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Molecular evolution

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Molecular evolution is the study of how inherited DNA and RNA change over long periods of time. These changes affect the proteins and other vital components within cells and organisms. By studying these molecular shifts, scientists can build a "tree of life" to show how different species are related.

Ortholog paralog analog examples
Ortholog paralog analog examples

This field overlaps with population genetics, particularly when looking at changes over shorter timescales. It explores how new genes originate and how complex traits develop through genetic changes.

The process of molecular evolution often begins with a mutation. A mutation is a permanent, transmissible change in the genetic material of a cell or virus. These can occur due to errors during DNA replication when a cell divides. Environmental stressors, such as radiation, chemicals, or viruses, can also cause these changes.

Hedgehog with Albinism
Hedgehog with Albinism

Mutations can be small, like a point mutation that affects only one base-pair. They can also be large, involving duplications, insertions, deletions, inversions, or translocations of DNA segments.

Different types of mutations happen at different rates. Most organisms have very low point mutation rates, roughly 10\u207b\(9\) to 10\u207b\(8\) per site per generation. However, some viruses have much higher rates, around 10\u207b\(6\) per site per generation. In humans, one common type of mutation involves changing the length of short tandem repeats. These changes can influence how evolution moves forward by creating a bias in the types of variation that appear.

Once a mutation exists, several forces determine if it stays in a population. Natural selection occurs when a specific version of a gene provides higher fitness. Fitness refers to an individual's ability to survive and reproduce on average. Selection can also happen at the gene level, sometimes causing conflict within the organism. For example, "selfish" genetic elements like transposable elements might benefit themselves even if they cost the host organism something.

Another force is genetic drift, which involves random changes in gene frequencies. This happens because of stochastic effects, or random sampling, in finite populations. In small populations, genetic drift is very strong. It can cause even slightly harmful mutations to become fixed, meaning they are shared by the whole group. For neutral mutations, which do not help or hurt, the rate of change is relatively constant. This constant rate allows scientists to use a "molecular clock" to estimate when species shared a common ancestor.

Scientists use molecular phylogenetics to classify organisms based on their evolutionary history. This involves aligning DNA or protein sequences to find homologous sites, which are parts that share a common origin.

Five Stages of Molecular Phylogenetic Analysis
Five Stages of Molecular Phylogenetic Analysis

Researchers use a substitution model to predict which patterns of change are common or rare.

Site pattern frequencies models
Site pattern frequencies models

By using computational tools, they can generate phylogenetic trees that represent these evolutionary relationships. Different genes evolve at different speeds; for instance, hemoglobin and cytochrome c change at different rates.

Evolution can also lead to massive changes in protein function. Within a single protein family, many different structural and functional mechanisms can evolve. One example is the ribonucleotide reductase (RNR) family, which has many structural variants. In some cases, only a few mutations are required to radically change a protein's job. A study showed that myoglobin could be turned into an efficient enzyme using only three mutations. This demonstrates the incredible flexibility of molecular systems over time.

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File:Site pattern frequencies models.jpg
Site pattern frequencies models.jpg
File:Five Stages of Molecular Phylogenetic Analysis.png
Five Stages of Molecular Phylogenetic Analysis.png
File:Ortholog paralog analog examples.svg
Ortholog paralog analog examples.svg
File:Hedgehog with Albinism.jpg
Hedgehog with Albinism.jpg
File:Animal cells SwissBioPics DL20221120.svg
Animal cells SwissBioPics DL20221120.svg
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