Where is the "genetic melting pot" in the history of tiger evolution? It's in China!

Produced by: Science Popularization China

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

Producer: China Science Expo

The tiger (Panthera tigris) is the largest cat species , belonging to the order Carnivora, family Felidae, genus Panthera. It is known as the king of beasts and is one of the most ferocious beasts in the world.

In China, the tiger is one of the twelve zodiac animals and has a very important cultural connotation. But in fact, do we really know this species?

Although tigers around the world belong to one biological species, there are many subspecies with unique characteristics, and they differ in appearance and body shape.

Image source: Veer Gallery

Classifying tigers: 6 separate subspecies

The current tiger subspecies are named by naturalists from the 19th century to the early 20th century, and are artificially divided based on morphological differences caused by geographical isolation. They are:

The Siberian tiger (Panthera tigris altaica), the South China tiger (Panthera tigris amoyensis), the Indochinese tiger (Panthera tigris corbeti), the Bengal tiger (Panthera tigris tigris), the Sumatran tiger (Panthera tigris sumatrae), the Malayan tiger (Panthera tigris jacksoni), the Bali tiger (Panthera tigris balica), the Caspian tiger (Panthera tigris virgata) and the Javan tiger (Panthera tigris sondaica).

Among them, the Bali tiger, Caspian tiger and Javan tiger have become completely extinct; the South China tiger has disappeared in the wild; the Siberian tiger, Indochinese tiger, Malay tiger, Bengal tiger and Sumatran tiger are all endangered.

Image source: Veer Gallery

The development of genetics in recent years has opened a new chapter in the study of animal origins, and tigers are no exception.

Previously, scientists have used genetic evidence to determine the subspecies of existing tiger species. This is because deoxyribonucleic acid (DNA), the most important genetic material, is the determining factor in the morphological differences of organisms and is passed between parents and children. The differences between different biological groups are fundamentally based on genetic differences. The greater the difference, the more distant the relationship between the populations.

Based on the above principles, in genetic research conducted based on existing samples, scientists collected samples of existing tigers from different regions of the world. Through genetic analysis, they proved that there are obvious genetic differences between regional populations of existing tigers, supporting the division of existing wild tiger populations into 6 independent subspecies .

Phylogenetic tree of the six existing tiger subspecies (Image source: self-made by the author, tiger subspecies image cited from WWF-Malaysia)

New discovery: The genetic mystery of the South China tiger

Although genetic research based on existing samples supports the division of the tiger into six subspecies, the evolutionary history of the tiger is still full of questions.

How to determine the origin and spread of tigers? How did tigers evolve into different subspecies and form their current distribution pattern? What is the relationship between recently extinct tigers and living tigers? Only living samples will not be able to answer these details of evolutionary history.

But fortunately, in recent years, the extremely small amounts of DNA fragments remaining in biological remains and sediments, combined with the emerging ancient DNA technology, have enabled scientists to obtain genome sequence information of ancient samples.

Preserved at the Zoological Museum in Strasbourg, France

The type specimen of the South China tiger from Hankou, Hubei in 1905 (Photo source: Peking University official website)

Through in-depth comparative analysis, scientists can dig deep into genetic information related to evolutionary history, which is crucial for understanding the origin and evolution of tigers and can provide us with a more accurate picture of the tiger's evolutionary story.

On August 31, 2023, Luo Shujin's research group at the School of Life Sciences of Peking University and their collaborative team published a paper titled "Ancient DNA reveals genetic admixture in China during tiger evolution."

Ancient DNA reveals genetic admixture in China during tiger evolution (Image source: Nature Ecology & Evolution magazine)

The research team conducted research on nine tiger subspecies, including extinct tigers, over a time span of about 10,000 years. It resolved decades of controversy over the division of tiger conservation management units (subspecies), clarified the genetic origins of the modern South China tiger, and demonstrated China's important role in the formation of the tiger distribution pattern. It also provided a scientific basis for the protection and reintroduction of tigers around the world.

Previous studies have shown that tiger speciation occurred approximately 2-3 million years ago, and the most recent common ancestor of modern tigers can be traced back to approximately 110,000 years ago.

Currently, due to habitat loss and fragmentation, as well as human hunting and other factors, the six existing subspecies of modern tigers are all endangered . The South China tiger is the most widely distributed subspecies in China and the only subspecies endemic to China .

A South China tiger specimen from Foping, Qinling Mountains, preserved in the Shaanxi Institute of Zoology in 1964 (Photo source: Peking University official website)

Previous analysis based on the mitochondrial genome showed that in addition to its own unique maternal types, captive South China tigers also contain maternal types from other subspecies, which has led to controversy over whether their genetic uniqueness is valid.

In this study, it was found that all South China tiger samples clustered into one branch from the perspective of nuclear genome, showing its uniqueness at the genome level and clarifying its subspecies classification status .

Not only that, from the perspective of the mitochondrial genome, it was observed that the South China tiger population presented multiple maternal types, reflecting its complex maternal genetic history.

Such results inevitably raise the question of why a population that is genetically unique enough would have such a complex mitochondrial origin?

Unique and complex: Genetic fusion between different populations

Typically, this phenomenon is explained as the result of gene fusion .

In this study, the results of mitochondrial genome showed that South China tiger samples that shared maternal types with other subspecies were limited to eastern China, and did not appear in samples from western places such as Shaanxi and Chongqing .

To further explore the reasons for this situation, scientists tested suitable habitats for tigers under climate fluctuations from the last ice age to the present day, and found two possible refuges during this period, a small area in the mountainous area of ​​southwestern China and an area located in the Japanese archipelago.

Based on the above results, scientists put forward a hypothesis that during the Last Glacial Maximum (referring to the period when the climate was the coldest and the glaciers reached the largest scale during the Last Glacial Maximum, about 26,000-19,000 years ago), the entire eastern Asia was affected by drastic climate changes, and the environment in the north changed dramatically, which greatly affected the population of South China tigers.

Global average surface temperature during the Last Glacial Maximum (Image source: Reference [3])

At this time, suitable habitats still existed in the mountains of southwestern China , making it an excellent refuge.

With the end of the ice age, the surviving South China tiger population hiding in the southwestern mountains gradually migrated eastward after the climate became suitable. In east China, they encountered tigers carrying other maternal types and exchanged genes , eventually forming the genetically unique modern South China tiger population.

Because of this, researchers speculate that eastern China may be the "genetic melting pot" in the history of tiger evolution.

In addition, scientists have discovered that the earliest tiger fossils can be traced back to the ancient Chinese tiger (Panthera palaeosinensis) in Henan and Gansu, China. Since then, tiger fossils have been discovered many times in East Asia and Southeast Asia, such as the Java Man Site and Zhoukoudian Site, indicating that China has long been the core area of ​​tiger evolution .

Ancient samples are often crucial for analyzing evolutionary history.

Among the sample data collected by scientists this time, an ancient sample from Russia's Far East is the oldest.

The results of the nuclear genome showed that it was most closely related to the Siberian tiger from the same region. However, the results of the mitochondrial genome showed that, unlike the modern Siberian tiger, this ancient sample from the Russian Far East had a certain maternal connection with the South China tiger in southern China, suggesting that there may be some connection between the modern South China tiger and the Russian Far East tiger population 10,000 years ago.

Overall, all Russian Far East tiger mitochondria may belong to three maternal types, corresponding to two major maternal branches. Two closely related maternal types (samples dating back about 10,600-8,600 years ago) and the unique maternal lineage of the South China tiger together form the basic maternal lineage of all modern tigers , while the remaining ancient sample (sample dating back about 1,800 years ago) is closely related to the maternal type of the existing Siberian tiger in the same region.

Considering that there were waves of migration of tiger populations from eastern and northern China to the Russian Far East after the Last Glacial Maximum, the researchers believe that the tiger may have migrated from China to Northeast Asia multiple times, and this ancient Russian Far East sample (the sample dates back about 10,600 years) may represent an earlier expansion event of the tiger population to Northeast Asia, and the later spread gradually formed the modern Siberian tiger population.

The Caspian tiger: a unique entity with no geographical connection

Among the three subspecies that have become extinct, the Caspian tiger is a relatively special existence as the only population on the Asian continent that has no geographical connection with any other tiger subspecies .

As we mentioned earlier, the formation of subspecies is due to geographical isolation caused by the spread of populations. This inevitably makes people curious. Since there is no geographical connection between the Caspian tiger and other subspecies, it means that it has experienced a more distant diffusion route. So what kind of diffusion history did it go through to form?

The nuclear genome results showed that there was a close genetic connection between the Caspian tiger and the Bengal tiger , while the mitochondrial genome results showed that the Caspian tiger samples had a maternal connection with the ancient tiger population in Northeast Asia and the South China tiger population .

Image source: Veer Gallery

To understand the cause of this conflict, scientists evaluated the genetic flow between populations and found that there was significant genetic flow between the extinct Caspian tiger samples and the Bengal tiger.

In such a complex genetic background, scientists speculate that the extinct Caspian tiger population may have originated from the ancient tiger population in Northeast Asia, moved westward across the Siberian Plain and arrived in Central Asia, and then experienced genetic exchanges with the Bengal tiger from the southern Indian subcontinent, thus forming the modern Caspian tiger.

History of the spread of modern tiger subspecies

Now that we know about the possible formation processes of several special subspecies, what kind of diffusion history did the formation of modern tiger subspecies go through as a whole?

Nuclear genome data indicate that the Sumatran tiger is at the base of all subspecies, suggesting the basal position of this subspecies in the history of subspecies differentiation of tiger species.

To further explore this issue, the researchers studied the genetic pedigree relationships of the populations. The results showed that the evolution of tiger subspecies can be divided into three main pedigree stages. One stage of evolution formed the Bengal tiger, another stage of evolution formed the Sumatran tiger (which may also be the ancestor of tigers on other continents), and the third stage established other subspecies on the Asian continent.

Image source: Veer Gallery

In general, the evolutionary history of modern tiger subspecies can be described as:

After the last ice age, an ancestral lineage carrying the South China tiger's unique maternal type may have survived in the mountains of southwestern China under cold climate conditions.

After the end of the last ice age, as the climate warmed and habitat recovered, tiger populations began to spread.

The initial rapid dispersal center may have been in Indochina, and then the Bengal tigers diverged to the Indian mainland. As the climate gradually improved, the ancient population in India increased and dispersed to eastern China, which was covered with suitable habitats such as forests and shrubs, and merged with the ancient South China tiger population that spread from southwestern China.

Siberian tiger (Photo source: Veer Gallery)

Over the past 12,000 years, after the last glacier retreated, tiger populations in eastern China gradually spread northwards. Due to climate fluctuations, the migration process of tiger populations occurred many times and finally reached Northeast Asia.

Tiger populations in Northeast Asia subsequently expanded to Central Asia through the Siberian Corridor and mixed with northern populations from the Indian mainland.

In summary, genetic evidence supports the classification pattern of nine tiger subspecies, and proves for the first time that China is a "genetic melting pot" in the history of tiger evolution, which is of great significance to the formation of the tiger distribution pattern.

The spread routes of the nine tiger subspecies, with the extinct subspecies marked with a red cross. (Image source: self-made by the author, tiger subspecies images cited from WWF-Malaysia, and the rest of the content is referenced from [4])

Interestingly, tigers are not an isolated case; similar “refuge” evolutionary history has also occurred in other animals.

Early fossil records show that southwestern China preserves a wealth of animal fossils dating back more than 10,000 years, including some species of antelope that were supposed to have lived in Russia's Lake Baikal region and the weasel that lived in Tibet and northern China.

These findings confirm that the area plays an important role as a "refuge" under harsh environmental conditions.

Glacier (Photo credit: Veer Gallery)

Likewise, genetic studies provide evidence for a similar evolutionary history.

For example, ancient DNA studies of wild boars have shown that southwestern China is the main source of the wild ancestors of East Asian domestic pigs, and that the migration routes of most wild boars can be traced back to the southwest.

In addition, the results also show that during the Last Glacial Maximum, wild boar populations experienced a clear population bottleneck (i.e., a significant decrease in population size), but as the climate warmed after the end of the ice age, their populations expanded rapidly and occupied suitable areas in East Asia.

Together, these studies reveal the special role of Southwest China in the history of animal evolution. As an important "refugium", Southwest China provided key support for the survival of diverse species and laid the foundation for the later population spread.

References:

[1]Liu YC, Sun X, Driscoll C, et al. 2018. Genome-wide evolutionary analysis of natural history and adaptation. in the world's tigers. Current Biology. 28: 3840-3849.

[2]Pang L, Chen S, Huang W, et al. 2014. Paleoenvironmental and chronological analysis of the mammalian fauna from Migong Cave in the Three Gorges Area, China. Quaternary International. 434: 25-31.

[3] Wu Yubin et al. "Impact of glacier changes on the Tibetan Plateau during the Last Glacial Maximum on the Asian climate." Journal of Peking University: Natural Science Edition 55.1(2019):12.

[4]Sun X, Liu YC, Tiunov MP, et al. 2023. Ancient DNA reveals genetic admixture in China during tiger evolution. Nature Ecology & Evolution.

[5]Zhang M, Liu YC, Li ZP, et al. 2022. Ancient DNA reveals the maternal genetic history of East Asian domestic pigs. Journal of Genetics and Genomics. 49: 537-546.