Phenotypic diversity from dogs to diseases

 

Whether you are trying to keep your neighbor’s German shepherd out of your yard or avoiding that biting Chihuahua on your way to the mail boxes – people have no problem identifying domestic dogs. Most can tell they are not foxes, wolves, or coyotes. There are approximately 400 different domestic dog breeds worldwide – but they all have the same taxonomic classification.

All domestic dogs belong to the same genus and species according to Linnean classification and that is Canis familiarus.  The genus was established in 1758 by Linnaeus to include dogs, wolves (C. rufus, C. lycaon, C. lupus, C. lupaster, C. simnesis) , coyotes (C. latrans), and jackals (C. aureus).  Foxes belong to the genus Vulpes and there are 12 species. This genus forms a clade meaning that they are all descended from a common ancestor.

Domestic dogs can be traced back to 15,000 to 100,000 years ago when they were originally descended from the Gray Wolf in East Asia (1).  Breeding programs have been used to select specific physical and behavioral characteristics of domestic dogs that had led to the observed phenotypic diversity.  The domestication process in general has selected for genetic changes and associated changes at the neurobiological level.  High prevalence illnesses are observed in some dog breeds suggesting that there are heritable loci that could be studied and provide some guidance for human diseases.  Purebred dogs can also have extensive genealogies including family histories and pathology data. 

In terms of comparative genomics (1) there are 4 clades of placental mammals  Afrotheria: ( elephants, manatees, and hyraxes), Xenartha: (sloths, anteaters, and armadillos),  Euarchontoglires: Euarchonta (primates, tree shrews, colugos) + Glires (rodents and lagomorphs), and Laurasiatheria: (shrews, hedgehogs, bats, and other carnivores including dogs).  The most extensively studied mammals at the genetic level all belong to Euarchontoglires (human, chimpanzee, mouse, rat). More detailed information on the dog genome allows for analysis for sections of conserved human DNA, reconstruction of the genetics of a common ancestor between clades, and investigations into the nature of polygenically determined illnesses.

One of the most interesting aspects of reference 1 is the phylogenic tree of the family Canidae showing the relationships between different phyla. This tree was constructed looking at 12 exons (8,080 base pairs (bp) and 4 introns (3029 bp). They were sequences in 30 of the 34 Canid species.  Note where domestic dogs are on the diagram. The boxer photo is used because the boxer genome was the prototypical analysis in this paper because it has some of the longest stretches of homozygosity (62%).  In the diagram clades are color coded (see legend). Each cladogram is constructed with Bayesian analysis generating the respective bootstrap values from Markov chain analysis and posterior probabilities (see legend for location). Indels are insertions-deletions.  Divergence times are in millions of years and are applied to the wolf-like clade discussed in the paper (color coded blue).   

The authors constructed a map of 2,559,519 SNPs (single nucleotide polymorphisms).  They were able to determine the SNP rate for domestic dog breeds and other Canids (wolves and coyotes) and determined it was essentially 1 SNP per 900 (bp) base pairs for all the dog breeds studied except the Alaskan malemute (~1/790 bp).  Wolves and coyotes had greater variation than dogs suggesting a bottleneck during dog domestication.   The authors also demonstrated limited haplotype diversity within dog breeds.  The boxer genome was shown to have homozygosity over 62% of the genome with long blocks having the same haplotype on both chromosomes. The authors looked at the haplotype structure and linkage disequilibrium (LD) across 224 dogs – 10 each from ten breeds and one each from an additional 24 breeds. They used this analysis to construct a population genetics picture of dogs. Among the conclusions is that the dog genome is older (9,000 generations) than the human genome (4,000 generations).   

This is probably a good spot to briefly discuss homozygosity and why that is important.  In terms of experiments. It reduces interindividual variation based on genetics.  Laboratory rats for example have nearly identical genomes after 20 crosses (sib-sib, parent-offspring).  There is a previous post on this blog that discusses stochastics based on behavioral variation in rats with nearly identical genotypes. Dog breeding is a variation on that theme. Dogs do not have the same high degree of homozygosity but they are in the intermediate range.  The majority of dogs in the US are not pure bred but are of mixed heritage.  They can still inherit morphological and behavioral traits as well as genetically based diseases.   The human genome has a lower level of homozygosity due to widespread migration from a common ancestor about 150,000 years ago, a longer life span, as well as cultural constraints such as limits on consanguinity or marriage or a reproductive relationship between two closely related individuals. In the case of marriage by first cousins there is data on consanguinity rates between countries. The medical concern with this practice is that as homozygosity increased the risk of genetically determined autosomal recessive illness increases. Autosomal dominant conditions remain problematic but are not contingent on inheriting identical genes from both parents.   

Species	Homozygosity - same alleles inherited from each biological parent
Norwegian Rat Rattus norvegicus	1: Considered genetically identical at 20 generations of crossbreeding but some heterozygous alleles can be found out to 40 generations. (7) 2:  Rat breeds (phenotypes) are analogous to dog breeds – as an example the albino lab rat is still Rattus norvegicus. 3:  Experimental results on one inbred colony cannot be generalized to the next.
Domestic dogs Canis familiarus	1:  Degree of homozygosity varies with breed and specifics of breeding procedure for pure bred dogs.  Pure bred dogs – 63% homozygosity (10) Mixed breed dogs – 53% homozygosity (10)
Humans Homo sapiens	1: 11% homozygosity in individuals who parents were first cousins (consanguineous) compared with the expected value of 1 out of 16 or 6% (8) applying basic models 2:   Range of homozygosity in humans is wide based on evolutionary factors (bottlenecks, founder effects, inbreeding, outbreeding, background relatedness).  Runs of homozygosity (ROH) are studied more often than whole genome comparisons.

 

In summary, the genetics of domestic dogs is interesting just considering the phenotypic diversity of Canis familiarus.  It highlights issues of classification and that have been discussed in many places on this blog. Students of biology are familiar with these issues from practically every course they have ever taken.  That does not appear to be the case for people who never studied these problems.  Medicine and psychiatry as branches of biology have similar degrees of freedom on an individual basis and for classification purposes.  Any physician knows that no two persons with the same diagnosis are identical and yet there are scores of critics, administrators, politicians, and healthcare companies operating under that illusion. There are similar illusions about social constructs describing some subpopulations.  All humans are still Homo sapiens.  Further subclassification at the genomic or molecular level may be possible but it does not negate the meaning of the Linnean classification.  

In terms of temperament, personality, and behavioral characteristics correlations exist at the genetic level.  Since most of the behavioral traits are polygenic in nature – they have to be considered very early results.   

 There are probably as many advocates that claim a diagnosis has a simplified meaning that they are either advocating for or against.  Socially constructed classifications like race are more problematic.  The basic observation that hundreds of obviously different looking dogs belonging to the same genus and species may drive the phenotypic diversity point home.  The fact that these dogs breeds are also morphologically and behaviorally diverse as well as the fact that that develop unique diseases – provides a potential opportunity for studying morphology and disease mechanisms in humans. Despite suggestions about dog being potential models for human neuropsychiatric disorders that may be too strong of an association.  The research I did for this post was interesting from an evolutionary and genomic standpoint.  It highlights potential genetic and neurobiological effects of domestication as a selective breeding process.

Considering the application of a similar phenotypical diversity concept to complex diseases – why would we not expect hundreds of phenotypes?  Current analyses seem to suggest very simple phenotyping.  In the case of major depression – a single item from a rating scale – emotional blunting or anhedonia and genetic correlates. Other complex diseases like asthma, systemic lupus erythematosus, and diabetes mellitus have similar problems.  On the other hand, we can look at the combinatorics of the verbal descriptions of depression and how many of those combination exist in a clinical population and find 126 subtypes of depression. The question for me is why a handful of rating scale phenotypes of depression would exist and not 126 or more? The same is true for any psychiatric disorder. And of those 126 or more types – what is happening at the genetic and molecular levels?  The idea of a better classification based on some verbal hierarchy or rearranging the verbal descriptions does not seem promising to me.  The dilemma of trying to classify natural phenomena by words is always a limitation. There is no better example than biological classification.       

 

George Dawson, MD, DFAPA

 

 

Graphics Credit:  From reference 1 with permission - Copyright Clearance Center License Number 6004620929064

 

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