Recombination and Gamete Mosaics

Run

Seed

The same seed gives the same crossovers every time.

Meioses to draw

Each meiosis makes four products; one of them is the gamete.

Speed

Steps per second during playback.

Chromosome

Physical length (Mb)

Human chromosome 1 is 249 Mb; chromosome 21 is 47 Mb.

Map length (cM)

1 cM is a 1% chance of an odd number of crossovers between two points per meiosis.

Markers

Evenly spaced along the physical chromosome, not the genetic map.

Crossover model

Interference

Interference makes a second crossover near the first less likely than chance.

Recombination map

Real human recombination puts most crossovers in narrow hotspots.

Model: map length is the expected number of crossovers per gamete, so a 120 cM chromosome averages 1.2. Under Poisson, crossovers fall independently along the map. Under the gamma model they form on the four-chromatid bundle at twice that rate with Gamma(nu, 2nu) gaps in Morgans and each involves a given chromatid half the time, so larger nu means more evenly spaced crossovers. nu = 1 is exactly Poisson.

On the Map distance tab, with no interference the observed points sit on Haldane. As nu rises they move toward Kosambi and then toward additivity, because evenly spaced crossovers produce fewer double crossovers.

The four products are drawn as a two-strand configuration, where the same pair of chromatids takes part in every crossover. Hotspots are drawn wider than real ones, which are 1 to 2 kb.

Generations tab

Generations

Rounds of random mating since two founding haplotypes.

Why it shrinks: generation 0 is a population of first-generation hybrids, every one of them carrying one founder A chromosome and one founder B chromosome. After that, mating is random within a population of 120.

Every generation adds crossovers, but a crossover only leaves a visible junction where the parent's two chromosomes carry different ancestry. At a 50:50 mix that is half the time, so the mean ancestry block after t generations settles at about 200/t cM.

This is why linkage disequilibrium is short-range in an old population and long-range in a recently founded one, and it is what local ancestry inference measures.

One meiosis, and the gametes it makes

Crossovers0

Mean0

cM per Mb0

Markers0

Gametes0