GENE221 Mod 7 - Natural selection & geno-phenotype assiociations in microbial genomes

Describe the three-domain tree of life and explain why molecular data changed our view of microbial diversity.

The three domains of life are bacteria, archea and eukarya. Historically the phylogenetic tree was thought of as dominated by eukarya but this was due to sampling bias. More recently, the prokarya branch has been split into bacteria and archaea. Archaea are also single-celled organisms but are difficult to grow and isolate in culture so only recent molecular data has illuminated our perception of them. They used to be thought of as extremophiles but recently have been found in more balmy environments like human guts.

Explain how ribosomal RNAs and conserved proteins can be used to infer evolutionary relationships.

Ribosomes are universal & conserved (essential DNA for translation). Their RNA & protein components especially useful for deep evolutionary comparisons. Hug et al. formed the first mostly complete phylogenetic tree by aligning 16 RNA proteins/genes that are essentially constant across all life and aligned all the samples they could get, then measured them by genetic differences to build a phylogenetic tree.

Define and distinguish the molecular clock, genetic drift, and the nearly neutral theory of molecular evolution.

The molecular clock: the number of mutations within biomolecules can be used to deduce when two or more species diverged i.e. closely related species have similar genomes (DNA, RNA & protein) sequences, more diverged species have dissimilar sequences

The nearly neutral theory of molecular evolution: Most genetic variation between species is either neutral or slightly deleterious and is fixed in the population due to genetic drift i.e. individuals in a population with and without a neutral variant will have almost no difference in fitness

Define homology and distinguish it from similarity and analogy.

A homologous trait is any characteristic of organisms that is derived from a common ancestor Eg. vertebrate forelimbs, or the coronaviruses. Analogy and similarity are commonalities in genotype or phenotype in organisms, usually do to convergent selection pressures causing convergent traits.

Explain why most observed variation in homologous protein-coding genes is neutral or nearly neutral.

Genes that are homologous across distantly related organisms are almost definitely essiential genes. Variation that are deleterious is removed from the population by negative selection (also called “purifying selection”). As a consequence of this sequence conservation over long time periods implies strong negative selection

What are some examples of common nucleotide or amino acid changes that point toward the nearly neutral mutation hypothesis.

• The most common kind of point mutation are ones that code for the same amino acid, as they have no effect on protein formation.

• Non-coding DNA and RNA are much more likely to have mutations in them.

• Indel mutations are mostly likely to be prevalent if they preserve frame (i.e are in multiples of three so do not cause a frame shift in the protein.)

What are the Dayhoff Classes?

Dayhoff classes are amino acids that are grouped together as they f=have functionally similar chemical proteperties that make them likely mutations of each other as they mainly make nearly neutral mutations.

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Recognize how evolutionary selection applies to RNA genes.

Nearly neutral evolution is highly preferred in RNA. RNA structure is conserved over RNA sequence, so nucleotides that are far away in the sequence could be changed in a way that still allows it to base-pair to another nucleotide when the RNA molecule folds up.

Explain why most observed variation in homologous ncRNA genes is neutral or nearly neutral.

There is a strong negative selection for changes in ncRNA since their structure often has to stay similar to be effective at its task. This means the structure of an ncRNA has to be conserved across mutations for that mutation to still be viable for the organism.