1
Coalescent Models
John Wakeley
Abstract
The standard neutral coalescent model and its extensions to include changes
in population size over time and population structure are reviewed. Gene
genealogies are shown to provide the hidden structure behind patterns of genetic
variation. Expressions for expected levels of genetic variation are presented and
explained, and tests of the standard neutral model based on the frequencies of
mutations at single-nucleotide sites (aka “site frequencies”) are outlined. Several
examples of deviations from the standard model are discussed, and their effects
on expected site frequencies are illustrated. Some attention is given to the fact
that coalescent theory has not fully grappled with the existence of underlying
population pedigrees.
1.1
Aims and Clarifications
The goal of the coalescent theory is the same as that of population genetics,
namely, to understand the forces which produce and maintain variation. The models
presented in this chapter support this endeavor. They are abstract and idealized tools
applicable to many different kinds of organisms or species. Due to the persistence of
racism, studies of human diversity call for a great deal of sensitivity. It is not enough
just to agree with Hochman (2019) that we have “changed the topic from ‘race’ to
‘population.’” We have to clarify that we are not just switching words. Rather, if
“race” is used to refer to a group of people, that group is not a “population” in the
population-genetic sense.
J. Wakeley ()
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
e-mail: wakeley@fas.harvard.edu
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021
K. E. Lohmueller, R. Nielsen (eds.), Human Population Genomics,
https://doi.org/10.1007/978-3-030-61646-5_1
3
Coalescent Models
John Wakeley
Abstract
The standard neutral coalescent model and its extensions to include changes
in population size over time and population structure are reviewed. Gene
genealogies are shown to provide the hidden structure behind patterns of genetic
variation. Expressions for expected levels of genetic variation are presented and
explained, and tests of the standard neutral model based on the frequencies of
mutations at single-nucleotide sites (aka “site frequencies”) are outlined. Several
examples of deviations from the standard model are discussed, and their effects
on expected site frequencies are illustrated. Some attention is given to the fact
that coalescent theory has not fully grappled with the existence of underlying
population pedigrees.
1.1
Aims and Clarifications
The goal of the coalescent theory is the same as that of population genetics,
namely, to understand the forces which produce and maintain variation. The models
presented in this chapter support this endeavor. They are abstract and idealized tools
applicable to many different kinds of organisms or species. Due to the persistence of
racism, studies of human diversity call for a great deal of sensitivity. It is not enough
just to agree with Hochman (2019) that we have “changed the topic from ‘race’ to
‘population.’” We have to clarify that we are not just switching words. Rather, if
“race” is used to refer to a group of people, that group is not a “population” in the
population-genetic sense.
J. Wakeley ()
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
e-mail: wakeley@fas.harvard.edu
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021
K. E. Lohmueller, R. Nielsen (eds.), Human Population Genomics,
https://doi.org/10.1007/978-3-030-61646-5_1
3