---
_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. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955.
    doi:<a href="https://doi.org/10.1111/1755-0998.13676">10.1111/1755-0998.13676</a>
  apa: Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess
    whether standard population genetic theory holds in the presence of spatio-temporal
    heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a
    href="https://doi.org/10.1111/1755-0998.13676">https://doi.org/10.1111/1755-0998.13676</a>
  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.” <i>Molecular Ecology Resources</i>. Wiley,
    2022. <a href="https://doi.org/10.1111/1755-0998.13676">https://doi.org/10.1111/1755-0998.13676</a>.
  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,” <i>Molecular Ecology Resources</i>, 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.”
    <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55,
    doi:<a href="https://doi.org/10.1111/1755-0998.13676">10.1111/1755-0998.13676</a>.
  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
  checksum: 3102e203e77b884bffffdbe8e548da88
  content_type: application/pdf
  creator: dernst
  date_created: 2023-02-02T08:11:23Z
  date_updated: 2023-02-02T08:11:23Z
  file_id: '12477'
  file_name: 2022_MolecularEcologyRes_Szep.pdf
  file_size: 6431779
  relation: main_file
  success: 1
file_date_updated: 2023-02-02T08:11:23Z
has_accepted_license: '1'
intvolume: '        22'
isi: 1
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:
  image: /images/cc_by_nc.png
  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'
...
---
_id: '8099'
abstract:
- lang: eng
  text: Sewall Wright developed FST for describing population differentiation and
    it has since been extended to many novel applications, including the detection
    of homomorphic sex chromosomes. However, there has been confusion regarding the
    expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome
    when comparing males and females. Here, we attempt to resolve this confusion by
    contrasting two common FST estimators and explain why they yield different estimates
    when applied to the case of sex chromosomes. We show that this difference is true
    for many allele frequencies, but the situation characterized by fixed differences
    between the X‐ and Y‐chromosome is among the most extreme. To avoid additional
    confusion, we recommend that all authors using FST clearly state which estimator
    of FST their work uses.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: William J
  full_name: Gammerdinger, William J
  id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
  last_name: Gammerdinger
  orcid: 0000-0001-9638-1220
- first_name: Melissa A
  full_name: Toups, Melissa A
  id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
  last_name: Toups
  orcid: 0000-0002-9752-7380
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
citation:
  ama: 'Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case
    study from  sex chromosomes. <i>Molecular Ecology Resources</i>. 2020;20(6):1517-1525.
    doi:<a href="https://doi.org/10.1111/1755-0998.13210">10.1111/1755-0998.13210</a>'
  apa: 'Gammerdinger, W. J., Toups, M. A., &#38; Vicoso, B. (2020). Disagreement in
    FST estimators: A case study from  sex chromosomes. <i>Molecular Ecology Resources</i>.
    Wiley. <a href="https://doi.org/10.1111/1755-0998.13210">https://doi.org/10.1111/1755-0998.13210</a>'
  chicago: 'Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement
    in FST Estimators: A Case Study from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>.
    Wiley, 2020. <a href="https://doi.org/10.1111/1755-0998.13210">https://doi.org/10.1111/1755-0998.13210</a>.'
  ieee: 'W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators:
    A case study from  sex chromosomes,” <i>Molecular Ecology Resources</i>, vol.
    20, no. 6. Wiley, pp. 1517–1525, 2020.'
  ista: 'Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators:
    A case study from  sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.'
  mla: 'Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study
    from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>, vol. 20, no. 6, Wiley,
    2020, pp. 1517–25, doi:<a href="https://doi.org/10.1111/1755-0998.13210">10.1111/1755-0998.13210</a>.'
  short: W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20
    (2020) 1517–1525.
date_created: 2020-07-07T08:56:16Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-09-05T16:07:08Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1111/1755-0998.13210
ec_funded: 1
external_id:
  isi:
  - '000545451200001'
  pmid:
  - '32543001'
file:
- access_level: open_access
  checksum: 3d87ebb8757dcd504f20c618b72e6575
  content_type: application/pdf
  creator: dernst
  date_created: 2020-11-26T11:46:43Z
  date_updated: 2020-11-26T11:46:43Z
  file_id: '8814'
  file_name: 2020_MolecularEcologyRes_Gammerdinger.pdf
  file_size: 820428
  relation: main_file
  success: 1
file_date_updated: 2020-11-26T11:46:43Z
has_accepted_license: '1'
intvolume: '        20'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1517-1525
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28842-B22
  name: Sex chromosome evolution under male- and female- heterogamety
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: 'Disagreement in FST estimators: A case study from  sex chromosomes'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 20
year: '2020'
...