LIFE SCIENCE

Genetic rescue: a silver lining for South China tigers


South China Tiger Photo courtesy of interviewee

Photo courtesy of Siberian Tiger interviewee

Towards the end of the Year of the Tiger, a high-quality genomic study of South and Siberian tigers led by a Chinese team was published as a cover story in Molecular Ecology Resources. This year, another team-led Bengal tiger genome was also published in a preprint.

High-quality genomes of 3 tiger subspecies are published a year, accounting for half of the 6 extant tiger subspecies. Anubhab Khan, an internationally renowned conservation geneticist, commented in the same journal that the Year of the Tiger in China is the year of the tiger genome, and the publication of high-quality tiger genomes is the best way to celebrate the Year of the Tiger.

Khan pointed out that this is one of the highest quality tiger reference genomes to date, and its assembly quality is even comparable to that of domestic cats, which has important implications for future tiger-related research and conservation efforts. The study fills in the genomic information of one of China’s most endangered species, the South China tiger, providing a more detailed scientific basis for a comprehensive understanding of the genetic decline of the South China tiger and the genetic rescue of the species.

The pathos of the apex predators

The tiger is the largest apex predator in Eurasia and includes 9 subspecies. Due to habitat loss, fragmentation and poaching, the population of all tiger subspecies declined dramatically, and the Bali tiger, Javan tiger and Caspian tiger became extinct in the 40s and 70s of the 20th century, leaving only six tiger subspecies left.

The South China tiger (Panthera tigris amoyensis) is ancestral among all tiger subspecies. But in the late 90s of the 20th century, it was declared functionally extinct in the wild and became one of the most endangered animals in China.

Liu Huan, co-corresponding author of the paper and a life science researcher at Shenzhen BGI, told China Science News that there are more than 200 captive South China tigers in China, but only from the descendants of six wild tigers. Although the population size, age structure and sex ratio are generally good, inbreeding is inevitable due to the small number of colonists and the uneven reproductive contribution of the colony. This can directly lead to the decline of inbreeding of the population.

Khan pointed out that tigers are not only scarce and mysterious, but also face a variety of threats to their survival. Because of these characteristics, tiger-related studies are difficult to conduct. Not only that, but tigers are a geopolitically sensitive species. Therefore, it is difficult to protect and conserve them in full accordance with the most ideal conservation strategies in conservation genetics, so as to better restore the population.

In such cases, the use of genetics to protect the South China tiger has become an option for scientists.

Three of the six extant tiger subspecies have reference genomes, of which there are a total of six chromosomal tiger genomes, including two South China tiger genomes, two Siberian tiger genomes, and two Bengal tiger genomes. In addition, the Malay tiger also has a good genome publication.

“Collectively, these genomes have greatly contributed to the understanding of the evolutionary history of tigers and how they will continue and develop tiger populations in the future.” These genomes could also allow scientists to develop more tools for tiger conservation and management. Khan emphasized that while about 170 whole tiger genome sequencing data at different depths have been published, there are only four whole genome data for South China tigers in the National Center for Biotechnology Information (NCBI) database. Given that the South China tiger is located in the ancestral position of all tiger subspecies, the whole genome data of the 16 South China tigers published in this paper are extremely valuable for tiger research. Khan said.

To track the history of inbreeding in South China tigers and explore viable genetic rescue strategies, the research team decided to systematically compare the high-quality genomes of South China tigers and Siberian tigers and resequence each subspecies on a small scale.

The team of Professor Xu Yanchun of Northeast Forestry University, together with the team of Lan Tianming, associate researcher of Shenzhen BGI Institute of Life Sciences, and the South China Tiger Breeding Institute of Meihuashan in Fujian, Heilongjiang Northeast Tiger Forest Park, Shanghai Zoo, Luoyang Zoo, Nanchang Zoo, Suzhou Zoo, Shaoguan Zoo and other South China tiger protection units successfully constructed chromosome-level genome sequence maps of South China tiger and Siberian tiger using multi-platform strategy.

“This is the highest quality and best continuity of the South China tiger and Siberian tiger genomes to date.” Khan said.

Demystify the history of population degradation and the extent of inbreeding

Through genomic analysis, they found that Siberian tigers and South China tigers diverged around 7,000 years ago.

Liu Huan introduced that the Siberian tiger and the South China tiger are different subspecies, and previous studies have concluded that the differentiation time between them is 65,000~100,000 years ago. “But we extrapolated from the latest genome-wide data that they diverged 7,000 years ago, much earlier than previously calculated.” This is mainly due to the advancement of the latest sequencing and bioinformatics analysis methods. ”

They then found that after the divergence of the two, the effective population size of both South China tigers and Siberian tigers has been declining. Zhang Le, the first author of the paper, said that especially in the past 5,000 years, the effective population of South China tigers has experienced a total of three stages of decline. The first stage was from 5,000 years ago to 1,000 years ago, from 14,700 to 200; the second stage was from 1,000 years ago to nearly 100 years; and the third stage was from 1963 to the present.

“The reason for this decline may be that the South China tiger population was already fragmented at that time, forming multiple relatively isolated small populations, and the rapid decline between the small populations due to the combined influence of genetic communication barriers, inbreeding, and human hunting and environmental damage.” Zhang Le told China Science News.

Khan pointed out that the high-quality genome published this time is very critical to accurately assess the degree of population inbreeding, because the long homozygous fragments on the genome are an important indicator for assessing inbreeding, and the evaluation of this indicator is highly dependent on genome continuity.

Lan Tianming, co-corresponding author of the paper and associate researcher at the Institute of Life Sciences of Shenzhen BGI, told China Science News that a variety of situations can cause homozygous fragments on the genome, the most important of which is the founder effect after inbreeding and population bottlenecks.

Inbreeding is the mating of individuals with the same genetic information, and the genomes of their offspring become more and more homozygous. The bottleneck effect is when the population size of a species declines rapidly, falling to a very small number of individuals (bottleneck), and then through this very small number of individuals (the founder), it returns to a large population. At this time, because the large population has only a few ancestors, its genome similarity will also be very high, and a large number of long homozygous fragments will appear on the genome.

“Our study found that a large number of long homozygous fragments in the genome of South China tigers are caused by inbreeding.” Moreover, the long homozygous fragments shared in the South China tiger population span more than 66 percent of the genome region, Lan said, and this inbreeding has a much larger genomic signal than Siberian tigers.

“This information is extremely important for the conservation of South China tigers, which are extinct in the wild, and these captive individuals are the only hope for the population to rejuvenate and return to the mountains and forests.” Khan said.

How to save South China tiger populations

Severe inbreeding of the South China tiger led to homozygosity of its genome. “Homozygosity will reveal recessive disease-causing genes that are otherwise harmful but not visible.” These harmful genetic mutations are the mutation load. Xu Yanchun, the corresponding author of the paper, said.

They found that the mutation load of the entire genome of the South China tiger was significantly higher than that of the Siberian tiger, which was expected. Interestingly, in the region of long homozygous fragments, the South China tiger had a lower mutation load than the Siberian tiger. This shows that the South China tiger purodied a large number of harmful mutation loads during inbreeding, and the homozygous mutation load showed greater body damage, and could not survive or reproduce, and was eliminated from the population. “This process is called the purification of harmful mutations, and this effect can be detected in many small populations.” But this is the first time this cleansing effect has been detected in South China tiger populations. Xu Yanchun said.

He further explained that because this purification effect is mainly achieved through the death of carriers and loss of reproductive ability, this finding explains the widespread phenomenon of 43% of young deaths and 30% of adult females not being able to reproduce in South China tigers.

That is, the superposition effect of inbreeding and genetic load leads to the death of young children and a decrease in reproductive rate, thereby clearing a portion of the homozygous mutational load. Xu Yanchun pointed out that all individuals in the current South China tiger population are related, mutation load is widely present in all individuals, and any paired breeding is inbreeding, so it will show a continuous state of high mortality and low reproductive rate. Therefore, “the removal and purification of mutational load does not improve the safety of the population.”

Khan believes that the data released this time and the existing genome-wide datasets can support the search for suitable tiger subspecies for genetic rescue of South China tigers to some extent. Due to the degree of local adaptability of the Sumatran tiger and Siberian tiger, Bengal tiger, Malay tiger and Indochinese tiger may be better candidates for genetic rescue.

Xu Yanchun told China Science News that suitable candidate subspecies mainly consider three aspects: whether they have had gene exchange in their natural state in history; After differentiation between them, do they already have the inherent ability to adapt to their respective environments, such as Siberian tigers adapt to cold environments, but South China tigers do not, if genetic exchange may lead to inability to adapt to the environment and further aggravate population decline; Whether harmful genes will be introduced between the two parties of genetic rescue.

“From our genomic analysis, we found that the distribution areas of Malay tigers, Indochinese tigers, and Bengal tigers have historically been interconnected, and they have always had more or less genetic exchange, and there is no significant difference in adaptation, so they may be more suitable as genetic rescue candidate subspecies, but more considerations are still needed.” Xu Yanchun said.

In addition, they found 170 mutations unique to South China tigers distributed in genes related to reproduction, growth and development. Khan believes that these sites are extremely important for the conservation of South China tigers, given the low reproductive rate of the South China tigers themselves. In the future, some single nucleotide site chips can be designed for captive populations to avoid the reproductive passage of these sites.

“This study shows that South China tiger populations may need genetic rescue to recover.” Khan said. The above findings provide rich clues and reference genomes for understanding the mechanism of inbreeding decline in big cats represented by tigers. At the same time, it provides strong scientific evidence and support for the formulation of effective and feasible genetic rescue strategies for South China tigers. (Source: Li Chen, China Science News)

Related paper information:https://doi.org/10.1111/1755-0998.13669



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