Coalescent models derived from birth–death processes
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Coalescent models derived from birth–death processes. / Crespo, Fausto F.; Posada, David; Wiuf, Carsten.
I: Theoretical Population Biology, Bind 142, 2021, s. 1-11.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Coalescent models derived from birth–death processes
AU - Crespo, Fausto F.
AU - Posada, David
AU - Wiuf, Carsten
N1 - Publisher Copyright: © 2021 The Author(s)
PY - 2021
Y1 - 2021
N2 - A coalescent model of a sample of size n is derived from a birth–death process that originates at a random time in the past from a single founder individual. Over time, the descendants of the founder evolve into a population of large (infinite) size from which a sample of size n is taken. The parameters and time of the birth–death process are scaled in N0, the size of the present-day population, while letting N0→∞, similarly to how the standard Kingman coalescent process arises from the Wright–Fisher model. The model is named the Limit Birth–Death (LBD) coalescent model. Simulations from the LBD coalescent model with sample size n are computationally slow compared to standard coalescent models. Therefore, we suggest different approximations to the LBD coalescent model assuming the population size is a deterministic function of time rather than a stochastic process. Furthermore, we introduce a hybrid LBD coalescent model, that combines the exactness of the LBD coalescent model model with the speed of the approximations.
AB - A coalescent model of a sample of size n is derived from a birth–death process that originates at a random time in the past from a single founder individual. Over time, the descendants of the founder evolve into a population of large (infinite) size from which a sample of size n is taken. The parameters and time of the birth–death process are scaled in N0, the size of the present-day population, while letting N0→∞, similarly to how the standard Kingman coalescent process arises from the Wright–Fisher model. The model is named the Limit Birth–Death (LBD) coalescent model. Simulations from the LBD coalescent model with sample size n are computationally slow compared to standard coalescent models. Therefore, we suggest different approximations to the LBD coalescent model assuming the population size is a deterministic function of time rather than a stochastic process. Furthermore, we introduce a hybrid LBD coalescent model, that combines the exactness of the LBD coalescent model model with the speed of the approximations.
KW - Bernoulli sampling
KW - Conditioned reconstructed process
KW - Founder population
KW - Kingman coalescence
KW - Variable population size coalescence
UR - http://www.scopus.com/inward/record.url?scp=85116898012&partnerID=8YFLogxK
U2 - 10.1016/j.tpb.2021.09.003
DO - 10.1016/j.tpb.2021.09.003
M3 - Journal article
C2 - 34563554
AN - SCOPUS:85116898012
VL - 142
SP - 1
EP - 11
JO - Theoretical Population Biology
JF - Theoretical Population Biology
SN - 0040-5809
ER -
ID: 283507588