Prokaryotic systematics - detailed explanations
In the previous article, I did not bother myself with a detailed description of the idea. It seemed to me intuitive and elementary. But after a discussion with Davidov, I realized that the idea was not so easy to grab. The fact is that now classical concepts in phylogenetics are based on one dogma, which distorts the worldview of biologists.
When we build an evolutionary tree, we of course want to know in what sequence the species were formed in time. But classical phylogenetics has declared that it is not scientifically to pose such a question. And in fact, she signed for her helplessness. Indeed, it is difficult to judge the time of speciation, while the evolutionary process is going on every minute. But you can. Explain how this is possible and called for this detailed explanation.
To examine on the fingers, it will not be speculatively speculative, therefore we will consider the problem with one particular example.
Be sure to watch the example in high resolution .
To begin with, what is the pinnacle of Cellvibrio. Cellvibrio is one genus of proteobacteria. There are several species in the genus. But not a species is sequenced, but one of the representatives of the species - the strain is called (it’s the same as taking the genome of a specific person –– this is the strain of the species). Now in this example, it turned out that now only one strain of Cellvibrio is sequenced - the species Cellvibrio japonicus, and the stamp was called Ueda107. Therefore, the graph on top of Cellvibrio has no connection with itself - no information.
Next, look at the other peak of Cellulomonas. This is a different genus, and sequenced two strains of different species. And near the top there is a connection with oneself. And there are numbers 8-8. This means that when comparing these strains (in this case, only two) of this genus, it turned out that they have 100 different 8 different tRNAs.
In general, the body typically has about 20 tRNA (for each amino acid). Further, as a rule, the body contains 2-3 variations of the same tRNA. But more ancient organisms do not even contain all 20 tRNAs, and often in one version. Younger ones have a wide variety. Therefore, within the genus, if 40-60 tRNAs coincide, then we can confidently say that this is a relatively young genus, and the strains are assigned to it correctly. In this case, we have 8 - this is not enough, but this is just the exception, because it is one of the oldest organisms.
Where does this follow (except from the small number of matching tRNAs)?
In a previous article, I gave a complete graph of the systematics of prokaryotes
There is an ideal point between the largest black spot (there are representatives of Gamma proteobacteria) and the area on the right where individual nodes are visible. This point is the pinnacle of Cellvibrio.
How is it remarkable? The genus Cellvibrio itself is classified as gamma proteobacteria, but we see that this genus has connections not only with a cluster of gamma proteobacteria, but also with another, for example, with the apex of Cellulomonas - and this genus is of the Actinobacteria type.
The question arises: what is more likely that representatives of the Cellvibrio genus aggregated tRNA from a dozen gammaproteobacteria and a dozen other species of different types, for example, from Actinobacteria?
(I emphasize separately that even the coincidence of one tRNA is not a random event, and here it coincides 5-7.)
Or should we conclude that the species Cellvibrio japonicus existed before proteobacteria and a number of types, such as Actinobacteria, were formed?
Naturally, the probability of having one species at first is greater than the aggregation of several tens of species into one species at once.
Yes, at present Cellvibrio japonicus - may differ from Cellvibrio japonicus which was a million years ago, but during this million years its 5-7 tRNAs have not changed at all, while proteins and, say, rRNA have undergone mutations.
This is one of the simplest and most vivid examples of how you can judge the age of species / genera in relation to others.
But there are very few such ideal points as we see on the general graph; it is rather an accident when it is so easy to judge which species is older and which is younger.
More often there is a layering of some genera to others, and it becomes more difficult to understand. We trace this along the first column. The Cellvibrio vertex has connections with all other vertices, with the exception of only one Nocardia, which is so connected by Cellvibrio - Cellulomonas - Nocardia. Those. we can say here that the genus Nocardia is younger in comparison with all the others, because requires the formation of an intermediate genus Cellulomonas.
How to analyze the rest of the relationship?
There are several ways depending on the desire for detail. If you look at the signature of the bonds there we will see the minimum-maximum number of identical tRNAs. For example, between the genera Cellvibrio and Isoptericola (located on the far left) there are 6 identical tRNAs. On the other hand, between Cellvibrio and Kocuria (rightmost) there is only 1 identical tRNA.
Thus, we can say that the genus is moving away from Cellvibrio gradually from left to right.
This is true for the first row at 100%. And again, this allows us to talk about the time of birth.
But with the second row is more difficult. The fact is that in the second row the peaks have two entrances from Cellvibrio and Cellulomonas, and it becomes not clear from which of the two the next genus was formed.
You can do statistically. For example, we compare two Cellvibrio bonds, Isoptericola and Cellulomonas, Isoptericola. The first has 6-6 identical tRNAs, the second 5-7. So, we can conclude that 6 identical tRNAs were transferred from Cellvibrio to Cellulomonas, and only then the genus Isoptericola was formed, to which another 1 tRNA was transmitted, and in some form, 1 tRNA was lost (5-7 were transferred). And then the Cellvibrio-Isoptericola bond is mediated and can be removed. And it becomes more accurately visible who comes from whom in time.
There are other options. There you can already look not statistically, but in detail whether there are specific tRNAs as a prerequisite for the subsequent formation of the genus. I will explain in more detail on the same example in the comments - if there is interest.
Those. the basic idea is that the Whole cannot be formed if there are no parts in nature that the whole should consist of.
When we build an evolutionary tree, we of course want to know in what sequence the species were formed in time. But classical phylogenetics has declared that it is not scientifically to pose such a question. And in fact, she signed for her helplessness. Indeed, it is difficult to judge the time of speciation, while the evolutionary process is going on every minute. But you can. Explain how this is possible and called for this detailed explanation.
Ideal point of divergence of species
To examine on the fingers, it will not be speculatively speculative, therefore we will consider the problem with one particular example.
Be sure to watch the example in high resolution .
To begin with, what is the pinnacle of Cellvibrio. Cellvibrio is one genus of proteobacteria. There are several species in the genus. But not a species is sequenced, but one of the representatives of the species - the strain is called (it’s the same as taking the genome of a specific person –– this is the strain of the species). Now in this example, it turned out that now only one strain of Cellvibrio is sequenced - the species Cellvibrio japonicus, and the stamp was called Ueda107. Therefore, the graph on top of Cellvibrio has no connection with itself - no information.
Next, look at the other peak of Cellulomonas. This is a different genus, and sequenced two strains of different species. And near the top there is a connection with oneself. And there are numbers 8-8. This means that when comparing these strains (in this case, only two) of this genus, it turned out that they have 100 different 8 different tRNAs.
In general, the body typically has about 20 tRNA (for each amino acid). Further, as a rule, the body contains 2-3 variations of the same tRNA. But more ancient organisms do not even contain all 20 tRNAs, and often in one version. Younger ones have a wide variety. Therefore, within the genus, if 40-60 tRNAs coincide, then we can confidently say that this is a relatively young genus, and the strains are assigned to it correctly. In this case, we have 8 - this is not enough, but this is just the exception, because it is one of the oldest organisms.
Where does this follow (except from the small number of matching tRNAs)?
In a previous article, I gave a complete graph of the systematics of prokaryotes
There is an ideal point between the largest black spot (there are representatives of Gamma proteobacteria) and the area on the right where individual nodes are visible. This point is the pinnacle of Cellvibrio.
How is it remarkable? The genus Cellvibrio itself is classified as gamma proteobacteria, but we see that this genus has connections not only with a cluster of gamma proteobacteria, but also with another, for example, with the apex of Cellulomonas - and this genus is of the Actinobacteria type.
The question arises: what is more likely that representatives of the Cellvibrio genus aggregated tRNA from a dozen gammaproteobacteria and a dozen other species of different types, for example, from Actinobacteria?
(I emphasize separately that even the coincidence of one tRNA is not a random event, and here it coincides 5-7.)
Or should we conclude that the species Cellvibrio japonicus existed before proteobacteria and a number of types, such as Actinobacteria, were formed?
Naturally, the probability of having one species at first is greater than the aggregation of several tens of species into one species at once.
Yes, at present Cellvibrio japonicus - may differ from Cellvibrio japonicus which was a million years ago, but during this million years its 5-7 tRNAs have not changed at all, while proteins and, say, rRNA have undergone mutations.
This is one of the simplest and most vivid examples of how you can judge the age of species / genera in relation to others.
Sorting by age
But there are very few such ideal points as we see on the general graph; it is rather an accident when it is so easy to judge which species is older and which is younger.
More often there is a layering of some genera to others, and it becomes more difficult to understand. We trace this along the first column. The Cellvibrio vertex has connections with all other vertices, with the exception of only one Nocardia, which is so connected by Cellvibrio - Cellulomonas - Nocardia. Those. we can say here that the genus Nocardia is younger in comparison with all the others, because requires the formation of an intermediate genus Cellulomonas.
How to analyze the rest of the relationship?
There are several ways depending on the desire for detail. If you look at the signature of the bonds there we will see the minimum-maximum number of identical tRNAs. For example, between the genera Cellvibrio and Isoptericola (located on the far left) there are 6 identical tRNAs. On the other hand, between Cellvibrio and Kocuria (rightmost) there is only 1 identical tRNA.
Thus, we can say that the genus is moving away from Cellvibrio gradually from left to right.
This is true for the first row at 100%. And again, this allows us to talk about the time of birth.
But with the second row is more difficult. The fact is that in the second row the peaks have two entrances from Cellvibrio and Cellulomonas, and it becomes not clear from which of the two the next genus was formed.
You can do statistically. For example, we compare two Cellvibrio bonds, Isoptericola and Cellulomonas, Isoptericola. The first has 6-6 identical tRNAs, the second 5-7. So, we can conclude that 6 identical tRNAs were transferred from Cellvibrio to Cellulomonas, and only then the genus Isoptericola was formed, to which another 1 tRNA was transmitted, and in some form, 1 tRNA was lost (5-7 were transferred). And then the Cellvibrio-Isoptericola bond is mediated and can be removed. And it becomes more accurately visible who comes from whom in time.
There are other options. There you can already look not statistically, but in detail whether there are specific tRNAs as a prerequisite for the subsequent formation of the genus. I will explain in more detail on the same example in the comments - if there is interest.
Those. the basic idea is that the Whole cannot be formed if there are no parts in nature that the whole should consist of.