Old Dog, New Dog: Genetic Map Tracks The Evolution Of Man’s Best Friend | @GrrlScientist

An extensive genomic map of dog breeds — the largest to date — published recently provides the first DNA evidence that dogs crossed the Bering land bridge alongside ancient humans, and it also will help veterinarians and researchers identify disease-causing genes in both dogs and men

by GrrlScientist for Forbes | @GrrlScientist

Figure 1. Genetic analysis of dog breeds reveals past migrations that led to the genetic mixing of multiple breeds. Colors correspond to those in figure 2. Breeds that form unique clades supported by 100% of bootstraps are combined into triangles. For all other branches, a gold star indicates 90% or better, black star 70% 89%, and silver star 50% 69% bootstrap support. Breeds are listed on the perimeter of the circle. A small number of dogs do not cluster with the rest of their breed, indicated as follows: *cane paratore, +Peruvian hairless dog, #sloughi, @country-of-origin salukis, and ^miniature xoloitzcuintle. (Credit: NIH Dog Genome Project / Cell Reports, 2017, doi:10.1016/j.celrep.2017.03.079.)

Dogs have been in the Americas for more than 10,000 years, probably because they traveled across the Bering land bridge from East Asia alongside the first humans. But mitochondrial DNA studies indicate that these original New World dogs were almost entirely replaced by dogs from the Old World when colonists arrived from Europe. But an extensive genomic map published today in the journal, Cell Reports, presents evidence for this original “New World Dog” in the genomes of two dog breeds from the Americas. Additionally, this genomic map identifies where and when many of the more than 350 modern dog breeds originated, and it will also help researchers identify disease-causing genes in both dogs and men.

A genomic family tree comprising 161 dog breeds identifies 23 closely-related breed clusters

All dogs — Canis lupus familiaris — are a single subspecies of the wolf, Canis lupus, but people have selectively bred them over thousands of generations to fill certain needs and to perform particular tasks. Modern dogs comprise a riot of shapes, sizes and abilities, and are now formally recognized as standardized “breeds”. But the essentials of how each breed was developed is often shrouded in the mists of time.

This genomic map of dog breeds is the most expansive yet published. To build it, the researchers attended dog shows and contacted dog breeders over a period of 20 years to obtain samples. They collected and genotyped samples from 938 dogs representing 127 breeds, as well as nine wild canids. They combined those data with genotypes retrieved from publicly available sources, and merged them into a single dataset comprising 1,346 dogs from 161 breeds developed on North America, Europe, Africa, and Asia.

Analyses of this dataset reveals 23 clades, or clusters, of dog breeds (Figures 1 & 2).

Figure 2. Representatives from each of the 23 clades of breeds. Breeds and clades are listed for each picture from left to right, top to bottom, and have a color-coded border around the photograph.
(A) Akita/Asian spitz.
(B) Shih tzu/Asian toy (by Mary Bloom).
© Icelandic sheepdog/Nordic spitz (by Veronica Druk).
(D) Miniature schnauzer/schnauzer.
(E) Pomeranian/small spitz.
(F) Brussels griffon/toy spitz (by Mary Bloom).
(G) Puli/Hungarian.
(H) Standard poodle/poodle.
(I) Chihuahua/American toy.
(J) Rat terrier/American terrier (by Stacy Zimmerman).
(K) Miniature pinscher/pinscher.
(L) Irish terrier/terrier.
(M) German shepherd dog/New World (by Mary Bloom).
(N) Saluki/Mediterranean (by Mary Bloom).
(O) Basset hound/scent hound (by Mary Bloom). (P) American cocker spaniel/spaniel (by Mary Bloom). (Q) Golden retriever/retriever (by Mary Bloom).
(R) German shorthaired pointer/pointer setter (by Mary Bloom). (S) Briard/continental herder (by Mary Bloom).
(T) Shetland sheepdog/UK rural.
(U) Rottweiler/drover
(V) Saint Bernard/alpine.
(W) English mastiff/European mastiff (by Mary Bloom).
(Credit: NIH Dog Genome Project / Cell Reports, 2017, doi:
10.1016/j.celrep.2017.03.079.)

The clades on this map represent clusters of 2–16 closely-related breeds of dogs that possess similar traits, for a total of 78% of the breeds included in this dataset.

“First, there was selection for a type, like herders or pointers, and then there was admixture to get certain physical traits,” said lead author Heidi Parker, a Staff Scientist in the Cancer Genetics Branch at the National Human Genome Research Institute of National Institutes of Health (NIH), in a press release.

For example, herding dogs, such as shepherds, collies and shelties, cluster into one clade, whereas hunting dogs, such as retrievers and setters, cluster into another clade. This clustering indicates that dogs were originally bred for specific purposes before breeders began selecting for specific physical traits that are commonly associated with distinct breeds today.

“I think that understanding that types go back a lot longer than breeds or just physical appearances do is something to really think about.”

Two breeds originating in the Americas are likely descendants of the ‘New World Dog’

Most of the breeds included in this study originated approximately 200 years ago in Europe and Asia, and this is reflected in the researchers’ genomic map. But several breeds did originate in the Americas.

“What we noticed is that there are groups of American dogs that separated somewhat from the European breeds,” said Dr. Parker.

These distantly related breeds, the xoloitzcuintle and the Peruvian hairless dog, which are both hairless, are likely descendants of the “New World Dog”; an ancient canine sub-species that migrated across the Bering land bridge alongside ancestors of Native Americans roughly ten thousand years ago. These New World dogs later disappeared, seemingly without leaving a trace, after European and Asian dogs arrived in the Americas. Although scientists previously unearthed archaeological evidence that the New World Dog did, in fact, exist, this study reports the first evidence of this animal in the genomes of modern dogs.

A champion toy Xoloitzcuintle.
The Toy Xoloitzcuintle (“Xolo” or Mexican hairless dog), is likely descended from dogs that crossed the Bering land bridge with ancestors of the Native Americans. (Credit: Penny Inman / Cell Reports, 2017, doi:
10.1016/j.celrep.2017.03.079.)

“We’ve been looking for some kind of signature of the New World Dog, and these dogs have New World Dogs hidden in their genome,” Dr. Parker said.

Dr. Parker mentioned that it’s unclear precisely which gene regions in these modern hairless dog breeds are from Europe and which are from their ancient New World ancestors, but she and her colleagues are planning to investigate that in future research.

New dog breeds often appeared when human society was undergoing big changes

Since dogs are so closely associated with people, critical junctures in human history correlate to the appearance of new dog breeds.

“Each time we come up with different changes into our own sort of society and the way we live, then there’s room for a new kind of dog, or a new shape, a new size,” Dr. Parker said.

For example, the so-called “gun dogs” (the Retrievers and the Setters), exploded into a plethora of new breeds around the Victorian era, when hunting with guns created new roles for dogs — detecting, flushing and fetching prey.

A black Standard Poodle retrieving a Mallard. Poodles are rarely used for retrieving any more, and are most commonly used as companions. (Public Domain.)

On the other hand, other breeds associated with more traditional forms of hunting, such as the Saluki from the Middle east, and the Chow Chows and Akitas from Asia, apparently diverged well before the “Victorian Explosion” in Europe and the United States.

Increasing leisure time also opened up new roles — and new breeds were created to fill them.

“For example, when dog fighting was a popular form of entertainment, many combinations of terriers and mastiff or bully-type breeds were crossed to create dogs that would excel in that sport,” write the authors in their paper (ref).

“In this analysis, all of the bull and terrier crosses map to the terriers of Ireland and date to 1860–1870. This coincides perfectly with the historical descriptions that, though they do not clearly identify all breeds involved, report the popularity of dog contests in Ireland and the lack of stud book veracity, hence undocumented crosses, during this era of breed creation.”

Cross breeding between diverse breeds added new traits

Although it samples almost half of all known dog breeds, this study did reinforce existing ideas that dog types were crossbred to fill certain roles; either to add new traits to old breeds, or to create entirely new breeds to fulfil new tasks. These crossbreeds also end up sharing large portions of their genomes.

One particularly interesting example of a newly-created breed that the research team examined is the Eurasier. Developed in Germany less than 50 years ago by people seeking an easily-trained companion that bonds strongly to its family, this new breed is the result of mixing chow chow with other spitz-type breeds. Although the Eurasier “breeds true” by consistently passing specific traits to its offspring, it still shares shares large portions of its genes with its closest relatives; the samoyed, keeshond (Nordic spitz), and chow chow (Asian spitz).

Eurasier.
Eurasiers originated in Germany in 1960, as a cross between the Chow Chow and the Wolfspitz. Twelve years later, these dogs were crossed with a Samoyed, named the “Eurasier” (Eurasian) and, after it was shown these dogs bred true, were formally recognized as a breed in 1973. (Credit:
PartnerHund / CC BY 2.0)

Although the recently-developed Eurasier is most obvious example of genome sharing identified in this study, 117 of the 161 breeds examined did show evidence of past crossbreeding events, these crosses were typically only between closely-related breeds. The low level of crossbreeding across diverse breed clusters suggests this was done after careful thought and for specific reasons, such as the introduction of a new trait or after immigration of a breed into a new geographic region.

Tracking recent crosses can identify the source of mutations in multiple breeds

Clarifying the origins of, and relationships between, dog breeds is useful for identifying populations that share both rare and common traits — and particularly for pin-pointing the origins of deleterious mutations. For example, collie eye anomaly (CEA) is a genetic disease that affects the development of the eye in several herding breeds, including the collie, Border collie, Shetland sheepdog, and Australian shepherd. This disease is present in all these breeds thanks to a common ancestor that suffered the affliction. But knowing that does not explain why another breed, the Nova Scotia duck tolling retriever, also suffers from the same disease. This genomic map reveals that this Canadian sporting breed has an undocumented collie or Shetland sheepdog ancestor, and this ancestor is the source of the CEA mutation in the Nova Scotia duck tolling retriever, too.

Another inherited condition is one that causes life-threatening reactions to a variety of drugs in many of herding breeds, and has been reported in 10% of German shepherd dogs. This condition is caused by a mutation in the MDR1 (multi-drug resistance 1) gene, and it demonstrates the previously undocumented contribution of the Australian shepherd to the development of the modern German shepherd dog. Additionally, this study indicates that the same gene region containing the deleterious MDR1 mutation is shared with the recently developed chinook breed, and also is present in the toy xoloitzcuintle — suggesting that this rare breed may also carry the mutation.

Three shelties pose for a photograph. Different herding is one of the oldest jobs for dogs and likely originated separately in several different places. (Credit: Dayna Dreger / Cell Reports, 2017, doi:10.1016/j.celrep.2017.03.079)

This study did turn up some other provocative findings. For example, the researchers found that herding breeds turned out to be surprisingly diverse, with distinct breeds originating in different geographic regions of Europe.

“When we were looking at herding breeds, we saw much more diversity, where there was a particular group of herding breeds that seemed to come out of the United Kingdom, a particular group that came out of northern Europe, and a different group that came out of southern Europe,” said Dr. Parker.

“Which shows herding is not a recent thing. People were using dogs as workers thousands of years ago, not just hundreds of years ago.”

Dogs from different herding breeds use very different strategies to do their jobs, so genomic map confirmed what many dog experts had previously suspected, the authors note in their paper.

“What that also tells us is that herding dogs were developed not from a singular founder but in several different places and probably different times,” said the study’s senior co-author and dog geneticist Elaine Ostrander, chief of the Cancer Genetics and Comparative Genomics Branch at the National Human Genome Research Institute of NIH.

Why invest so much into learning about the evolution of dog breeds?

This comprehensive genomic map will certainly help veterinarians identify potential genetic problems so pet owners can be alert to the possibilities. It will also help human health researchers identify dog breeds that may suffer the same diseases that people do, such as diabetes, kidney disease, epilepsy, and cancer.

“Using all this data, you can follow the migration of disease alleles and predict where they are likely to pop up next, and that’s just so empowering for our field because a dog is such a great model for many human diseases,” said Dr. Ostrander in a press release.

“Every time there’s a disease gene found in dogs it turns out to be important in people, too.”

Because the prevalence of these diseases varies so widely and so predictably between breeds, it can narrow down the time needed to identify which dog breeds may provide useful models for studying these conditions in humans.

Source:

Heidi G. Parker, Dayna L. Dreger, Maud Rimbault, Brian W. Davis, Alexandra B. Mullen, Gretchen Carpintero-Ramirez, and Elaine A. Ostrander (2017). Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development, Cell Reports, 19, published online on 25 April 2017 before print. doi:10.1016/j.celrep.2017.03.079


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Originally published at Forbes on 25 April 2017.