Evolution

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Gene transfer

Evolution refers to the changes over time experienced by living things, associated with genomic variation. The genetic material embodied by DNA transcends organisms in a few ways.

One of them is vertical inheritance from parents to offspring via asexual or sexual reproduction. Another path is horizontal transmission between unrelated individuals, as seen between bacteria that exchange antibiotic resistance genes through the sharing of their plasmids.

Genetic variation in bacteria in the context of evolution of antibiotic resistance is a good case study.

(1) Genetic - why? All of the characteristics of bacterial organisms are a result of the blueprint for the various proteins coded in their DNA, the same DNA that all life has on Earth (except for the specific base sequence). Genetic simply means arising from DNA.

(2) Variation - bacteria have variation? Who would have thought? I mean, I always thought they were just a bunch of tiny hot dogs without the sausage in the middle, hanging around causing trouble. Well, I found out, no, they're not hot dogs. They're beautiful organisms in their own right, and if it wasn't for our inherent bias of being on the receiving end of their infection, they wouldn't be baddies. They could be heroes. In fact, some of them are heroes! Some bacteria do contribute positively to our life. The undeniable evidence for that is pickles.

(1+2) So, the variation is genetic.

(3) Bacteria - why bacteria? Due to bacteria being a common cause of disease, as well as their fast life cycle, they are a good case study for explaining selection and resistance. This is done in the light of antibiotic resistance. Things are complicated on Earth; antibiotics literally murder bacteria in a very efficient way. What could go wrong?

As generations of bacteria come to life, their DNA doesn't stay completely identical. Random mutations sometimes arise. Mutations are changes in DNA which result in different characteristics. No, not bacteria with fangs, but subtle changes in, say, the shape of a certain protein which sits on the cell wall. These mutations and the bacteria don't "know" which, or if, these changes will turn out favourable or unfavourable. This depends on their environment. Some mutations may even be irrelevant or neutral.

The key point is that sometimes, some bacteria develop mutations which just so happen to give them resistance to an antibiotic. 

This resistance, being genetic, is passed on to the offspring by vertical transmission (bacteria dividing; called binary fission - which literally means splitting in two). It's called vertical because it happens from top to bottom, as multiple generations arise.


As you can see, this happens "vertically". In reality, there is no such thing as vertical. Bacteria divide any which way, clearly. But silly humans can't understand the concept of no direction... A way of looking at it is that the transmission only occurs if the given bacterium divides.

In horizontal transmission, the given bacterium doesn't divide. It exchanges genetic material from its plasmid (circular bit of DNA) by replicating the plasmid and passing it along via a tube to a different bacterium, even of another species. This process is called conjugation, and many a cheeky teachers have compared it to sex.




No worries about the F factor (it's the factor which enables the receiving bacterium to initiate conjugation).

In the above picture think of the plasmid - the black circle being copied and transferred - as a bit of DNA which contains the allele responsible for antibiotic resistance. Now the other fellow has it. Damn.


Prokaryotic and viral DNA transmission to eukaryotes

Horizontal transmission can also occur between different life kingdoms. Whenever a virus infects a host, e.g. retroviruses such as HIV in humans, it can potentially integrate its DNA into the genome of the host by using an enzyme. This DNA can result in further copies of the virus being made at a later date, and is one of the ways that viruses replicate.




When this horizontal gene transfer takes place in an embryo, all the resulting cells and their DNA will carry the viral DNA, passing it on vertically to the host's offspring.

Human genomes have been found to contain retroviral DNA dated millions of years old. Some research indicates that some of these ex-viral DNA sequences may have evolved to take part in key human development functions, such as enabling embryonic stem cells to be pluripotent. A study found that disabling the viral segment left the stem cells unable to differentiate into multiple types of cell, which is crucial to development.

Bacterial DNA has also been found to have integrated itself into the eukaryotic, human genome. The billions of bacterial cells residing in a human carry out horizontal gene transfer between themselves. However, it is possible for them to also pass some genes onto human cells. Curiously, it has been found that more of these lateral gene transfers (LGT) are present in cancerous cells, which proliferate faster. It could be that these cells are more prone to taking up the bacterial DNA, or that the DNA itself makes initially healthy cells turn cancerous.


Natural and sexual selection

In the wild, each species may exist as one population or multiple populations. Different populations correspond to defined areas - habitats.

The sum of all present alleles for a given gene in a given population is known as the gene pool.

This is essentially a way of thinking about all the individuals in a population contributing their alleles towards the overall allele frequency. The extent of different alleles present gives the genetic diversity of a population.




The allele frequency in a population's gene pool can change as a result of selection. The effectors of selection can be varied, yet the outcome is similar: advantageous or preferred alleles and the traits associated with them increase in frequency, while detrimental or disfavoured alleles and the traits associated with them decrease in frequency.

Here is an all-time classic example. The most frequent initial moth colour in a population landing on tree trunks was dark, to match that of the tree trunks. Few moths could get away with being light-coloured. Once the tree trunks were painted white, the former moths became very apparent to predators, and so the light-coloured moths evaded predation much better and survived to reproduce. Essentially, the tables had turned!

This resulted in the allele for light colour to spread and become the most frequent compared to that for dark colour. The latter sharply dropped in frequency and became the minority.




This is an example of directional selection. It tends towards an extreme, either the light-coloured or the dark-coloured, depending on scenario. 

Selection can also tend towards a "happy medium" and avoid either extreme. This is stabilising selection. If really small lions don't survive long, but really large lions can't supply themselves enough food, then the average lions are selected for and achieve the highest frequency.




Directional selection also takes place when antibiotics are used against bacteria. The adaptive pressure favours bacteria that have the antibiotic resistance gene and can survive the hostile environment.

On the other hand, a scenario such as human birth weight showcases stabilising selection. The average weight is large enough to keep the newborn healthy and increasingly able to survive independently, but small enough to enable the actual birth.

Natural selection therefore results in species increasingly and consistently adapted to their environment via anatomical, physiological or behavioural changes.

The train of thought leading to natural selection includes these key points:

1. Individuals within a population exhibit variety of phenotypical traits caused by both their alleles and the environment.


Primarily the source of this variation is mutation. Secondarily it is meiosis and the random fertilisation of gametes in the case of sexual reproduction.

2. The balance of survival and reproduction is affected by factors including predationdisease and competition. Some appearances and behaviour can attract more predators while others such as camouflage can avert them.

Disease can impede survival and reproduction, while competition enables hidden traits that might have gone unnoticed or been "neutral" before to come in handy when unforeseen selection pressures arise. If the positive outcome of such competition, such as resources needed for survival, are limited relative to the population seeking them, then competition acts further to select certain traits.


3. Any favourable traits controlled by alelles will end up in more offspring, thereby shifting the alelle frequency and over time, the entire gene pool of a population or species.

Sexual selection differs from natural selection in that the selection pressure exists within the population rather than from the outside, and the medium of its propagation is reproductive success directly rather than as a proxy of survival.

Within a population, individuals may have the ability to determine the direction of selection through their reproductive activity. This is indirectly steered by the reproductive outcomes of individuals, and the aspects associated with individuals with a high rate of offspring survival versus low rate of offspring survival.

In this sense, sexual selection can be viewed as the non-random increase in frequency of DNA sequences that are associated with the selected reproductive outcomes.


Types of selection

We looked at stabilising and directional selection previously.

There is a third type called disruptive selection. Instead of shifting the traits towards an end, or towards a middle ground, disruptive selection splits the pool down the middle, where both extremes of a trait are favourable, but not a middle value.



An example of this is an original population of purple individuals which stand out quite a lot amongst red and blue flowers in a field. They will end up shifting towards either red or blue, but not staying purple as this attracts predators.


Genetic drift

The background fluctuation of allele frequency in a population that is not a result of any selection pressure, just chance, is called genetic drift. This can be due to deaths and sampling variables. For example, if offspring are the basis of the allele assessment, that does not provide the information regarding any alleles their parents might have had. Data on many generations would need to be obtained in order to draw conclusions regarding changes in allele frequency due to selection pressures. 





The founder effect

Suppose a boat travelled from one island to another. In the process, several lizards were transferred from the first island to the other. The lizards breed and settle down to form a new lizard population on their new island. This is called the founder effect. The small number of founding lizards formed the genetic base on which the whole population was built. This genetic base is significantly smaller than that of the original lizard population on the first island.

Therefore, the genetic diversity of the new population is lower than that of the original population.


Speciation

In the old days, a species was known as a collection of individuals similar enough in resemblance to be put in the same box. This was purely based on physical features. Today we know that similar physical characteristics on their own aren't enough to define a species.

species is defined in terms of observable physical features as well as the ability to produce fertile offspring.


What is at the heart of new species formation? It all starts with a single population of a species which for whatever reason (genetic bottlenecks, founder effect, etc.) ends up being split geographically to the point where no interbreeding occurs for a certain length of time. 

Given that the two habitats are different, the individuals in each population will adapt differently to counteract different selection pressures. Say for example the ants in the forest experience a warmer and more nutrient-rich surrounding compared to the emigrated ants on a nearby, although disconnected, beach.

The adaptations acquired by both populations over a long time will get increasingly disparate. When these pass a threshold, the two populations can no longer interbreed, even if the opportunity were given (due to excessive genetic difference). They have now become separate species! This process is called speciation.



Speciation due to an established barrier such as geographical separation is termed allopatric. Speciation can also occur in absence of a barrier. The individuals of a starting species can share the same physical space and be able to come into contact with each other, yet for other reasons subspecies can still separate within that population in what is termed sympatric speciation.


Sympatric speciation may occur as a result of different members of the former species occupying different niches within the same habitat. Perhaps they start feeding on different sources, behaving differently, having different mating signals, etc.

At the point where diverging species meet again, or have maintained an area where the original forms still interbreed, there is a hybrid zone.




There are many hybrid zones around the globe with species such as mice and birds maintaining interbreeding areas with their respective related species. The outcomes of hybrid zones can be different.

One outcome is that the hybrids are well adapted and continue to be produced (stability). If the purebred species are well adapted while the hybrids are not, the two emerging species will stay separate and the hybrids will disappear (reinforcement). Lastly, it could be that whatever barriers exist between the two species reproducing are taken down, resulting in the gradual re-establishment of a single species throughout (fusion).

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