Abstract
Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale—analogous to the Kingman coalescent—we find that the ancestral process can be rescaled to its timehomogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 323-338 |
| Number of pages | 16 |
| Journal | Genetics |
| Volume | 208 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 1 2018 |
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Keywords
- Coalescent theory
- Maximum likelihood
- Multiple mergers
- Population growth
- Site-frequency spectrum
ASJC Scopus subject areas
- Genetics
Cite this
Coalescent processes with skewed offspring distributions and nonequilibrium demography. / Matuszewski, Sebastian; Hildebrandt, Marcel E.; Achaz, Guillaume; Jensen, Jeffrey.
In: Genetics, Vol. 208, No. 1, 01.01.2018, p. 323-338.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Coalescent processes with skewed offspring distributions and nonequilibrium demography
AU - Matuszewski, Sebastian
AU - Hildebrandt, Marcel E.
AU - Achaz, Guillaume
AU - Jensen, Jeffrey
PY - 2018/1/1
Y1 - 2018/1/1
N2 - Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale—analogous to the Kingman coalescent—we find that the ancestral process can be rescaled to its timehomogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
AB - Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale—analogous to the Kingman coalescent—we find that the ancestral process can be rescaled to its timehomogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
KW - Coalescent theory
KW - Maximum likelihood
KW - Multiple mergers
KW - Population growth
KW - Site-frequency spectrum
UR - http://www.scopus.com/inward/record.url?scp=85040096909&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85040096909&partnerID=8YFLogxK
U2 - 10.1534/genetics.117.300499
DO - 10.1534/genetics.117.300499
M3 - Article
C2 - 29127263
AN - SCOPUS:85040096909
VL - 208
SP - 323
EP - 338
JO - Genetics
JF - Genetics
SN - 0016-6731
IS - 1
ER -