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10/13/2011: Notes on evolution course

The four principles of evolution:

  1. The number of offsprings is at least as large as the number of parents
  2. Genetic mutations occur
  3. Mutations are heritable
  4. ?

Neo-Darwinism is the combination of the theory of natural selection with Mendelian genetics. Its principles are:

  1. Only mutations in germline contribute to heritable variation
  2. Natural mutations are subtle, evolution is gradual – not a series of hopeful monsters (Natura non facit saltus: Nature does not leap)
  3. Traits that seem to blend are simply those that are encoded by many alleles (similar to the reason why Gaussian distributions are often found in Nature: because they are the results of many different processes)

Sex

Only a small branch of the tree of life practices sexual reproduction. Most species practice asexual reproduction and a minority (most plants) practices both.

Sexual reproduction is the combination of two independent acts: 1. Sex: the sharing of genetical information and 2. and Reproduction: the reprication of the genetical information. There are species that have sex without reproducing: E. Coli exchanges genes without replicating the cells.

Asexual reproduction is cheap (does not cost as much energy as sexual reproduction) and it assures that the next generation is exactly a copy of your, assuring that your genetic material is saved in the future. So why sexual reproduction? Fisher (1932) first proposed that sex enables to speed up the adaptative evolution. If mutations A, B and C occur and are all beneficials, it will take more time for three mutations to appear in one organism with asexual reproduction than with sexual reproduction. With asexual reproduction, the mutation needs to occur one by one over the same genetic material; it does not help that one population may have A+C and another A+B. On the other hand, with sexual reproduction, a population separately with A+B and A+C will produce quickly a generation with all three mutations.

Williams (1971), however, noticed a problem with Fisher’s model. Because asexual reproduction is so much cheaper than sexual reproduction then once a population has adapted to its environment thanks to its sexual reproduction, it should have given up the sexual aspects of reproduction and becomes asexual. (Did I get that right?). Williams proposed that there ought to be a short-term advantage to sexual reproduction as well. He proposed that over a short term, it enables a species to quickly adapt to a changing environment. Indeed, species that are both sexual and asexual shift between the two modes of reproduction depending on the environement: if the environment is stable, they use asexual reproduction but once the environment changes it shifts to sexual reproduction. Bugs who live on a plant are asexual but once they used so much of the plant that the plant dies, they become sexual.

The red queen hypothesis: Large living things (like mammals) that have a slow rate of reproduction use sexual reproduction in order to always fight extinction threatened by parasites and viruses that are small, asexual and reproduce quickly.

Definition of female: It is the pattern that contribute the most to the next generation. A woman’s egg is maany order of magnitude larger than a man’s spermatozoid.

Why the males (except human) are spending so much energy to produce traits to attract females, traits that can be unfitting to the environment (like a peacock and its bright colors, not very fit for hiding in the bush)? Because it is a way to tell the female that its genetic material is good, clean and parasite-free: “My genetic material is so good that I can afford so much energy to show you I am healthy.” Indeed, when we are sick, the apparent part of the body (skin, etc) usually shows a signature of the disease.

Ecological explanation of why there are females and males (why one partner contributes more to the other): The partner investing 51% will have more to lose if fertilization does not lead to a viable offspring so the pattern put more energy. Inversely, because this pattern put more energy, the other (the male) does not have to put as much. There is a positive feedback that explains the order of magnitude difference in the size of the male and female’s gametes (Triver 1972).

The unit of selection

The unit of selection is the gene.

The exampe of the lemmings: let’s say there is a population of lemmings on a planet, limited in resources. One species of lemmings kill themselves once the carrier capacity of the planet is reached; the other species do not kill themselves whatever the quality and quantity of resources. One might think of a Gaian mechanism where the species that naturally stabilizes its population would be selected because it is the one that enables to optimize the size of the population. But this is wrong because this altruistic population will always be vulnerable, from the natural selection point of view, to other species that are more selfish. This is identical to the point of Kirchner that both Gaian and anti-Gaian traits can be selected. What matters is only the relative number of offspring not if the member of a species live a “good life”.

Example of “the geometry of the selfish herd”: A herd forms not because individuals are altruistic and want to increase the chance of the whole herd to survive but because each individual try to put at least one other individual between him and, say, a nearby forest. From this simple and selfish rule emerges a collective behavior. This explain the behavior of the whole herd from the selfishness of individuals.

Adaptative landscape (03/11/2011)

The adaptative landscale of a species has as many dimensions as the species has variety of traits.

Fisher came up with the first theory of evolution over this landscape. The theory, called microscope theory, states that evolution is gradual and proceeds in small steps. Once the organism reaches a peak, natural selection works to eliminate variations, a stabilizing effect.

Landscape of a species is made of a large part by other organisms themselves so that the landscape is dynamic.

The fitness of an organism is governed by its phenotype (the expression of the genes), itself governed by the genotype. The first discovery in microbiology was that each phenotype corresponds to a protein (read Dawkins’ chapter on that). Proteines are either structural or enzymatic and they are made of 20 different amino acids. The second discovery was that there is a lot of variation within the same species of proteins. This seems first inconsistent with the purifying effect of evolution discussed earlier. Maybe, these proteins have not effect on fitness. Indeed, this is the case as discussed further below.

Three out of four nucleotides are necessary to produce the twenty amino acids. A triplet of nucleotides is called a codon. This codon is then transcripted into a tRNA which is then translated into an amino acid. Notice, however, that there 64 possible different codons, yet, only 20 amino acids are coded: most amino acids are assigned to more than one codon.

What we know the is that there is many-to-one mapping, not only between the genotype and the phenotype but also between the phenotype and the fitness. Most mutations and most variations within the genetic material of a species have not impact on the phenotype and is thus invisible to natural selection.

Next, we will see what governs then the dynamics of these invisible mutations.