Sizes of genomes: The C‑value paradox 1
its commonly claimed, that in order to get more complex organisms, a increase of information in the genome is required. And that increase was due to evolution. This view has been abandoned fourty years ago, but there are still papers that make that claim:
Genome increase as a clock for the origin and evolution of life 2
The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. I propose a hypothesis that biological complexity increased exponentially during evolution. The increase of functional non-redundant genome size in macro-evolution was consistent with the exponential hypothesis.
Paris japonica, however , an unremarkable and slow-growing plant, has a genome, 50 times bigger than that of our own species. - it boasts more than 150 billion base pairs – the basic building block that links together to form DNA – in its genome. Humans have just three billion base pairs. This means obviously, that Genome size does not necessarily relate to the complexity of an organism. Therefore, above cited science paper makes unaccurate claims. Genome size is not equivalent of the complexity of the organism. 3
Its very difficult to define what complexity is in biological systems, and how to measure it. Nobody has given a good answer to that question.
What's in a genome? The C-value enigma and the evolution of eukaryotic genome content 4
The discovery that eukaryotic genomes contain vast quantities of non-protein-coding DNA resolved the ‘paradox’ of a general lack of correspondence between genome size and organismal complexity. At the same time, it has raised a number of important new questions that persist as major subjects of investigation. What kinds of sequences are present in eukaryotic genomes, and which of these contribute to the extensive variability in total genome size? How do these elements accumulate or become lost in genomes over evolutionary timescales? Does this non-coding majority have any effects (positive or negative) on organismal biology, or even functions for which it has been subject to natural selection at the organismal level (sensu )? Why do some genomes remain (or become) streamlined, whereas others reach staggering sizes? Collectively, these questions have been considered part of a complex puzzle known as the ‘C-value enigma’ .4
Natural selection is taken as granted, but what does all this mean in regard of natural selection as a mechanism of adaptation, survival, and increase of complexity and biodiversity and speciation of organisms ?
The C-value paradox 1 is basically this: how can we account for the amount of DNA in terms of known function? Very similar organisms can show a large difference in C-values (e.g. amphibians). The amount of genomic DNA in complex eukaryotes is much greater than the amount needed to encode proteins.
Our current understanding of complex genomes reveals several factors that help explain the classic C-value paradox:
Introns in genes
Regulatory elements of genes
Pseudogenes
Multiple copies of genes
Intergenic sequences
Repetitive DNA
The facts that some of the genomic DNA from complex organisms is highly repetitive, and that some proteins are encoded by families of genes whereas others are encoded by single genes, mean that the genome can be considered to have several distinctive components.
Epigenetic factors - are in play that define body development, shape, and complexity. Regulatory elements had to emerge together with genes coding for proteins. That alone puts Darwins natural selection in question.
Natural Selection, Genetic Drift, and Gene Flow Do Not Act in Isolation in Natural Populations
Natural selection occurs when individuals with certain genotypes are more likely than individuals with other genotypes to survive and reproduce, and thus to pass on their alleles to the next generation. As Charles Darwin (1859) argued in On the Origin of Species, if the following conditions are met, natural selection must occur:
There is variation among individuals within a population in some trait.
This variation is heritable (i.e., there is a genetic basis to the variation, such that offspring tend to resemble their parents in this trait).
Variation in this trait is associated with variation in fitness (the average net reproduction of individuals with a given genotype relative to that of individuals with other genotypes).
Directional selection leads to increase over time in the frequency of a favored allele.
http://www.nature.com/scitable/knowledge/library/natural-selection-genetic-drift-and-gene-flow-15186648
1.https://bio.libretexts.org/TextMaps/Map%3A_Working_with_Molecular_Genetics_(Hardison)/Unit_I%3A_Genes%2C_Nucleic_Acids%2C_Genomes_and_Chromosomes/4%3A_Genomes_and_chromosomes/Sizes_of_genomes%3A__The_C%E2%80%91value_paradox
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526419/
3. http://www.telegraph.co.uk/news/science/science-news/8196572/Worlds-largest-genome-belongs-to-slow-growing-mountain-flower.html
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571570/#RSTB20140331C7
its commonly claimed, that in order to get more complex organisms, a increase of information in the genome is required. And that increase was due to evolution. This view has been abandoned fourty years ago, but there are still papers that make that claim:
Genome increase as a clock for the origin and evolution of life 2
The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. I propose a hypothesis that biological complexity increased exponentially during evolution. The increase of functional non-redundant genome size in macro-evolution was consistent with the exponential hypothesis.
Paris japonica, however , an unremarkable and slow-growing plant, has a genome, 50 times bigger than that of our own species. - it boasts more than 150 billion base pairs – the basic building block that links together to form DNA – in its genome. Humans have just three billion base pairs. This means obviously, that Genome size does not necessarily relate to the complexity of an organism. Therefore, above cited science paper makes unaccurate claims. Genome size is not equivalent of the complexity of the organism. 3
Its very difficult to define what complexity is in biological systems, and how to measure it. Nobody has given a good answer to that question.
What's in a genome? The C-value enigma and the evolution of eukaryotic genome content 4
The discovery that eukaryotic genomes contain vast quantities of non-protein-coding DNA resolved the ‘paradox’ of a general lack of correspondence between genome size and organismal complexity. At the same time, it has raised a number of important new questions that persist as major subjects of investigation. What kinds of sequences are present in eukaryotic genomes, and which of these contribute to the extensive variability in total genome size? How do these elements accumulate or become lost in genomes over evolutionary timescales? Does this non-coding majority have any effects (positive or negative) on organismal biology, or even functions for which it has been subject to natural selection at the organismal level (sensu )? Why do some genomes remain (or become) streamlined, whereas others reach staggering sizes? Collectively, these questions have been considered part of a complex puzzle known as the ‘C-value enigma’ .4
Natural selection is taken as granted, but what does all this mean in regard of natural selection as a mechanism of adaptation, survival, and increase of complexity and biodiversity and speciation of organisms ?
The C-value paradox 1 is basically this: how can we account for the amount of DNA in terms of known function? Very similar organisms can show a large difference in C-values (e.g. amphibians). The amount of genomic DNA in complex eukaryotes is much greater than the amount needed to encode proteins.
Our current understanding of complex genomes reveals several factors that help explain the classic C-value paradox:
Introns in genes
Regulatory elements of genes
Pseudogenes
Multiple copies of genes
Intergenic sequences
Repetitive DNA
The facts that some of the genomic DNA from complex organisms is highly repetitive, and that some proteins are encoded by families of genes whereas others are encoded by single genes, mean that the genome can be considered to have several distinctive components.
Epigenetic factors - are in play that define body development, shape, and complexity. Regulatory elements had to emerge together with genes coding for proteins. That alone puts Darwins natural selection in question.
Natural Selection, Genetic Drift, and Gene Flow Do Not Act in Isolation in Natural Populations
Natural selection occurs when individuals with certain genotypes are more likely than individuals with other genotypes to survive and reproduce, and thus to pass on their alleles to the next generation. As Charles Darwin (1859) argued in On the Origin of Species, if the following conditions are met, natural selection must occur:
There is variation among individuals within a population in some trait.
This variation is heritable (i.e., there is a genetic basis to the variation, such that offspring tend to resemble their parents in this trait).
Variation in this trait is associated with variation in fitness (the average net reproduction of individuals with a given genotype relative to that of individuals with other genotypes).
Directional selection leads to increase over time in the frequency of a favored allele.
http://www.nature.com/scitable/knowledge/library/natural-selection-genetic-drift-and-gene-flow-15186648
1.https://bio.libretexts.org/TextMaps/Map%3A_Working_with_Molecular_Genetics_(Hardison)/Unit_I%3A_Genes%2C_Nucleic_Acids%2C_Genomes_and_Chromosomes/4%3A_Genomes_and_chromosomes/Sizes_of_genomes%3A__The_C%E2%80%91value_paradox
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526419/
3. http://www.telegraph.co.uk/news/science/science-news/8196572/Worlds-largest-genome-belongs-to-slow-growing-mountain-flower.html
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571570/#RSTB20140331C7
