancestors first encountered them. They would have been great hunting companions.

I think Boswell would be happy to know his ancestor was a wolf. I doubt, however, I will ever be able to get my wife to overlook the biting as “wolf genetic baggage” inherited from nobel ancestors. In my house, science only stretches so far. © Txtwriter Inc

As so often happens, for reasons quite beyond me, when I am pursuing an article idea something else crops up that is highly relevant to my musings.  This was no exception.

A recent article in the Christian Science Monitor describes finding a fragment of dog bone in North America dating back some 9,400 years.  Here’s a flavour of that article.

By Associated Press / January 19, 2011

PORTLAND, MaineNearly 10,000 years ago, man’s best friend provided protection and companionship — and an occasional meal.

That’s what researchers are saying after finding a bone fragment from what they are calling the earliest confirmed domesticated dog in the Americas.

University of Maine graduate student Samuel Belknap III came across the fragment while analyzing a dried-out sample of human waste unearthed in southwest Texas in the 1970s. A carbon-dating test put the age of the bone at 9,400 years, and a DNA analysis confirmed it came from a dog — not a wolf, coyote or fox, Belknap said.

Because it was found deep inside a pile of human excrement and was the characteristic orange-brown color that bone turns when it has passed through the digestive tract, the fragment provides the earliest direct evidence that dogs — besides being used for company, security and hunting — were eaten by humans and may even have been bred as a food source, he said.

Belknap wasn’t researching dogs when he found the bone. Rather, he was looking into the diet and nutrition of the people who lived in the Lower Pecos region of Texas between 1,000 and 10,000 years ago.

The article then, a little later, goes on to say:

Dogs have played an important role in human culture for thousands of years.

There are archaeological records of dogs going back 31,000 years from a site in Belgium, 26,000 years in the Czech Republic and 15,000 years in Siberia, said Robert Wayne, a professor of evolutionary biology at UCLA and a dog evolution expert. But canine records in the New World aren’t as detailed or go back nearly as far.

Darcy Morey, a faculty member at Radford University who has studied dog evolution for decades, said a study from the 1980s dated a dog found at Danger Cave, Utah, at between 9,000 and 10,000 years old. Those dates were based not on carbon-dating or DNA tests, but on an analysis of the surrounding rock layers.

“So 9,400 years old may be the oldest, but maybe not,” Morey said in an e-mail.

Morey, whose 2010 book, “Dogs: Domestication and the Development of a Social Bond,” traces the evolution of dogs, said he is skeptical about DNA testing on a single bone fragment because dogs and wolves are so similar genetically.

My last extract is as follows:

Darcy Morey, a faculty member at Radford University who has studied dog evolution for decades, said a study from the 1980s dated a dog found at Danger Cave, Utah, at between 9,000 and 10,000 years old. Those dates were based not on carbon-dating or DNA tests, but on an analysis of the surrounding rock layers.

“So 9,400 years old may be the oldest, but maybe not,” Morey said in an e-mail.

Morey, whose 2010 book, “Dogs: Domestication and the Development of a Social Bond,” traces the evolution of dogs, said he is skeptical about DNA testing on a single bone fragment because dogs and wolves are so similar genetically.

Fascinating.

Finally, going back to the photograph at the top of the page, this came from an article here in ImpactLab.  It’s well worth a read.