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currently prevailing. Random changes (mutations), natural selection, and reproduction

(replication) work together to achieve this. Sexual reproduction also allows new gene

combinations in the offspring through recombination of the paternal and maternal genome.

Depending on the environment, a mutation can thus be beneficial or detrimental or insig­

nificant (neutral). Although this makes the evolution of genetic material a very complex

process in populations, it is now possible to determine how these representative sequences

change over time and how different they are in different populations by systematic

sequence comparison of typical sequences for a population. One can then calculate from

many such sequence comparisons (see Sects. 10.3 and 10.4) how different different popu­

lations are (one often compares species) and can then calculate back how the precursor

populations looked (also extinct species).

This is all surprisingly difficult when looked at in detail, e.g. which sequences are rep­

resentative of the population? Answer: The most frequent sequences in the population. So

ideally you have to sequence many individuals, like in the 1000 genomes project for the

human genome. However, when do I have a new species? This is not a problem for verte­

brates and mammals, but it is not at all easy to determine with certainty for all other living

organisms. Originally, individuals were classified morphologically (differing in appear­

ance) and then simply called species. Later, a species was defined as a sexually fertile

reproductive community between individuals in a population. This does not work for bac­

teria. Here, genetic exchange is complex with many transitions and reproduction is usually

asexual, so that a three percent difference in the genome is often pragmatically defined as

a new species. One also has to look carefully at the resulting phylogenetic trees in order

not to make any mistakes, for example whether one can determine an original species

(“root”) or whether it is better not to do so because of the unclear data situation. Another

example error in reconstruction is the tree-building error (long branch attraction), since

systematic errors can often occur, in particular distantly related species are wrongly con­

sidered closely related or closely related species are wrongly considered unrelated, which

arises when sequences of different lengths are compared or when a single sequence is

quite long and the taxa have a different number of mutations.

10.1

A Brief Overview of Evolution from the Origin of Life

to the Present Day

Evolution always takes place in a population. The individual living being or protein is,

after all, determined within a narrow framework by the specific genome. There are always

new species (colloquially: “living beings always evolve over time”). In reality, there are

always new populations with always new typical characteristics (by mutation and, in the

case of sexual reproduction, by recombination) that allow near-optimal adaptation to the

prevailing environment. Less environmentally related traits are less often passed on in the

population (selection). However, many variants are also neutral. Even more exciting is that

10  Understand Evolution Better Applying the Computer