TY - JOUR

T1 - On the genealogy of a sample of neutral rare alleles

AU - Wiuf, Carsten

PY - 2000/1/1

Y1 - 2000/1/1

N2 - This paper concerns the genealogical structure of a sample of chromosomes sharing a neutral rare allele. We suppose that the mutation giving rise to the allele has only happened once in the history of the entire population, and that the allele is of known frequency q in the population. Within a coalescent framework C. Wiuf and P. Donnelly (1999, Theor. Popul. Biol. 56, 183-201) derived an exact analysis of the conditional genealogy but it is inconvenient for applications. Here, we develop an approximation to the exact distribution of the conditional genealogy, including an approximation to the distribution of the time at which the mutation arose. The approximations are accurate for frequencies q < 5-10%. In addition, a simple and fast simulation scheme is constructed. We consider a demography parameterized by a d-dimensional vector α = (α1,..., α(d)). It is shown that the conditional genealogy and the age of the mutation have distributions that depend on a = qα and q only, and that the effect of q is a linear scaling of times in the genealogy; if q is doubled, the lengths of all branches in the genealogy are doubled. The theory is exemplified in two different demographies of some interest in the study of human evolution: (1) a population of constant size and (2) a population of exponentially decreasing size (going backward in time). (C) 2000 Academic Press.

AB - This paper concerns the genealogical structure of a sample of chromosomes sharing a neutral rare allele. We suppose that the mutation giving rise to the allele has only happened once in the history of the entire population, and that the allele is of known frequency q in the population. Within a coalescent framework C. Wiuf and P. Donnelly (1999, Theor. Popul. Biol. 56, 183-201) derived an exact analysis of the conditional genealogy but it is inconvenient for applications. Here, we develop an approximation to the exact distribution of the conditional genealogy, including an approximation to the distribution of the time at which the mutation arose. The approximations are accurate for frequencies q < 5-10%. In addition, a simple and fast simulation scheme is constructed. We consider a demography parameterized by a d-dimensional vector α = (α1,..., α(d)). It is shown that the conditional genealogy and the age of the mutation have distributions that depend on a = qα and q only, and that the effect of q is a linear scaling of times in the genealogy; if q is doubled, the lengths of all branches in the genealogy are doubled. The theory is exemplified in two different demographies of some interest in the study of human evolution: (1) a population of constant size and (2) a population of exponentially decreasing size (going backward in time). (C) 2000 Academic Press.

KW - Age of mutation

KW - Coalescent theory

KW - Genealogy

KW - Rare allele

KW - Sampling scheme

UR - http://www.scopus.com/inward/record.url?scp=0033856339&partnerID=8YFLogxK

U2 - 10.1006/tpbi.2000.1469

DO - 10.1006/tpbi.2000.1469

M3 - Journal article

C2 - 10944476

AN - SCOPUS:0033856339

VL - 58

SP - 61

EP - 75

JO - Theoretical Population Biology

JF - Theoretical Population Biology

SN - 0040-5809

IS - 1

ER -