BSC2010-evolution-6-2024

Organisms listed in order of evolutionary complexity:
- Mammals, Birds, Reptiles, Frogs, Salamanders, Lungfishes, Teleosts, Chondrichthyes, Agnathans, Non-vertebrate Chordates, Crustaceans, Insects, Arachnids, Myriapods, Molluscs, Annelids, Echinoderms, Tardigrades, Flatworms, Rotifers, Angiosperms, Gymnosperms, Pteridophytes, Bryophytes, Nematodes, Cnidarians, Sponges, Fungi, Algae, Protozoa, Eubacteria, Archaea.
C-value (pg): Range indicated from 10^-4 to 10^3.

Neutral vs. Selective Processes of Genotypic Evolution
- Synonymous and Nonsynonymous substitutions
- Purifying vs positive selection of genotypic variation
- Kimura’s Neutral Theory of Evolution and the molecular clock
- Types of Genotypic Change
  - Insertions, deletions, frameshifts
  - Hox Genes
  - Lateral Transfer
  - Evolution of genome size and gene number

Genome Definition:
- The collective set of genes and noncoding DNA of an organism.
- Comprises genes, regulatory sequences, structural elements, and extensive noncoding regions.
- Evolution occurs through changes in gene sequences, locations, and expressions.

Synonymous Substitution:
- No effect on protein functioning (silent).
Nonsynonymous Substitution:
- Often harmful but can be neutral or beneficial; mutation probability’s effect on protein depends on codon position.

Rates of Substitution:
- Higher in regions where changes have negligible effect.
- Lower in regions affecting amino acid expression.
Pseudogenes:
- Non-functional gene copies resulting from mutation.

Testing for Selection Using dN/dS Ratio:
- dN/dS (or Ka/Ks) ratio calculated as:
  - dN = non-synonymous substitutions / total possible non-synonymous
  - dS = synonymous substitutions / total possible synonymous
- Interpretation:
  - dN/dS > 1: Positive selection
  - dN/dS = 1: Neutral evolution (null hypothesis)
  - dN/dS < 1: Purifying selection (common for most codons)

Adaptive Variation vs. Neutral Variation:
- Traits can vary on multiple scales (molecular, morphological, etc.).

Positive (Darwinian) Selection:
- Favours beneficial alleles, evident through higher nonsynonymous substitution rates.
Purifying Selection:
- Reduces prevalence of harmful alleles, correlating to higher synonymous substitution rates.

Most genetic variation stems from neutral mutations.
Neutral mutations accumulate via genetic drift.
The fixation rate of neutral mutations is mutation rate independent of population size.

DNA Substitution Rate:
- Used to estimate evolutionary time scales (divergence times, rates of neutral evolution).

Measure % base pair differences (D) between species, estimate time (T) from fossils:
Divergence rate = D / T.

Applications in determining the timeline of HIV in humans, dating significant events like the Cambrian explosion and human origins.

Insertions/Deletions/Frameshifts:
- More impactful than point mutations in gene sequences.

Hox genes dictate cell fates and are conserved across all animals; mutations can significantly alter body structure.

Transfers genetic material between unrelated organisms, prevalent in prokaryotes, contributing to genetic diversity.
Key events include the endosymbiosis of mitochondria and chloroplasts.

Complexity not directly correlating with genome size or gene number; variations often arise from non-coding DNA quantities.

Comparative analysis of gene numbers across different species highlighting diversity and evolutionary complexity.