Where did your dog come from? Scientists use ancient DNA technology to find the answer!

Produced by: Science Popularization China

Author: Wang Caihui (School of Cultural Heritage, Northwest University)

Producer: China Science Expo

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The domestic dog (Canis lupus familiaris) is the most loyal companion of humans and the earliest domesticated animal. Dogs belong to the genus Canis of the family Canidae of the order Carnivora. They are one of the "six domestic animals" along with horses, cattle, sheep, pigs and chickens. They are one of the twelve zodiac signs and have very important cultural connotations.

Domestic dogs are inextricably linked to the development of human civilization. From hunting, guarding to companionship, dogs have played an important role in every stage of human civilization. As early as about 12,000 years ago in the Natufian culture in northern Israel, tombs of people and dogs were buried together, showing the special feelings of the ancients for dogs.

Yet, despite the long history of the bond between domestic dogs and humans, our understanding of our companions remains limited.

As we all know, the origin of the "Six Domestic Animals" originated from the domestication of wild animals by humans. The results of comprehensive animal taxonomy, archaeology and genetics research have confirmed that all domestic dogs in the world originated from the gray wolf (Canis lupus).

But there are undoubtedly big differences between the ferocious gray wolf and the docile domestic dog.

So how did the gray wolf evolve into the domestic dog of today? And where did the domestic dog originate?

(Photo source: veer photo gallery)

The origins of domestic dogs: complex and controversial

There are many questions about the domestication of domestic dogs: How were dogs domesticated? Where did the first dogs come from? How did they evolve? What unexpected stories are hidden behind them?

In fact, the process of dog domestication is very complicated and controversial.

According to statistics, there are more than 400 domestic dog breeds registered with the World Canine Federation (FCI), and dogs around the world vary greatly in size and appearance. British biologist Darwin once questioned the origin of domestic dogs in "The Origin of Species": "Do these domestic dogs of different appearances all originate from the same wolf?"

To answer the mystery of the origin of domestic dogs, the earliest remains of domestic dogs may be the key.

Through investigation, researchers have discovered a series of early domestic dog remains around the world, for example, in Europe it can be traced back to 15,000 years ago, in the Far East it can be traced back to 12,000 years ago, and the latest research has found that domestic dog remains in northern East Asia can be traced back to 13,000 years ago.

However, gray wolves were widely distributed in Eurasia and North America in history, and the domestic dogs that were originally domesticated were very similar in appearance to wolves. These interfering factors make it extremely difficult to directly determine the origin of domestic dogs based solely on morphological evidence. Therefore, it seems a bit inadequate to answer the mystery of the origin of domestic dogs based solely on archaeological evidence.

A 33,000-year-old fossil of a domestic dog was found in the Altai Mountains of Siberia.

(Image source: PLoS ONE magazine)

With the development of genetics in recent years, research on the origin and evolution of animals is no longer completely limited to archaeological evidence. Researchers have begun to try to use genetic methods to analyze the origin and domestication history of domestic dogs.

DNA (deoxyribonucleic acid) is the genetic code between the parents and offspring of an organism. No matter where the organism migrates to or what form it evolves into, the organism's kinship and evolutionary history are always hidden in the genetic code. Therefore, we can reveal the evolution and genetic history of animals by deciphering DNA information.

Considering that species usually have higher genetic diversity in their center of origin, after comparing the genetic diversity of modern domestic dog populations around the world based on genetic studies of living individuals, it is believed that domestic dogs originated in southern East Asia, and the southern East Asian origin hypothesis of domestic dogs was proposed.

However, animal archaeological evidence in East Asia contradicts this hypothesis. Specifically, compared with northern East Asia, the remains of domestic dogs in southern East Asia appeared relatively late and were less, so animal archaeologists believe that domestic dogs in East Asia appeared at least earlier in northern East Asia, which conflicts with the hypothesis that domestic dogs originated in southern East Asia.

Ancient DNA: Cracking the code of the "wordless book"

Obviously, the only living samples cannot explain the contradiction between the two views. Obtaining more information about historical nodes is the key to solving the problem. Ancient samples, as carriers of genetic information, are high-quality materials for solving the details of the evolutionary history of different species.

In recent years, the rapid development of ancient DNA technology has enabled us to obtain rich genetic information from ancient materials and, through more in-depth excavations, provide a more accurate and complete picture of the evolutionary story.

Therefore, according to the hypothesis that domestic dogs originated from the south, if we can find evidence that the southern gray wolf population is the wild ancestor of domestic dogs, it will provide great support for the hypothesis that domestic dogs originated from the south of East Asia. However, due to a variety of factors, the number of wild gray wolf populations has dropped sharply, making it extremely difficult to obtain fresh samples.

In response to this situation, the researchers took a different approach in 2019: they chose to use samples of gray wolf skins from southern China preserved in museums, and successfully obtained the whole genome sequence information of these samples by improving the ancient DNA extraction method. They then combined it with the whole genome data of gray wolves and domestic dogs published in other parts of Eurasia for a joint analysis.

However, the study found that this existing southern gray wolf population has no special connection with domestic dogs, that is, they are not the wild ancestors of domestic dogs.

So, how can we solve the mystery of the origin of domestic dogs?

In order to gain a deeper understanding of the origin of domestic dogs, researchers conducted the first systematic ancient DNA study of domestic dogs in China in 2020. They collected 83 ancient domestic dog samples from the Yangtze River and Yellow River basins, and successfully obtained high-quality mitochondrial whole genome data of 26 of them (7000-2000 years ago) through ancient DNA capture technology.

Distribution map of the 26 sample source sites

(Image source: Molecular Biology and Evolution magazine)

The study showed that about 7,000 to 2,000 years ago, a type of mitochondrial DNA was common in the Yangtze and Yellow River basins, but this type is now very rare in domestic dogs north of the Yangtze River. This may be because domestic dogs in northern China have experienced a large-scale population replacement in the past 2,000 years.

Interestingly, some domestic dogs with this common type may have successfully reached the Pacific Islands, Australia, and eastern Siberia before the replacement occurred. Among them, those domestic dogs on the Pacific Islands that existed before the arrival of European colonists may have originated from the Yangtze River and Yellow River basins. They may have spread to different islands in the deep Pacific Ocean with Austronesian peoples through the Southeast Asian continent and Indonesia.

In addition, the study found that the domestic dog population had experienced a population expansion about 7,500 years ago, which coincided with the time when humans in the region shifted from hunting and gathering to farming, indicating that the growth of the domestic dog population may be related to the expansion of the human population.

The route of domestic dogs' spread to the Pacific Islands and other regions

(Image source: Molecular Biology and Evolution magazine)

However, did domestic dogs originate from the north or south of East Asia? How were they domesticated? Limited by the source area and time span of the samples in the current study, these questions have not been well answered. Therefore, to solve the mystery of the origin of domestic dogs, we need more ancient samples and research with a wider time span.

On April 9, 2024, Zhang Ming's research group at the School of Cultural Heritage of Northwest University and a collaborative team published a paper titled "Ancient mitogenomes reveal the maternal genetic history of East Asian dogs."

(Image source: Molecular Biology and Evolution magazine)

Mitochondrial DNA is an important basis for researchers to study population history. It is usually defined as different haplotypes based on differences. In this study, researchers successfully obtained the earliest domestic dog samples in northern East Asia (Harbin, Heilongjiang, about 12,900 years ago) and the earliest domestic dog remains in southern East Asia (Jingtoushan site in Yuyao, Zhejiang, about 8,300 years ago), and collected high-quality mitochondrial genome data of more than 100 domestic dog samples from other sites. This is the most extensive and data-rich study of ancient domestic dog DNA in East Asia to date.

Distribution map of more than 100 ancient domestic dog origin sites

(Image source: Molecular Biology and Evolution magazine)

Northeastern Eurasia: The Possible Ancestral Homeland of Domestic Dogs

This study reveals the possible origin of domestic dogs in East Asia and further reveals the diffusion pattern of domestic dogs in East Asia.

In previous studies, researchers compared population genetics of humans and domestic dogs from Siberia, Beringia, and North America, and hypothesized that the ancestors of domestic dogs were domesticated in Siberia due to coexistence with humans in the harsh environment of the Last Glacial Maximum (approximately 23,000–19,000 years ago).

(Photo source: veer photo gallery)

In this study, the researchers found that the remains of domestic dogs in northern East Asia were significantly earlier and more abundant than those in southern East Asia by counting the archaeological records of animals in East Asia. After further comparing the archaeological records of other animals, the researchers ruled out the possibility that acidic soil caused the destruction of the remains, thus leading to the lack of domestic dog remains in southern East Asia. In fact, the reason why there are few domestic dog remains in southern East Asia may be that there were no domestic dogs in the ancient southern region, which further shows that northern East Asia seems to be more in line with the characteristics of the origin of domestic dogs.

In addition, genetic results show that the mitochondrial lineages of ancient domestic dogs in northern East Asia are much older than those of ancient and modern domestic dogs from the southern region. And some ancient samples from northeastern Eurasia are at the base of the main lineages of East Asian domestic dogs, indicating that this part of the lineage is more ancient in the domestic dog population.

Based on the above evidence, the research team believes that domestic dogs may have originated in the northeastern region of Eurasia. As for the specific origin and ancestral population, further research is needed to explain.

Multidirectional diffusion and internal and external integration: the complex evolutionary history of East Asian domestic dogs

Seeing this, you may inevitably wonder: How did the domestic dog population in East Asia evolve from the domestic dog population in the distant northeast of Eurasia?

In this study, researchers analyzed ancient domestic dog data and found that the number of domestic dogs experienced a rapid expansion between about 23,000 and 17,000 years ago. Surprisingly, this period coincided with the end of the last ice age and a period after it ended.

Therefore, after integrating information from ancient and modern samples and multiple genetic results, the researchers speculated that with the end of the last ice age and the warming of the climate, living conditions began to develop in a favorable direction, and it was in this context that the domestic dog population rapidly expanded and spread in multiple directions, for example, spreading southward into East Asia.

The southward spread of East Asian domestic dogs can be divided into two directions, namely, southward spread to eastern China and southwestward spread to western China. The genetic differences between domestic dog populations in these two regions were formed approximately 8,000 to 5,000 years ago.

In addition, some domestic dog populations later spread further to southern East Asia and spread to Southeast Asia, New Guinea, and other areas in the Pacific. Similarly, multiple mitochondrial types of domestic dogs spread from eastern Eurasia to the Americas and other regions.

Within East Asia, researchers have found that there were also special diffusion events in domestic dog populations. For example, there were at least two waves of diffusion to the Qinghai-Tibet Plateau, one was the diffusion of A1b and A3 type domestic dogs to the northeastern edge of the Qinghai-Tibet Plateau 5,000-4,000 years ago, and the other was the diffusion of A1a type domestic dogs from the west to the Qinghai-Tibet Plateau about 2,600 years ago. The revelation of this diffusion event also provides an important reference for the time node of the diffusion of related populations.

So, after the domestic dog populations from East Asia and Eurasia formed genetic differences, was there any genetic exchange?

The answer is yes.

By analyzing ancient domestic dog data, the researchers found that about 3,000 years ago, the mitochondrial type of domestic dog populations in northern East Asia changed significantly. The proportion of the previously dominant A1b type dropped significantly, while the proportion of the A1a type that replaced it increased rapidly.

At the same time, genetic information from western Eurasia was found in ancient East Asian domestic dogs (mitochondrial types B and C) dating back about 4000-3500 years, indicating that genetic exchanges had existed between domestic dogs in eastern and western Eurasia at least about 3500 years ago.

In addition, the study also found that the A1a type domestic dog population in East Asia has a diffusion trend "from west to east" and may also spread further by sea. For example, an individual from the Xiaolongtou site in Jiangsu (about 1,000 years ago) showed genetic links with ancient dogs in the Middle East. Interestingly, this may be related to the extensive trade activities in East Asia and the Middle East during the Song Dynasty or earlier.

Trends in mitochondrial types in East Asian domestic dogs over time

(Image source: Molecular Biology and Evolution magazine)

However, even in the face of multiple introgressions from external domestic dogs, domestic dog populations in southern East Asia and Southeast Asia still retain most of their original mitochondrial types.

Within East Asia, studies have shown that there was also close genetic exchange between ancient western Chinese populations and eastern domestic dog populations, which may have originated from the frequent east-west exchanges during the Spring and Autumn Period and the Warring States Period.

summary

In general, genetic studies of ancient mitochondrial genomes have enabled us to gain a deeper understanding of the origins of domestication and the details of the diffusion history of domestic dogs in East Asia.

However, in order to reveal the full picture of the genetic evolutionary history of domestic dogs, nuclear genome research that contains richer genetic information is very necessary, especially research on older samples in northeastern Eurasia, which may, in the future, add a key contribution to the revelation of the genetic evolutionary history of domestic dogs.

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