PMID- 30293985
OWN - NLM
STAT- MEDLINE
DCOM- 20191028
LR  - 20210218
IS  - 1365-2540 (Electronic)
IS  - 0018-067X (Print)
IS  - 0018-067X (Linking)
VI  - 121
IP  - 6
DP  - 2018 Dec
TI  - The IICR and the non-stationary structured coalescent: towards demographic 
      inference with arbitrary changes in population structure.
PG  - 663-678
LID - 10.1038/s41437-018-0148-0 [doi]
AB  - In the last years, a wide range of methods allowing to reconstruct past 
      population size changes from genome-wide data have been developed. At the same 
      time, there has been an increasing recognition that population structure can 
      generate genetic data similar to those produced under models of population size 
      change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any 
      model of population structure, it is always possible to find a panmictic model 
      with a particular function of population size changes, having exactly the same 
      distribution of T(2) (the coalescence time for a sample of size two) as that of 
      the structured model. They called this function IICR (Inverse Instantaneous 
      Coalescence Rate) and showed that it does not necessarily correspond to 
      population size changes under non-panmictic models. Besides, most of the methods 
      used to analyse data under models of population structure tend to arbitrarily fix 
      that structure and to minimise or neglect population size changes. Here, we 
      extend the seminal work of Herbots (PhD thesis, University of London, 1994) on 
      the structured coalescent and propose a new framework, the Non-Stationary 
      Structured Coalescent (NSSC) that incorporates demographic events (changes in 
      gene flow and/or deme sizes) to models of nearly any complexity. We show how to 
      compute the IICR under a wide family of stationary and non-stationary models. As 
      an example we address the question of human and Neanderthal evolution and discuss 
      how the NSSC framework allows to interpret genomic data under this new 
      perspective.
FAU - Rodriguez, Willy
AU  - Rodriguez W
AD  - Institut de Mathematiques de Toulouse, Universite de Toulouse, Institut National 
      des Sciences Appliquees, 31077, Toulouse, France.
FAU - Mazet, Olivier
AU  - Mazet O
AD  - Institut de Mathematiques de Toulouse, Universite de Toulouse, Institut National 
      des Sciences Appliquees, 31077, Toulouse, France.
FAU - Grusea, Simona
AU  - Grusea S
AD  - Institut de Mathematiques de Toulouse, Universite de Toulouse, Institut National 
      des Sciences Appliquees, 31077, Toulouse, France.
FAU - Arredondo, Armando
AU  - Arredondo A
AD  - Institut de Mathematiques de Toulouse, Universite de Toulouse, Institut National 
      des Sciences Appliquees, 31077, Toulouse, France.
FAU - Corujo, Josue M
AU  - Corujo JM
AD  - Facultad de Matematica y Computacion, Universidad de La Habana, La Havana, Cuba.
FAU - Boitard, Simon
AU  - Boitard S
AD  - GenPhySE, Universite de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France.
FAU - Chikhi, Lounes
AU  - Chikhi L
AD  - Laboratoire Evolution & Diversite Biologique (EDB UMR 5174), Universite de 
      Toulouse Midi-Pyrenees, CNRS, IRD, UPS. 118 route de Narbonne, Bat. 4R1, 31062, 
      Toulouse cedex 9, France. lounes.chikhi@univ-tlse3.fr.
AD  - Instituto Gulbenkian de Ciencia, Rua da Quinta Grande, No. 6, P-2780-156, Oeiras, 
      Portugal. lounes.chikhi@univ-tlse3.fr.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20181007
PL  - England
TA  - Heredity (Edinb)
JT  - Heredity
JID - 0373007
SB  - IM
EIN - Heredity (Edinb). 2021 Apr;126(4):706. PMID: 33597719
MH  - *Demography
MH  - Humans
MH  - Models, Theoretical
MH  - *Population Density
PMC - PMC6221895
COIS- The authors declare that they have no conflict of interest.
EDAT- 2018/10/09 06:00
MHDA- 2019/10/29 06:00
PMCR- 2018/10/07
CRDT- 2018/10/09 06:00
PHST- 2018/07/15 00:00 [received]
PHST- 2018/09/15 00:00 [accepted]
PHST- 2018/09/14 00:00 [revised]
PHST- 2018/10/09 06:00 [pubmed]
PHST- 2019/10/29 06:00 [medline]
PHST- 2018/10/09 06:00 [entrez]
PHST- 2018/10/07 00:00 [pmc-release]
AID - 10.1038/s41437-018-0148-0 [pii]
AID - 148 [pii]
AID - 10.1038/s41437-018-0148-0 [doi]
PST - ppublish
SO  - Heredity (Edinb). 2018 Dec;121(6):663-678. doi: 10.1038/s41437-018-0148-0. Epub 
      2018 Oct 7.