How do the eukaryotic genomes evolve? (part I)

In the previous post, I wrote about the book “Molecular and Genome Evolution” by Dan Graur. It contains thirteen chapters as shown below. Chapters 7-11 may be considered the heart of the book, where Graur discusses how the genomes evolve and how new genes come into existence. Among those, the chapters 6-8 present three mechanisms for genome evolution, namely DNA duplication, molecular tinkering and mobile elements. Subsequently, chapters 10 and 11 discuss evolutionary aspects of the prokaryotic and the eukaryotic genomes respectively.

  1. The Molecular Basis of Biology and Evolution (30 pages)
  2. Allele Dynamics in Populations (44 pages)
  3. DNA and Amino Acid Sequence Evolution (32 pages)
  4. Rates and Patterns of Molecular Evolution (58 pages)
  5. Molecular Phylogenetics and Phylogenetic Trees (72 pages)
  6. Reticulate Evolution and Phylogenetic Network (36 pages)
  7. Evolution by DNA Duplication (66 pages)
  8. Evolution by Molecular Tinkering (52 pages)
  9. Mobile Elements in Evolution (60 pages)
  10. Prokaryotic Genome Evolution (60 pages)
  11. Eukaryotic Genome Evolution (84 pages)
  12. The Evolution of Gene Regulation (22 pages)
  13. Experimental Molecular Evolution (15 pages)

You can see that chapter 11 is the longest. Also, it is highly relevant to all biologists working on human, mouse, fish, plants, insects, yeasts and other eukaryotic organisms. For the benefit of many of those, who focus on only one (or a few) organisms, I will discuss some common patterns seen in the genomes of all eukaryotic organisms in this two part blog series.

How do the eukaryotic genomes evolve?

With the availability of hundreds of eukaryotic genomes, it is now possible to compare and look for evolutionary patterns regarding genome size, number of chromosomes, gene count, distribution of genes within genome, nucleotide content and distribution, etc. Such comparative analysis can tell us about how the genomes evolve, and guide us in building analytical tools to study the genomes of individual organisms.

Different views on genome evolution

Unbiased vs human-centric view

To explain the genomic differences based on biology, scientists match the observed patterns with some hierarchical ranking of the organisms. In the literature, such hierarchies tend to get built in two ways. One method can be described as unbiased, where the organisms are ranked according to clearly-stated criteria (e.g. multicellular organisms are considered more complex than the unicellular organism). The other approach is human-centric, where the humans are considered the epitome of evolutionary perfection, while the other organisms are ranked based on human perception of their inferiority.

To make the human-centric ranking appear objective, brain size is sometimes considered as a metric. In such ranking, the plants, fungi and other brainless multicellular organisms are placed near the bottom of the ladder, whereas the animals evolutionarily closest to humans are placed near the top. Unicellular eukaryotes tend to get excluded from this analysis, because human-centric biologists are usually unaware of them (apart from the sole exception of baker’s yeast).

Selectionist vs Neutral View

Selectionists argue that every biological feature in an organism got “carefully selected” by nature. In the neutral view, many such features came into existence through random processes. However, they continue to exist because they are harmless, and therefore the evolutionary processes did not get a chance to get rid of them.

When taken to the genomic scale, a selectionist view regards the entire genome as functional, whereas the neutral view considers a substantial part as neutral or functionless. In the neutral view, only 3-10% (15% to be generous) of the human genome have any function.

“Onion test”

The genome of domestic onion (Allium cepa) is 16Gb long. The “onion test” asks - “If most DNA is functional, why does an onion require 5 times as much DNA as the human?” We note that although any other organism with a large genome can be used in this argument, brain-less onion provides the highest shock value to the human-centric selectionists, who consider brain size as the objective metric of evolutionary superiority.

In part II of this series, we will discuss the observed patterns regarding genome size, number of chromosomes, gene count, distribution of genes within genome, nucleotide content and distribution in the eukaryotic genomes sequenced so far.

Written by M. //

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