Lectures 11-13

From Biol301

• Prehistory dates back to the earliest known writings of 3500 BC (about 5000 years as per old exam)

• Homo sapiens started to spread across the earth about 70,000 years ago (or 100,000 to the nearest 100,000 years)

• Human population growth has been exponential with little to no struggle for survival so natural selection has been weak with probably more genetic drift.

• Lewontin (1973): there is more genetic variation within races than between races, hence race is primarily cultural not genetic.

• Humans and chimps diverged 6-8 million years ago from a common ancestor.

• There are two theories that attempt to explain the neoteny of the human skull.

1. There were selection pressures for increased intelligence.
2. Prolonged sexual selection for beauty that equates to child like characteristics with intelligence as an accidental byproduct.

• The Cenozoic era is known as the age of mammals with the Pleistocene epoch being when the humans emerged and all other large mammals seemed to go extinct when humans arrived to the area. It is known as the age of mammals because mammal bones were the predominate bones found. The age of insects would be a better name since there are far more insects than mammals. (Although not really touched on, there was already an age of insects in the Carboniferous period of the Paleozoic era therefore we cannot use insects again).

• The ecological significance of the Isthmus of Panama is that it allowed the interchange of species between North and South America. Occurred around 3 million years ago

• Tectonic plates are the divisions of land mass that are free to move around and change the surface of the earth.

• The Mesozoic was the age of reptiles and it lasted for 190 million years.

• The KT mass extinction was the mark of the end of the Mesozoic era. It occurred 65 million years ago and was the result of prolific volcanic activity and a meteorite about 10 km across hitting just off the Yucatan Peninsula. The sun was blocked out and the earth grew cold and many things died.

• During the late Paleozoic era all the land masses converged for the first and only time in the history of multicellular life. This land mass was known as Pangea. The convergence allowed for the large Tetrapods to dominate the land.

• The world’s coal was produced in the Carboniferous period. The atmospheric oxygen was at 35% (compared to today’s 16%) and this allowed for larger creatures. This was the age of arthropods (insects).

• The Devonian period was known as the age of fish and ended about 360 million years ago.

• The Cambrian explosion occurred 543 – 490 million years ago. The burgess shale shows the fossils of this period where there are many strange and unusual unknown body shapes.

• The Pikaia fossil was representative of the group that gave rise to all vertebrates.

• Stephen J Gould asked if we re-ran the tape of life would today’s world look anything like the one we see around us? Meaning that instead of there being a steady diversity, life was more diverse early on and today we see diversification within a few major groups that are a near random sample left over.

• The origin of multicellular life was roughly 750 million years ago.

• Stanley A. Tyler (1953) investigates the formation of gun flint formation from 2,100 million years ago an iron rich rock that straddles the US-Canadian border. When he examined the rocks under a microscope he realized the Precambrian was teeming with life which are now called microfossils.

• Stromatolites are the oldest living fossils, they are known as microbial rainforests. The oldest known stromatolite is 2.3 billion years old. Today stromatolites can be found in shark bay.

• Banded Iron Formations (aka BIF’s) are the result of the oceans rusting due to the abundance of oxygen from the oxygen producing cyanobacteria.

• Eukaryotes use mitochondria to process oxygen (and thus control its corrosive properties). Mitochondria are about the same size as bacteria, have a lipid bilayer and retain small amounts of DNA with clear homology to alpha-proteobacteria. This evidence lead us to believe that mitochondria are endosymbionts used to handle the toxic oxygen that couldn’t otherwise be handled by eukaryotes. The same is true of chloroplasts.

• Protein is the biochemical basis of phenotypes. By 1924 the first proteins were being analyzed and found to be composed of amino acids. Chains of amino acids fold into proteins.

• Stanley Miller created the spark tube experiment where he took water and heated it in an atmosphere of ammonia, methane and hydrogen. Then he added a spark and waited to see what happened. He discovered that amino acids were formed.

• Protein polymorphism was discovered by Lewin and Hubby (1966); it means that there are variations in the naturally occurring proteins.
  • If high levels of protein polymorphism are to be sustained by natural selection then natural populations should be full of sick or dying individuals this is known as genetic load. It would seem that in terms of Neo-Darwinism the less fit proteins should be selected against by purifying selection but this is not the case. One answer to this problem was that perhaps some variation in the protein sequence has no effect on fitness.

• Watson and Crick (1953) discovered DNA along with Rosalind Franklin and found that it was composed of 4 nucleotides (2 purines and 2 pyrimidines).

• The genetic code is the set of relationships between the 64 codons and the 20 amino acids. A codon is a triplet of three nucleotides. The genetic code should not be confused with the genome which is the entire sequence of all the genes of an individual.

• The central dogma of molecular biology is that DNA is transcribed into RNA (mRNA) then translated to protein (by means of tRNA). There are some genes that never get translated to proteins. (For example ribosomes.) These molecules are known as ribozymes which are metabolically active RNA molecules. They are also known as molecular fossils from when RNA based molecules did the job of proteins. This can also be described as the RNA world hypothesis where RNA carried the genetic material and performed catalytic reactions.

• About 10% of the human genome codes for protein and of that 10%, 90% is introns which get spliced out. Also, because there are 64 codons and 20 amino acids, multiple codons code for one amino acid normally with the final position being variable. Hence there is genetic redundancy.

• With genetic redundancy and lots of non-coding, DNA many variations in genetic material do not affect the phenotype of the organism. In summary many possible genotypes encode for one protein then many proteins map to one phenotype. This appears to be contrary to the Neo-Darwinian view. However if you consider that things can have equal fitness then the Neo-Darwinian view still appears to hold.

• Motoo Kimura developed the neutral theory saying that most molecular evolution is neutral and produces no change in fitness. Thus natural selection does not select for these neutral changes. He goes on to say that the rate at which neutral mutations feed into a population is proportional to its size. And the rate at which they wander to fixation is inversely proportional to the population size. These two statements cancel out the dependency on population size saying that the rate at which neutral mutations contribute to molecular evolution is constant.

• So if tested he should see a simple linear function of time for the number of changes. Kimura looked at homologous gene sequences (those coming from a common ancestor). The time since common ancestor against the percent difference in DNA have a linear relationship.

• Different types of genetic material have different rates of neutral mutations. For instance: non-coding DNA evolves more quickly than protein coding DNA which evolves quicker than the gene for Ribosomal RNA (not translated to protein so no redundancy).

• More "important" parts of DNA evolve more slowly than the less "important" parts. For instance the third position of a codon evolves fastest because multiple codons map to one amino acid and the third position is where this variation is located (hence it is less important). Also non-coding DNA changes quickly compared to the coding because a change in a used sequence could change the fitness and be selected against whereas non-coding region changes do not matter.

• The human genome suggests a typological human which there is not. This idea that things come in types goes back to Aristotelian Essentialism.

• The sequence alignment algorithm removes any bias from the data say for example the removal of a codon which would shift everything and show more change when comparing nucleotide by nucleotide. The alignment algorithm puts the gaps back.

• NCBI (National Center for Biotechnology Information) is a NIH division focusing on making scientific data available to everyone so that conclusions can be made.

• Neutral mutations are ones that do not affect the phenotype and thereby fitness of an organism.

• Phylogeny is the evolutionary development and history of an organism.b