evolution

name	evolution
description	Biological evolution and adaptation
license	MIT
compatibility	opencode
metadata	{"audience":"evolutionary biologists, researchers, students","category":"biology"}

What I do

• Study mechanisms of evolutionary change
• Analyze natural selection and adaptation
• Research speciation and biodiversity
• Construct phylogenetic trees
• Investigate molecular evolution
• Study population genetics

When to use me

• When studying evolutionary relationships
• When analyzing adaptation mechanisms
• When constructing phylogenies
• When studying speciation
• When researching molecular evolution
• When analyzing population genetics

Key Concepts

Mechanisms of Evolution

• Natural selection: Differential reproductive success
• Genetic drift: Random allele frequency change
• Gene flow: Migration between populations
• Mutation: Source of genetic variation
• Non-random mating: Assortative/disassortative

Natural Selection

# Example: Selection coefficient calculation
def selection_coefficient(w1, w2):
    """
    Calculate selection coefficient.
    w1, w2: Fitness values of genotypes
    """
    return 1 - (w2 / w1)

def allele_frequency(p, q, s, t):
    """
    Calculate allele frequency change under selection.
    p: Frequency of dominant allele
    q: Frequency of recessive allele
    s: Selection coefficient against dominant
    t: Selection coefficient against recessive
    """
    delta_p = (p * q * (p*s - q*t)) / (1 - s*p**2 - t*q**2)
    return delta_p

Phylogenetics

Tree Construction Methods

• Maximum parsimony
• Maximum likelihood
• Neighbor-joining
• UPGMA

Molecular Evolution

• dN/dS ratio: Nonsynonymous vs synonymous substitutions
• Molecular clock: Constant mutation rate
• Positive selection: Adaptive evolution

Evidence for Evolution

• Fossil record
• Comparative anatomy
• Molecular biology
• Biogeography
• Direct observation