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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