---
_id: '11640'
abstract:
- lang: eng
text: Spatially explicit population genetic models have long been developed, yet
have rarely been used to test hypotheses about the spatial distribution of genetic
diversity or the genetic divergence between populations. Here, we use spatially
explicit coalescence simulations to explore the properties of the island and the
two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal
variation in deme size. We avoid the simulation of genetic data, using the fact
that under the studied models, summary statistics of genetic diversity and divergence
can be approximated from coalescence times. We perform the simulations using gridCoal,
a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical
Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change
arbitrarily across space and time, as well as migration rates between individual
demes. We identify different factors that can cause a deviation from theoretical
expectations, such as the simulation time in comparison to the effective deme
size and the spatio-temporal autocorrelation across the grid. Our results highlight
that FST, a measure of the strength of population structure, principally depends
on recent demography, which makes it robust to temporal variation in deme size.
In contrast, the amount of genetic diversity is dependent on the distant past
when Ne is large, therefore longer run times are needed to estimate Ne than FST.
Finally, we illustrate the use of gridCoal on a real-world example, the range
expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using
different degrees of spatio-temporal variation in deme size.
acknowledgement: ES was supported by an IST studentship provided by IST Austria. BT
was funded by the European Union's Horizon 2020 research and innovation programme
under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project
received further funding awarded to KC from the Swiss National Science Foundation
(SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick
Barton for many invaluable discussions and his comments on the thesis chapter and
this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions
and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for
providing us with the raw data from the LPX-Bern model for silver fir, and Willy
Tinner for helpful insights about the demographic history of silver fir. We also
thank the editor Alana Alexander for useful comments and advice on the manuscript.
Open access funding provided by Eidgenossische Technische Hochschule Zurich.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Katalin
full_name: Csilléry, Katalin
last_name: Csilléry
citation:
ama: Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 2022;22(8):2941-2955.
doi:10.1111/1755-0998.13676
apa: Szep, E., Trubenova, B., & Csilléry, K. (2022). Using gridCoal to assess
whether standard population genetic theory holds in the presence of spatio-temporal
heterogeneity in population size. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13676
chicago: Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to
Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal
Heterogeneity in Population Size.” Molecular Ecology Resources. Wiley,
2022. https://doi.org/10.1111/1755-0998.13676.
ieee: E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether
standard population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size,” Molecular Ecology Resources, vol. 22, no. 8. Wiley,
pp. 2941–2955, 2022.
ista: Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 22(8), 2941–2955.
mla: Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic
Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.”
Molecular Ecology Resources, vol. 22, no. 8, Wiley, 2022, pp. 2941–55,
doi:10.1111/1755-0998.13676.
short: E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022)
2941–2955.
date_created: 2022-07-24T22:01:43Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-03T12:11:01Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13676
ec_funded: 1
external_id:
isi:
- '000825873600001'
file:
- access_level: open_access
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creator: dernst
date_created: 2023-02-02T08:11:23Z
date_updated: 2023-02-02T08:11:23Z
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intvolume: ' 22'
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issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2941-2955
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- 1755-0998
issn:
- 1755-098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using gridCoal to assess whether standard population genetic theory holds in
the presence of spatio-temporal heterogeneity in population size
tmp:
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legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2022'
...