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Quite other important processes of evolution are, for example, genome modifications by

selfish DNA, repetitive DNA and jumping gene elements (transposons). For illustration,

there is a recent review of mobile genes in the human microbiome and how they are con­

structed (Brito et al. 2016). Other important factors in evolution include sexual selection

(Connallon and Hall 2016), parasite-host interplay (Tellier et al. 2014), and the newly dis­

covered important role of RNAs in genome evolution (e.g., pi-RNAs; Vourekas et al. 2016).

What is significant for the fascination of bioinformatics is that with the new data and

their evaluation by bioinformatics, but also with new simulations and calculations about

evolution, the formative diversity of these processes of evolution is revealed.

Conclusion

• Evolution is central to understanding the development of life. It always takes

place in a population. The individual living being or protein is, after all, deter­

mined within a narrow framework by the specific genome. There are always new

species (colloquially: “living beings always evolve”). 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 a near-optimal adapta­

tion to the prevailing environment. Less environmentally related characteristics

are less often passed on in the population (selection).

• However, many variants are also neutral, or new structures only appear abruptly when

enough mutations are present (neutral pathways in RNA structures; “punctuated

equilibrium” according to Gould). Over time, there has been no directed “higher evo­

lution”. But there has been spread of life to the land and air, more species and biomass

formed. Bacterial (prokaryotic) cells, still clearly dominant in numbers, have consoli­

dated and become increasingly robust. In the case of eukaryotes, in addition to many

new species (99.9% are extinct!), more and more complex organisms and complex

behaviour emerged (dominant on land: insects, from the Tertiary onwards the state-

forming insects; from Holocene onwards: humans and civilisation).

• Phylogeny (family tree science) helps to infer the evolution of different species

based on shared or non-shared traits via calculated ancestors. There are faster

(neighbour joining) and more accurate methods (parsimony, most accurate maxi­

mum likelihood). Accompanying sequence and secondary structure analyses

reveal conserved and variable regions as well as the evolution of functional

domains. Basic techniques for this are easy to learn (see tutorials). Most accurate

phylogenetic trees require much practice and systematic comparison of all avail­

able information (e.g. alternative phylogenetic trees, also macroscopic features,

molecular sequences, marker proteins). Phylogeny and other data from paleon­

tology and molecular biology as well as from protein structure analyses, embry­

ology, genetics and simulations also allow the analysis of evolution. This provides

fascinating new insights into the evolution of life, such as the endosymbiont

hypothesis and the RNA world, but also into the mechanisms of evolution.

10  Understand Evolution Better Applying the Computer