🧬 Evolution — Advanced#

Scope — Quantitative population genetics, molecular evolution, coalescent theory, adaptive landscapes, and evolutionary developmental biology (evo‑devo).

Key concepts#

• Selection coefficients and fitness landscapes — quantify selective advantage and visualize adaptive peaks and valleys.
• Coalescent theory — retrospective model describing genealogical relationships and time to common ancestry.
• Molecular evolution — neutral theory, dN/dS ratios, and models of sequence evolution.

Seed Q&A triads#

• Q: What does a dN/dS ratio greater than 1 indicate?
  A: Elevated nonsynonymous substitution rate relative to synonymous rate, consistent with positive selection on protein-coding changes.

• Q: How does the coalescent framework inform demographic inference?
  A: Coalescent patterns (branch lengths, topology) reflect past population size changes, structure, and migration, enabling parameter estimation from genetic data.

• Q: What is an adaptive landscape and how does it shape evolutionary trajectories?
  A: An adaptive landscape maps genotypes/phenotypes to fitness; populations move on the landscape via mutation, selection, and drift, potentially becoming trapped on local peaks.

Contributor prompts and extensions#

• Provide a worked example estimating selection coefficient from allele frequency change across generations.
• Add a short primer on methods: site-frequency spectrum analysis, PSMC for demographic history, and basic coalescent simulations.
• Discuss evo‑devo case studies where regulatory changes drive morphological innovation.

Advanced exercises#

• Compare neutral and selection models using simulated sequence data and compute dN/dS for a set of orthologs.