Coalescent Theory


Coalescent theory is a very useful tool in the interpretation of genomic variation data.

Keywords: coalescent; genealogy; recombination; haplotype blocks; selection; inference

Figure 1.

Coalescent trees for samples of size 6 and 32.

Figure 2.

Coalescent tree of a sample of size 6 (constant population size in the left panel, exponentially growing population in the right panel).

Figure 3.

Ancestral history of three chromosomal segments. See text for details.

Figure 4.

Ancestral recombination graph. Dot‐dash lines indicate coalescence events; dotted lines indicate recombination events.

Figure 5.

Coalescent trees in an ancestral recombination graph. The shaded points indicate mutations, which are represented as dots in each coalescent tree.

Figure 6.

Nucleotide diversity and time to most recent common ancestor (MRCA) across a segment.

Figure 7.

Decay of haplotype sharing.



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Further Reading

Beaumont MA, Zhang W and Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162: 2025–2035.

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Reich DE, Schaffner SF, Daly MJ, et al. (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genetics, 32: 135–142.

Tang H, Siegmund DO, Shen P, Oefner PJ and Feldman MW (2002) Frequentist estimation of coalescence times from nucleotide sequence data using a tree‐based partition. Genetics 161: 447–459.

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Tavaré, Simon(Jul 2006) Coalescent Theory. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005458]