The role of selection in the genetics of populations

• Describe genetic structure of populations
• Make theories about the evolutionary forces acting on populations.
• Concerned mainly with understandiong vsriation within species
• Typically one focuses on the evolution of one or two loci at a time.

Evolutionary Forces

• Mutations (mistakes are unavoidable)
• Natural selections (there is extensive variability in fitness within populations)
• Migration (populations are structured)
• Genetic Drift (every population is finite, and subject to stochastic events)

Note: Evolution involves the interplay with all the forces.

• Hardy-Weinberg equilibrium: first milestone in Population Genetics in sexual diploids.
• Mutation rate is around $10^{-9}$ per nucleotide site per generation.

Effects of mutations

1. Neutral (don’t affect fitness)
2. Effectively neutral (-1 < $N_s$ < 1)
3. Beneficial (causes adaptation)
4. Deleterious (cause degeneration)

Neutral Theory of Molecular Evolution

• Kimura’s neutral model: Assumes that most variation observed within and across species can be explained by an equilibrium between variation generating mechanisms — mutation — and a variation erosion mechanism — genetic drift.

• One such test is pN/pS: the ratio of observed non-synonymous to synonymous polymorphism, compared to that expected if one assumes uniform mutation rates across the gene.

  pN/pS should be 1 under neutral evolution.

• Selection as an evolutionary force — constant fitness.

Frequency-dependent selection

• Here fitness depend on the frequencies of genotypes in the population.
• “A rare phenotype may be more popular in terms of sexual preference.” — negative frequency dependedent selection.
• There is also positive frequency based selection, which is the more obvious case.

Probability of Fixation of Mutations under Selection

• Not every good allele is fixed and not every bad one is lost!

• Time of Fixation of a Benefitial Mutation: A mutation that confers a 1% benefit will take ~200 generations to reach a frequency close to fixation.

• The decrease in populations , deleterious mutations can depart from their equilibrium frequency, be lost or go to fixation, all by stochastic drift.

• Clonal interference: adaptations muttations arise faster tahn the time it takes for an individual mutation to get fixed.

• When can populations avoid clonal interference? By using sexual recombination.

Using Wright-Fisher model to understand the mechanisms of evolution

1. Genetic Drift
2. Mutation
3. Selection

Experimental evolution applied to cell biology

• Cell Perturbations:
  • Gene deletion
  • Paralog (Express something which doesn’t bwlong there)
  • Ortholog (Insert a foreign gene)
  • Ancestral allele
  • Partial loss of function (disturb a gene partially)
• The ‘Evolutionary repair’ approach — as a methodology to study evolution.
  • DNA replication stress: specially visible in cancer cells, because they keep on dividing incessantly.

Ageing in Cells

• Three hypothetical reasons:
  • Harmful mutations
  • Antagonistic Pleiotrophy

Community Ecology

• Read: Modern Coexistance Theory (Chesson 2000)

• Metabolism scales predictibly with size (mass)

• Energy fluxes: intake and expenditure

• Some concepts not discussed in the lecture:

  • Intraspecific trait variation
  • Priority effectss (species arrivaal)
  • Metacommunities (interacting communities)

• Are all species equally important? Foundation Species.

• Biodiversity is important because it gives you functional redundancy.

Ecology and Evolution in communities

• Niche differences enables coexistence within different species.

• Evolution in a stable environment maximizes carrying capacity $K$. [theory]

• Density-dependence, resource competition, mortality affect life history traits (size, age at reproduction, etc)

• Bacteria are the most common model organisms for studying ecology.

• Malebra & Marshall 2019 Ecol [Danallelia micro-algae paper]

• WTF is the Metabolics theory?

  • TODO

Evolution of microbial Genomics

• What do we measure?

  • G + C content (the composition of these amino acids)

  • Gernome size

  • Structural arrangements

  • Coding & non-coding content

• Genome Size: Why are some bigger (or smaller) than others?

  • More genes == bigger genomes

  • Linear relationship in most bacteria & archaea ~1 kB, but thus relationship falls apart in prokaryotes.

  • In bacterial genomes: Use it or lose it!

  • How do bacteria lose the genes?

    • Selective advantage? or

      • Lower the $dN/dS$, stronger is the purifying selection.
      • Conclusions from the study: Purifying selection (probably) doesn’t have a major impact on (bacterial) genome streamlining!
      • No relationship between genome size and growth rate or cell size!

    • Neutral Process ?

      • Neutral process — strong deletion bias, and is well established for baceria as of now.

        graph LR Deletion-Bias --> Small-Genome Positive-Selection --> Big-Genome Purifying-Selection --> ??

    • Genetic Drift results in fixation of alleles inspite of the fluctuating frequencies fo alleles.

• Genome Erosion - reduction to the extreme, which often leads to coupling of the bacteria with a certain host.

  • Disadvantages:
    • Rapid evolution, extreme drift
    • Fixation of deleterious mutations due to drift
    • Irreversible loss of genes
  • Muller’s Ratchet: is genetic erosion a one way street to genetic oblivion?
    • Becuase in large and unrestricted populations — deleterious mutations are removed through recombination and these dewleterious mutations are less likely to get fixed by genetic drift.
    • In small, clonal populations — no way to recombine and more likely to fix and repeat cycle.
    • There are some mechanisms that are know, that help these bacterias avoid this trap:
      • Compensatory mutations
      • Just-enough recombination
      • Strong purifying selection
      • Symbiont replacement (doom for microbe, but not the host)

• C - value paradox

• Population size in eukaryotes: as in bacteria, effective population size (Ne) is postulated to strongly effect genome composition.

  • Eukaryotes have smaller populations than prokaryotes.
  • General trend upheld but variation depending on taxonomic group.

• Whole Gene Duplication

• Horizontal Gene transfer: What. is it? How common?

  • Upto 30% of thr genome of a bacteria may be acquired by HGT.
  • Pan genome of HGT: a prokaryotic species have no single defined gene set.

• Euk. genomes have continued to evolve and gain complexity via endosymbiosis.

• Constructive Neutral Evolution: complex functions can evolve with neutral changes to the network.

Seminars

• Horizontal gene transfer is common is prokaryotes (30% of genome can be acquired).