Rat Affairs: An Epic History of the Splitting of Zokor Rat Clans

Produced by | Science Popularization China

Author: Zhao Xumao (Young Researcher, Lanzhou University), Lei Kexin (School of Journalism, Chongqing University)

Producer | China Science Expo

There is a saying: The general trend of the world is that long-term division will inevitably lead to unification, and long-term unification will inevitably lead to division. In biological taxonomy, long-term division does not necessarily lead to unification, but long-term unification will inevitably lead to division. Among China's mammals, rodents can be said to be a "big family" among them. They roam "mountains, rivers, forests, fields, lakes, grasses, and sands", and their footprints cover most of China's ecological environments. Among rodents, the mole-shaped rat family is relatively mysterious. They live underground for a long time, comparable to the "Ancient Tomb School" in the animal martial arts world.

Zokor丨Photographed by Li Kexin in Qinghai

The subfamily of Zokor can be further divided into the genera of convex-headed zokor and flat-headed zokor. Among them, there are 6 species of convex-headed zokor distributed only in my country, which are endemic to China, including Chinese zokor, Gansu zokor, Luo's zokor, Qinling zokor, plateau zokor, and Smith's zokor; there are two species of flat-headed zokor distributed in my country - Northeastern zokor and steppe zokor. These mice have "many factions" and complex species, which once troubled taxonomists: what is the relationship between them and how did they evolve?

On May 6, 2022, a research result titled "Genomic insights into zokors' phylogeny and speciation" was published online in the internationally renowned journal PNAS (Proceedings of the National Academy of Sciences) led by Lanzhou University and jointly with the Northwest Plateau Institute of Biology of the Chinese Academy of Sciences and the University of Haifa of Israel, finally resolving the issue of the "division" of zokors in the world's rodents.

Screenshot of the paper. The paper is co-first authored by Liu Xi, Zhang Shangzhe, master's students from the School of Ecology of Lanzhou University, Cai Zhenyuan, associate researcher at the Northwest Plateau Institute of Biology of the Chinese Academy of Sciences, and Kuang Zhuoran, a master's student from the School of Ecology. Professor Li Kexin is the corresponding author of the article. The research was supported by the National Natural Science Foundation of China, the 14th Five-Year Plan Key R&D Program, the Gansu Province Basic Research Innovation Group and other funds.

For us humans, we can learn about intergenerational relationships by looking up family trees, but due to the time when writing appeared and the limitations of its preservation, we cannot trace back to a very long time ago. For animals like mice, which have neither civilization nor a very long evolutionary history, how can we learn about their "family trees" or origins?

When scientists study such problems now, they often use molecular biology techniques to build phylogenetic trees (evolutionary trees) of organisms. Phylogenetic trees are based on the genetic mutation rate of species. All species are constantly undergoing genetic mutations, and their mutation rates are roughly the same. The number of mutations accumulated in a certain evolutionary branch is proportional to the time it evolved. This is like a physics problem we have done before, where we know the speed of a car and the distance it has traveled, and find out how long it has traveled. In this way, we can calculate the time when each species evolved, and thus build a phylogenetic tree. This technology can trace the evolution of organisms over millions or even hundreds of millions of years.

There are many ways to build a phylogenetic tree. The study mentioned above used whole genome sequencing (the genome of a species is represented digitally as a set of orderly arranged ACGT letters. A lot of biological information can be analyzed based on the order of these letters, such as the origin and differentiation time of the species) to construct a complete chromosome-level genome of the Chinese zokor, which is more accurate than previous studies.

Based on genome analysis, we know the family evolution history of mice: the first three subfamilies of the family Mole-shaped rats were the Zokorinae, Bamboo Ratinae, and Mole-shaped rats, which is known as the "Three Families Dividing Jin" in the family Mole-shaped rats. 28.9 million years ago, the Mole-shaped rats began to differentiate from the family Mole-shaped rats, and then 2 million years later, the Zokorinae and Bamboo Ratinae completed their differentiation. So far, the three subfamilies have completed their differentiation.

Bamboo rat subfamily, this is a delicacy in many southern provinces丨Image source: wikipedia-Roadnottaken

Mole subfamily, because they live underground all year round, most of these creatures have degenerated eyes. Image source: wikipedia-GalinaGouz

Although they are divided into different subfamilies, the connection between the three is not broken. The three subfamilies can still form interspecific introgression through hybridization, forming a phenomenon of "you have me, I have you" in each other's genes. It is this mutual genetic exchange that has caused the classification dilemma of "inseparable and confusing" for later scientists.

There are many different phylogenetic trees, depending on the "materials" (data) selected. If the differentiation of species is likened to a breakup between lovers, if they no longer contact each other after the breakup, then the results of different phylogenetic trees will be consistent; if they still have some connection with each other after the breakup, then there will be inconsistent results. This is mainly reflected in the fact that the Chinese zokor appears on many branches on the phylogenetic tree, so it is impossible to accurately determine its branch. This may be due to two factors:

First, incomplete lineage sorting (ILS). There are many fragments in the genome, and different fragments have different evolutionary rates and conservation. This is like a family splitting up. Since the splitting time is relatively short, there are no certain rules when splitting up - such as the eldest son inheriting or the youngest son inheriting, so the "genes" inherited by the descendants from the ancestors are relatively random.

Second, introgression is the exchange of genes between different branches, which is generally referred to as gene flow caused by mating. This is similar to the "breakup" mentioned above that produces a lingering connection.

So, why does this happen?

"Since ancient times, rats have been romantic, and all the trouble is caused by romanticism." The Chinese zokor and other related species have been constantly hybridizing, resulting in genetic connections between species. Specifically, there is a lot of genetic exchange between the ancestors of the Chinese zokor and the ancestors of the plateau zokor, the Chinese zokor and the Qinling zokor and the Luo's zokor, indicating that their ancestors intermarried frequently. The position on the phylogenetic tree is unstable.

In the subsequent evolution, the rise of the Qinghai-Tibet Plateau played a crucial role in the population differentiation of zokors.

As the saying goes, heroes are made by the times, and heroes wait for the times. For the formation of species, the "times" and "wind and cloud" here refer to changes in the environment or geological structure. If species want to adapt to such changes in the environment, there is only one way - change, adapt to the new environment through genetic mutation.

3.6 million years ago, with the rise of the Qinghai-Tibet Plateau, one branch of the genus convex-cranial zokor started a life pattern from the plains to the plateau, while the other branch continued to live in low-altitude areas. The separation of altitudes made different populations lose the opportunity to communicate and integrate, thus forming reproductive isolation. The branch that followed the rise of the Qinghai-Tibet Plateau gradually adapted to the life on the plateau. The plateau environment brought about changes at the genome level, so 3.22 million years ago, the branch of convex-cranial zokor that followed the rise of the Qinghai-Tibet Plateau became independent and became a new species - the plateau zokor.

Plateau zokor | Image source: wikipedia- Xiao Sa

780,000-500,000 years ago, the world entered a new ice age. Due to the high latitude in the north, the climate was colder, so there was a shortage of food. In order to obtain better food resources and a warmer living environment, a branch of the plateau zokor family began to migrate south of the Qinhuai River. During the migration to the south, due to changes in the environment, their genetic material changed again, and the Smithsonian zokor was born 750,000 years ago.

A branch of zokors that did not rise with the Qinghai-Tibet Plateau formed the Chinese zokor 2.4 million years ago.

1.6 million years ago, the Loess Plateau underwent a huge change. C4 plants (carbon four plants, plants are mainly divided into two categories according to the type of organic matter formed by photosynthesis, C4 plants are more efficient in photosynthesis) began to expand. C4 plants are the food that zokors rely on for survival. Therefore, some zokors started a new round of "leaving their homes" to obtain food. They expanded from the Qinling Mountains to the northern Loess Plateau and differentiated into the Gansu zokor 1.46 million years ago.

The process of species formation in the genus Pseudocranopterygii. Image source: Reference [1]

135,000-194,000 years ago, the Qinling Mountains were covered by glaciers, and some zokor populations had to migrate south of the Qinhuai River, where they differentiated into Rothschild's zokor 440,000 years ago.

Phylogenetic trees can clarify the "generations" between species, so the effective population size (in layman's terms, the number of individuals that reproduce under a species, and individuals that do not participate in reproduction cannot be counted) can tell the size of the species family in the historical period. Population history research shows that the ice age significantly affected the effective population size of the genus Convex-headed zokor, and the altitude affected the fluctuation of the effective population size of the zokor by affecting the vegetation.

At this point, the entire zokor family has split up. To us humans, it’s just a few more species, but to the zokor it’s an epic story of family separation as they strive to survive in a changing environment.

References

[1]Liu X, Zhang S, Cai Z, et al. Genomic insights into zokors' phylogeny and speciation in China[J]. Proceedings of the National Academy of Sciences, 2022, 119(19): e2121819119.

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