Student assignment. (requirement for course by Peter Kabai)

Relaxation of selective constraint on dog mitochondrial DNA following domestication

In this assignment I worked with the article Relaxation of selective constrain on dog mitochondrial DNA following domestication by Susanne Bjornfeldt, Matthew T.Webster and Carles Vila. (http://www.genome.org/cgi/content/full/16/8/990)

They had a theory that after the dog was domesticated the selective constraint on the dogs mutations decreased, so that more weakly deleterious mutation could accumulate. They thought that this could have had a great impact on the dog species as we see it today.

The dog is the mans best friend, and inspires and interests us in so many ways. He is our companion and a part of our family. We are able to get a dog that is compatible to our life and requirements. How is it that the dog went from a wild animal, hunting and struggling for life, to such a diverse domesticated breed?

There has been several theories regarding how the dog became domesticated and who were its ancestors. There has also been several theories of when this happened. Earlier the fossil founds has been the scientific answer for the dogs history. The fossils at the proposed sites all date from between 10,000 and 20,000 years ago, times that slightly predate the origins of agriculture. Writes Christine Mlot in her article Stalking the ancient dog (http://www.sciencenews.org/pages/sn_arc97/6_28_97/bob1.htm).

However with todays molecular biology science has been able to unchart the dogs genome, and since we have representatives from its ancestors it is possible to just do so; Stalk the ancient dog.

Recent studies show that the dog might be as much as 100 000 years old. Instead of a 10,000- to 20,000-year time frame, Robert K. Wayne of the University of California, Los Angeles and his colleagues now have evidence that dogs could have been domesticated 100,000 years ago -- if not earlier. Christine Mlot also writes in her article, (http://www.sciencenews.org/pages/sn_arc97/6_28_97/bob1.htm).

This is interesting when questioning how the dog managed to get such a genetic diversity that the dog could become the most diverse species both appearance and behavioural.

It is scientifically proved that the wolf is the dogs ancestor, so why do the dog show this great variation compared to wolves, which have excised for a much longer time? Do the dog show bigger genetic diversity and why?

After the dog was domesticated it has changed dramatically and in different directions, no other species show these great differences. Over the years there has been developed a large diversity of breeds, which differ greatly from each other. So how is it that the Chihuahua and the Grand Danios can be the same species, and how did this happen?

This question the researchers from the Department of Evolutionary Biology from Uppsala in Sweden asked themselves and did a scientific research on the matter. They had the hypothesis that the domestication of the dog, which changed the dogs lifestyle, also had an impact on the dogs genome. They thought that after the dog was domesticated the natural selection was relaxed and weakly deleterious mutations could survive. These mutations would never have stayed in the species in the wild because they would have lead to less fitness. But after humans took in the dog, the survival constraint was not the same problem as earlier. The fact that these mutations were carried on to the next generations could have a lot to say regarding the dogs genetic material today.

The researchers used mitochondrial DNA to track the evolution of the dogs genome. There is no change in mtDNA from parent to offspring and the mutation rate is much higher then for regular DNA and is easily measured. This makes mtDNA good for tracking ancestry for species.

The researchers knew from previous studies that the dog mtDNA showed that most likely the dogs today come from four different sites of domestication. Therefor they needed to sample mtDNA from representatives from each of these clades. They sampled 88 dogs from 53 breeds, where 14 were selected. Previous studies also show that most of the dog breeds today derived from only one of these clades.

They also sampled wolves from different parts of the world to be good representatives of the earlier wolf population, which was in much greater magnitude the time of the dogs domestication. There were wolf representatives from Spain, Russia, Saudia Arabia, North America and Sweden.

Three coyotes were also sampled. Both wolf, jackal and coyote has been theories for the dogs ancestors, because these can mate and produce fertile offspring. But we now know that the wolf is the only ancestor, due to gene tracking. The coyotes was used as outgroups in this study.

They constructed a phylogenetic gene tree from the mtDNA sequences. Using Bayesian approach[1] and neighbor joining approach[2].

The mtDNA sequences showed that the dog + wolf and cayote genes diverged at a much higher rate then between dogs and wolves.

The gene sequencing also supported the four clades of domestication.

The researchers did not find any significant difference between dog and wolf branches although synonymous evolution was on a average of 10,9% higher where leading to dogs.

This makes no evidence of any difference in mutation rate of dogs compared to wolves.

The study showed that the non-synonymous/synonymous evolution ratio was much higher in the dog linages compared to wolf. This was surprising since the dog species was such a growing population and this would indicate that it would be more likely to loose its deleterious allels. The researchers concluded that this could indicate the relaxation of the dogs mtDNA.

They also estimated non-synonymous/synonymous evolution ratio for ATP genes, NADH genes and cytochrome c oxidase genes. The results did not show any difference in non-synonymous/synonymous evolution ratios, this therefor indicates that dogs may have slowly accumulated weakly deleterious changes.

The researchers also used a method to examine the phenotypic effects of the mutations and the effects were categorized.The results of conservative to radical changes did not show any remarkable difference between the wolf, dog or coyote. This was probably because damaging mutations are most likely lost because they will not allow the animal to survive. This also supports their hypothesis that the less selective pressure of dog genes has lead to the accumulation of weakly deleterious genes.

The researchers believe that these weakly deleterious mutations not only lead to the great diversity of phenotypic traits of todays dog population, but also the diversity of diseases that we see among the different dog breeds today. The researchers also concluded that since the humans controlled the breeding they would favour dogs with the ability to cooperate and to be tamed compared to dogs with the best metabolic traits. This could lead to an increase in functional genetic diversity.

My opinion and believes is that living with humans gave the wolves a big advantage in their survival. They got food and protection, in return they probably made a good protection for the humans as well. This may be the start of the good relationship between the humans and dogs.

When the dog lived together with the humans the survival of the fittest did not so much affect them as earlier. This way the genes of their pack was no longer regulated by natural selection, and deleterious genes that would probably die out in nature got to survive. This lead to a greater genetic pool in the dog species. After further domestication the humans could affect the breeding of their domestic animals. This way they could chose which genes they wanted their future dogs to have. This selection was no longer based on the individuals ability to survive or reproduce, but rather on their ability to cooperate with humans. This probably had a great impact on the dogs genes today.

This also gives an explanation for how the dog can be so diverse. This great magnitude of individuals in the species along with their great gene pool was probably what made the diverse breeding possible.

I think the theory that the dog was domesticated earlier then first assumed is a good explanation for how the dog could have such a genetic diversity. I also believe the domesticated dog was a more similar looking dog until about 14 000 years ago, when agriculture began. The humans then needed dogs for different purposes, and would breed the dog to form different types of wanted behaviour. This could be the start of the more precise breeding and the great difference and magnitude of breeds today.

Links:

Research paper: http://www.genome.org/cgi/content/full/16/8/990

http://canidae.ca/dog.htm

http://www.trussel.com/prehist/news24.htm

http://www.sciencenews.org/pages/sn_arc97/6_28_97/bob1.htm

www.wikipedia.com

Madeleine Austgulen

[1] Probability suggested by Bayesian theory, the probability can be defined after whether a person believes a proposition or not. (Wikipedia)

[2] Neighbor joining is a bottom up cluster type of method to create a phylogenetic tree, usually used for DNA or protein sequence data. It is essential that you know the distance between each pair of taxa in the tree.

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Relaxation of selective constraint on dog mitochondrial DNA following domestication In this assignment I worked with the article Relaxation of selective constrain on dog mitochondrial DNA following domestication by Susanne Bjornfeldt, Matthew T.Webster and Carles Vila. (http://www.genome.org/cgi/content/full/16/8/990) They had a theory that after the dog was domesticated the selective constraint on the dogs mutations decreased, so that more weakly deleterious mutation could accumulate. They thought that this could have had a great impact on the dog species as we see it today. The dog is the mans best friend, and inspires and interests us in so many ways. He is our companion and a part of our family. We are able to get a dog that is compatible to our life and requirements. How is it that the dog went from a wild animal, hunting and struggling for life, to such a diverse domesticated breed? There has been several theories regarding how the dog became domesticated and who were its ancestors. There has also been several theories of when this happened. Earlier the fossil founds has been the scientific answer for the dogs history. The fossils at the proposed sites all date from between 10,000 and 20,000 years ago, times that slightly predate the origins of agriculture. Writes Christine Mlot in her article Stalking the ancient dog (http://www.sciencenews.org/pages/sn_arc97/6_28_97/bob1.htm). However with todays molecular biology science has been able to unchart the dogs genome, and since we have representatives from its ancestors it is possible to just do so; Stalk the ancient dog. Recent studies show that the dog might be as much as 100 000 years old. Instead of a 10,000- to 20,000-year time frame, Robert K. Wayne of the University of California, Los Angeles and his colleagues now have evidence that dogs could have been domesticated 100,000 years ago -- if not earlier. Christine Mlot also writes in her article, (http://www.sciencenews.org/pages/sn_arc97/6_28_97/bob1.htm). This is interesting when questioning how the dog managed to get such a genetic diversity that the dog could become the most diverse species both appearance and behavioural. It is scientifically proved that the wolf is the dogs ancestor, so why do the dog show this great variation compared to wolves, which have excised for a much longer time? Do the dog show bigger genetic diversity and why? After the dog was domesticated it has changed dramatically and in different directions, no other species show these great differences. Over the years there has been developed a large diversity of breeds, which differ greatly from each other. So how is it that the Chihuahua and the Grand Danios can be the same species, and how did this happen? This question the researchers from the Department of Evolutionary Biology from Uppsala in Sweden asked themselves and did a scientific research on the matter. They had the hypothesis that the domestication of the dog, which changed the dogs lifestyle, also had an impact on the dogs genome. They thought that after the dog was domesticated the natural selection was relaxed and weakly deleterious mutations could survive. These mutations would never have stayed in the species in the wild because they would have lead to less fitness. But after humans took in the dog, the survival constraint was not the same problem as earlier. The fact that these mutations were carried on to the next generations could have a lot to say regarding the dogs genetic material today. The researchers used mitochondrial DNA to track the evolution of the dogs genome. There is no change in mtDNA from parent to offspring and the mutation rate is much higher then for regular DNA and is easily measured. This makes mtDNA good for tracking ancestry for species. The researchers knew from previous studies that the dog mtDNA showed that most likely the dogs today come from four different sites of domestication. Therefor they needed to sample mtDNA from representatives from each of these clades. They sampled 88 dogs from 53 breeds, where 14 were selected. Previous studies also show that most of the dog breeds today derived from only one of these clades. They also sampled wolves from different parts of the world to be good representatives of the earlier wolf population, which was in much greater magnitude the time of the dogs domestication. There were wolf representatives from Spain, Russia, Saudia Arabia, North America and Sweden. Three coyotes were also sampled. Both wolf, jackal and coyote has been theories for the dogs ancestors, because these can mate and produce fertile offspring. But we now know that the wolf is the only ancestor, due to gene tracking. The coyotes was used as outgroups in this study. They constructed a phylogenetic gene tree from the mtDNA sequences. Using Bayesian approach[1] and neighbor joining approach[2]. The mtDNA sequences showed that the dog + wolf and cayote genes diverged at a much higher rate then between dogs and wolves. The gene sequencing also supported the four clades of domestication. The researchers did not find any significant difference between dog and wolf branches although synonymous evolution was on a average of 10,9% higher where leading to dogs. This makes no evidence of any difference in mutation rate of dogs compared to wolves. The study showed that the non-synonymous/synonymous evolution ratio was much higher in the dog linages compared to wolf. This was surprising since the dog species was such a growing population and this would indicate that it would be more likely to loose its deleterious allels. The researchers concluded that this could indicate the relaxation of the dogs mtDNA. They also estimated non-synonymous/synonymous evolution ratio for ATP genes, NADH genes and cytochrome c oxidase genes. The results did not show any difference in non-synonymous/synonymous evolution ratios, this therefor indicates that dogs may have slowly accumulated weakly deleterious changes. The researchers also used a method to examine the phenotypic effects of the mutations and the effects were categorized.The results of conservative to radical changes did not show any remarkable difference between the wolf, dog or coyote. This was probably because damaging mutations are most likely lost because they will not allow the animal to survive. This also supports their hypothesis that the less selective pressure of dog genes has lead to the accumulation of weakly deleterious genes. The researchers believe that these weakly deleterious mutations not only lead to the great diversity of phenotypic traits of todays dog population, but also the diversity of diseases that we see among the different dog breeds today. The researchers also concluded that since the humans controlled the breeding they would favour dogs with the ability to cooperate and to be tamed compared to dogs with the best metabolic traits. This could lead to an increase in functional genetic diversity. My opinion and believes is that living with humans gave the wolves a big advantage in their survival. They got food and protection, in return they probably made a good protection for the humans as well. This may be the start of the good relationship between the humans and dogs. When the dog lived together with the humans the survival of the fittest did not so much affect them as earlier. This way the genes of their pack was no longer regulated by natural selection, and deleterious genes that would probably die out in nature got to survive. This lead to a greater genetic pool in the dog species. After further domestication the humans could affect the breeding of their domestic animals. This way they could chose which genes they wanted their future dogs to have. This selection was no longer based on the individuals ability to survive or reproduce, but rather on their ability to cooperate with humans. This probably had a great impact on the dogs genes today. This also gives an explanation for how the dog can be so diverse. This great magnitude of individuals in the species along with their great gene pool was probably what made the diverse breeding possible. I think the theory that the dog was domesticated earlier then first assumed is a good explanation for how the dog could have such a genetic diversity. I also believe the domesticated dog was a more similar looking dog until about 14 000 years ago, when agriculture began. The humans then needed dogs for different purposes, and would breed the dog to form different types of wanted behaviour. This could be the start of the more precise breeding and the great difference and magnitude of breeds today. Links: Research paper: http://www.genome.org/cgi/content/full/16/8/990 http://canidae.ca/dog.htm http://www.trussel.com/prehist/news24.htm http://www.sciencenews.org/pages/sn_arc97/6_28_97/bob1.htm www.wikipedia.com Madeleine Austgulen [1] Probability suggested by Bayesian theory, the probability can be defined after whether a person believes a proposition or not. (Wikipedia) [2] Neighbor joining is a bottom up cluster type of method to create a phylogenetic tree, usually used for DNA or protein sequence data. It is essential that you know the distance between each pair of taxa in the tree.

Notes (if any) by Peter Kabai:
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