Only the fittest survive in evolution? Earth's ancient inhabitants give another possibility
Genetic drift is the random fluctuation of gene frequency caused by changes in the number of offspring individuals produced by individuals of different genotypes.
In contrast to natural selection, genetic drift is a randomly occurring genetic change that greatly affects the gene pool of a small population.
For example, in a population with a frequency of 1% of a certain gene, if the population has 1 million individuals, there are thousands of individuals with this gene.
If the population has only 50 individuals, then only 1 individual has this gene.
Prochlorococcus, which lived on the earth as early as hundreds of millions of years ago, is considered to be an important primary producer of the ocean. It can fix about 4 billion tons of carbon every year through photosynthesis, making an important contribution to the ocean carbon sink.
For a long time, the academic community defaulted that the evolutionary adaptation process of Prochlorococcus was mainly the result of natural selection.
This inherent perception has recently been broken.
The team of Prof. Yao Zhang from the State Key Laboratory of Offshore Marine Environmental Science (MEL) of Xiamen University and Prof. Haiwei Luo's team of the Chinese University of Hong Kong, after four years of experimental research, found that during the evolution of Prochlorococcus, the well-known natural selection was not as good as the traditional one. Cognition is so important, and genetic drift, which has been overlooked, plays a key role.
The research results were published in the international journal Nature Ecology and Evolution.
Prochlorococcus has different characteristics in different environments
Prochlorococcus, known as the primary producer of the ocean, absorbs and utilizes the energy from sunlight to separate oxygen and hydrogen from water, so that oxygen begins to accumulate in the atmosphere, bringing prosperity to the originally "anoxic" earth." The "Great Oxidation" era provided important conditions for the rapid development of subsequent biological evolution.
Its "ancestors" began to evolve some 2.5 billion years ago and changed the planet in many ways.
What evolutionary mechanism did Prochlorococcus follow in its long history?
Understanding this problem can help humans better understand the marine ecological cycle and use resources in a green way.
The constant changes in genes contribute to the evolution of species.
The more common view at present is that the genetic changes of species are mainly attributable to natural selection, that is, survival of the fittest, beneficial individual differences and variations in the evolutionary process are preserved, while those harmful variations are eliminated by nature.
Prochlorococcus has a huge population and a wide geographical distribution in the ocean. For many years, the academic community has also defaulted that natural selection is extremely effective in the evolutionary adaptation of Prochlorococcus.
However, the latest research by Prof. Zhang Yao's team found that although Prochlorococcus is widely distributed, different niches are occupied by isolated populations with different metabolic characteristics. Various populations are isolated from each other, and there is no gene exchange. Recombination levels are low.
"It's like people living in different regions will have different characteristics in order to adapt to their environment." Zhang Yao further explained that during the evolution of Prochlorococcus, the well-known natural selection is not as good as traditional cognition. So important, genetic drift that has been overlooked plays a key role.
Genetic drift is the random fluctuation of gene frequency caused by changes in the number of offspring individuals produced by individuals of different genotypes.
In contrast to natural selection, genetic drift is a randomly occurring genetic change that greatly affects the gene pool of a small population.
For example, in a population with a frequency of 1% of a certain gene, if the population has 1 million individuals, there are thousands of individuals with this gene.
If the population has only 50 individuals, then only 1 individual has this gene.
In this case, because the individual may die by chance or not mate, the probability of the gene disappearing from the population is extremely high.
Inherently, there are few very small populations in nature, so genetic drift is likely to occur at a low frequency.
In recent years, some research points of view believe that many populations are not a large group, but are composed of many small populations, and there is an aggregate population of gene flow with each other.
When considering the evolution of these small populations, genetic drift plays a role.
This study shows that the effective population size of Prochlorococcus is not as large as the academic community defaults, but smaller than many typical free-living bacteria in the ocean, so genetic drift plays a key role in the evolution of Prochlorococcus.
So how do you study the tiny Prochlorococcus algae that live in the ocean?
How to know its effective population size?
How does effective population size help us understand how Prochlorococcus evolved?
Too small to be discovered more than 30 years ago
According to the researchers, effective population size is a key parameter for understanding the ecological, molecular and population genetic characteristics of Prochlorococcus populations.
To determine the effective population size of Prochlorococcus, it is necessary to carry out a mutation accumulation experiment to measure the accurate mutation rate of Prochlorococcus.
This study carried out the gene mutation accumulation experiment of Prochlorococcus for the first time through the continuous passage of large-scale single clones for 3 consecutive years. The characteristics of low mutation rate and small effective population size of algae subvert the traditional cognition that "the evolution of Prochlorococcus is dominated by natural selection".
Although it has been an ancient inhabitant that has lived on the earth for hundreds of millions of years, because it is too small, Prochlorococcus was not discovered by humans until more than 30 years ago.
Zhang Yao said, "There are as many as 100,000 Prochlorococcus in 1 milliliter of seawater, but because it is so small, it cannot be observed by backward equipment and technology, which makes people realize it so late." .
Due to its characteristics, it is very difficult to cultivate Prochlorococcus, and slight changes in the seawater used in the medium, the agarose concentration of the solid medium, the light intensity and temperature set during cultivation may affect the growth of Prochlorococcus. It has a huge impact, and even the early academic circles thought it could not be cultivated.
After years of exploration, there are only a handful of laboratories in the world that can successfully feed it.
In order to clarify the evolutionary mechanism of primary marine producers from the perspective of "evolutionary ecology", the research team continuously adjusted the experimental parameters to overcome the difficulty of culturing Prochlorococcus in the laboratory and the slow growth, and explored a set of stable single clones. training program.
The protocol starts with a single Prochlorococcus cell and keeps it dividing, eventually forming a population of cells derived from a common progenitor cell.
Not only that, Prochlorococcus has a long growth cycle, and the rate of gene mutation is very slow. To master the number of gene mutations in Prochlorococcus in the passage, it needs to accumulate a certain amount for effective statistical analysis, which makes the experimental results. The time span spanned 4 years.
Some species may just get away with it
In the experiment, the researchers set up the origin from one cell, and then developed it into 150 independent cell lines. Each cell line was serially passaged 39 times in 1065 days. Finally, 141 cell lines survived, providing data support for later experiments.
The whole genome sequencing analysis showed that the mutation rate of Prochlorococcus was at the normal level of prokaryotes, which indicated that Prochlorococcus did not obtain a faster mutation rate due to the lack of various DNA repair enzymes.
Based on the accurate mutation rates measured, the study conducted a rigorous species division of 418 Prochlorococcus genomes and calculated that the effective population size of Prochlorococcus is smaller than many typical marine free-living bacteria.
The researchers further analyzed that the widely distributed Prochlorococcus has a large number of coexisting isolated populations, different niches are occupied by isolated populations with different metabolic characteristics, and at the same time, the level of genetic recombination within these isolated populations is low.
Based on this, the study proposes a mechanism of enhanced genetic drift in Prochlorococcus—periodic selection.
Under conditions of low recombination levels, natural selection acts to fix the entire genome containing the dominant gene and knock out the entire genome that does not contain the dominant gene, thereby reducing the neutral genetic polymorphism and effective population size of Prochlorococcus, strengthen its role in genetic drift.
This study provides an innovative perspective and theory for the common gene reduction phenomenon of dominant taxa in oligotrophic environments, in addition to the traditional view of adaptation to oligotrophic environments.
"There are so many species in the world, and they are not necessarily the best selected by natural selection. Some species may just be lucky to survive. Although the role of natural selection is widely understood and believed in the public, we Therefore, the role of genetic drift cannot be ignored." Zhang Yao said that some of the experimental results obtained so far are in line with the existing theories, and some do not. This is because the theory is not the truth, and it is always in the process of dynamic development. , which needs to be continuously verified, revised, and developed in constant revision.
Our reporter Fu Xiaobo correspondent Zeng Wencui