Natural Selection (Lectures 24-29)

Who are Carl Linnaeus and Ernst Haeckel?

Founders of taxonomy and early developers of tree of life models based on phenotypic traits.

What is a major limitation of early phylogenetic trees?

They were eukaryote-centric and ignored microbes.

What discovery redefined the tree of life >40 years ago?

Archaea were discovered as a separate domain using rRNA comparisons.

What are the three domains of life?

Bacteria, Archaea, Eukaryotes.

What does LUCA stand for?

Last Universal Common Ancestor.

What is the Candidate Phyla Radiation (CPR)?

A massive clade of unculturable bacteria with small genomes and limited metabolism.

How did Hug et al. build their phylogenetic tree?

Aligned 16 ribosomal proteins from thousands of genomes using single-cell sequencing and conserved sequences.

What does molecular clock theory propose?

Mutations accumulate at a roughly constant rate, allowing estimation of divergence times.

What is the nearly neutral theory of molecular evolution?

Most mutations are neutral or slightly deleterious and spread by genetic drift.

What is genetic drift?

Random changes in allele frequency, not caused by selection.

What is the main takeaway from modern tree-building?

Most of life’s diversity is microbial, not eukaryotic.

What is a homologous trait?

A trait derived from a common ancestor.

What is an analogous trait?

A trait similar due to convergent evolution, not shared ancestry.

What does sequence alignment show?

Functional, structural, or evolutionary relationships between sequences.

What is negative (purifying) selection?

Removal of harmful mutations, leading to conserved sequences.

What kind of mutation is more frequent: synonymous or non-synonymous?

Synonymous mutations (don’t change amino acid).

What does it mean if a site is conserved over long periods?

It is likely under strong negative selection.

What is a conservative amino acid substitution?

One that replaces an amino acid with another of similar biochemical properties.

Why is protein sequence more conserved than DNA?

Protein function constrains acceptable mutations more tightly.

What is BLOSUM62?

A matrix scoring how often one amino acid replaces another in evolution.

What’s a mnemonic for Dayhoff classes?

"MILV went to a STAGParty, DEQN went home WYF HRK. C stayed home and studied."

• Hydrophobic: MILV

• Small/Flexible: STAGP

• Charged: DEQN

• Aromatic: WYF

• Basic: HRK

• Disulfide Bridges: C

What was unusual about Omicron’s spike protein?

It had an unusually high number of non-synonymous mutations.

What defines a Variant of Concern (VOC)?

A VOI that increases transmission or disease severity.

What is the RNA world hypothesis?

RNA once played all key roles in life: storage, replication, and catalysis.

What are core non-coding RNAs in all cells?

rRNA, tRNA, RNase P RNA, SRP RNA.

What are examples of regulatory ncRNAs in bacteria?

• sRNAs,

• tmRNAs,

• riboswitches,

• PrfA thermosensor in Listeria.

What is the role of CsrB RNA?

It acts as a sponge for the CsrA protein, a master regulator.

What drives RNA folding?

Hydrogen bonding and base-pairing (Watson-Crick + GU wobble).

What are the two ways RNA secondary structure is represented?

Dot-bracket notation and “wiggle” diagrams.

What is GU wobble pairing?

A non-canonical but common RNA base pair.

What makes RNA structure predictions difficult?

Thousands of near-optimal alternative structures for one sequence.

What does covariation in RNA alignments indicate?

Structural conservation—compensatory mutations preserve base pairing.

What kind of evolution preserves RNA structures?

Negative (purifying) selection.

Why are RNA sequences more variable than protein-coding sequences?

They are not constrained by the genetic code, allowing more flexible mutation patterns.

What does it mean if an RNA structure is conserved but sequence varies?

Functional structure is under selective pressure, not individual bases.

What is currently the major cost in genomics?

Data analysis, not sequencing.

Define phenotype and genotype.

Phenotype = observable traits; Genotype = complete genetic material.

What is a core gene in pangenome analysis?

A gene found in all (or nearly all) genomes under study.

What is an accessory gene?

A gene found in some but not all genomes under study.

Name three types of bacterial recombination.

Conjugation, Transduction, Transformation.

Why is recombination a double-edged sword in GWAS?

It confounds phylogeny but increases resolution by breaking up linkage blocks.

What is a SNP?

A DNA variant found in >1% of the population.

Define linkage in a genome.

Physical proximity of variants that tend to be inherited together.

What does an odds ratio >1 indicate in GWAS?

Increased likelihood that the genotype is associated with the phenotype.

What is a Manhattan plot used for?

Displaying GWAS results: x-axis = genome position, y-axis = -log(P).

What are common GWAS pitfalls?

Biased controls, small sample size, multiple testing, population stratification.

What is mecA in MRSA?

A gene encoding a penicillin-binding protein (PBP2A) resistant to β-lactams.

What phenotype was measured in MRSA GWAS?

Toxicity (via vesicle lysis assay).

How many loci were significantly associated with toxicity in MRSA?

121 loci (100 SNPs, 22 INDELs).

What is PLINK used for?

Identifying statistical associations between genetic variants and traits in GWAS.

What does the MRSA study reveal about GWAS reliability?

It can identify candidate loci, but results may include false positives.

How many isolates were studied in the S. pneumoniae GWAS?

3701 (3085 Thailand, 616 USA).

Why is recombination helpful in this GWAS?

It breaks linkage blocks, increasing statistical power.

Which genes were strongly associated with β-lactam resistance?

pbp2x, pbp1a, pbp2b.

What method was used for phenotyping in Study 2?

Disk diffusion assay to test antibiotic susceptibility.

What percentage of resistance variation was explained by SNPs in S. pneumoniae?

100% of variation in resistance explained by co-detected SNPs.

Name some weaker but significant loci from Study 2.

mraW, mraY (cell wall); ftsL, gpsB (cell division); clpL, clpX (chaperones); recU (recombination).

What are the two definitions of gene function?

Causal effect (direct activity) and selected effect (maintained by natural selection).

What is a “pathogenic” variant in human genetics?

A variant that increases susceptibility to disease.

What does a “sequence logo” show?

Frequency of amino acids/nucleotides at positions in aligned sequences.

How do you tell if a SNP is synonymous?

It doesn’t change the amino acid encoded (e.g. GGA → GGG both = Gly).

What are transitions and transversions?

Transition = purine↔purine or pyrimidine↔pyrimidine;
Transversion = purine↔pyrimidine.

What does strong conservation of a sequence suggest?

Functional importance and likely negative selection.

What is the significance of the 2nd codon position?

It strongly influences amino acid properties.

What are some types of coding variation?

Synonymous, non-synonymous, INDELs, frameshifts, premature stop codons.

What types of non-coding variation are functionally important?

Variants in promoters, ncRNAs, conserved secondary structures.

What tools help assess protein coding impact?

Dayhoff classes, BLOSUM62 matrix, conservation, structure prediction.