Selective Sweep & Genetic Hitchhiking Simulator

Population & Selection

Selection coefficient s 0.20

Recombination rate r 0.020

Population size N 40

Live Readouts

Generation

Beneficial allele freq.

2.5%

Diversity at locus (H)

0.97

Swept block width

0 kb

How it works

Each generation is an individual-based, discrete-time Wright-Fisher model. A chromosome is 41 linked sites (positions -20…+20, ~2 kb apart); site 0 is under selection. Every one of N offspring picks a "primary" parent with probability proportional to fitness:

w = 1 + s   (carries the beneficial allele)
w = 1       (ancestral allele)
P(parent = i) = w_i / Σ w_j

This is the standard haploid selection model — biased fitness sampling reproduces the deterministic recursion p' = p(1+s)/(1+ps) on average, with genetic drift from finite N added on top.

Linked neutral sites hitchhike unless recombination breaks them free. For a site at genetic distance d from the selected locus, the per-generation probability of recombining onto a random second parent is:

P(recombine) = 1 - e^(-r·d)

Near d = 0 this probability is tiny, so those sites are dragged to fixation along with the sweeping allele — the classic genetic hitchhiking effect (Maynard Smith & Haigh, 1974). Far sites recombine often and keep reshuffling among the population's original lineages, so diversity there stays high. The result is a valley of reduced diversity — a long, low-recombination haplotype block — centred on the selected locus.

Selection coefficient s — fitness advantage of the beneficial allele; higher s sweeps faster and leaves a wider hitchhiking footprint.
Recombination rate r — how quickly linkage decays with distance; higher r narrows the swept block.
Population size N — more individuals means more distinguishable lineages (colours) and stronger selection relative to drift.
Diversity H — Simpson heterozygosity 1 − Σ(freq_k)² over the distinct ancestral lineages still present at a site; it collapses toward 0 as one lineage sweeps to fixation.

Real-world relevance: this exact signature — a dip in nucleotide diversity flanked by an extended haplotype of low recombination — is how genome scans detect recent positive selection, e.g. around the human LCT lactase-persistence locus.

Founder lineage (site 0 carrier) Other ancestral lineages Rows = individuals · columns = linked sites

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