---
_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
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. Molecular Ecology Resources. 2020;20(6):1517-1525.
doi:10.1111/1755-0998.13210'
apa: 'Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in
FST estimators: A case study from sex chromosomes. Molecular Ecology Resources.
Wiley. https://doi.org/10.1111/1755-0998.13210'
chicago: 'Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement
in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources.
Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.'
ieee: 'W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators:
A case study from sex chromosomes,” Molecular Ecology Resources, 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.” Molecular Ecology Resources, vol. 20, no. 6, Wiley,
2020, pp. 1517–25, doi:10.1111/1755-0998.13210.'
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
license: https://creativecommons.org/licenses/by/4.0/
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'
...
---
_id: '6821'
abstract:
- lang: eng
text: To determine the visual sensitivities of an organism of interest, quantitative
reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify
expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable,
high‐throughput method for measuring expression, it comes with inherent normalization
issues that affect the interpretation of results, especially as opsin expression
can vary greatly based on developmental stage, light environment or diurnal cycles.
We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr
increments and examined how normalization affects a data set with fluctuating
expression levels using qRT–PCR and transcriptome data from the retinae of the
cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression
relative to (a) the average of three stably expressed housekeeping genes (Ube2z,
EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific
subunit of transducin), (d) total opsin expression and (e) only opsins expressed
in the same cone type. Normalizing by proportion of cone type produced the least
variation and would be best for removing time‐of‐day variation. In contrast, normalizing
by housekeeping genes produced the highest daily variation in expression and demonstrated
that the peak of cone opsin expression was in the late afternoon. A weighted correlation
network analysis showed that the expression of different cone opsins follows a
very similar daily cycle. With the knowledge of how these normalization methods
affect opsin expression data, we make recommendations for designing sampling approaches
and quantification methods based upon the scientific question being examined.
article_processing_charge: No
article_type: original
author:
- first_name: Miranda R.
full_name: Yourick, Miranda R.
last_name: Yourick
- first_name: Benjamin A.
full_name: Sandkam, Benjamin A.
last_name: Sandkam
- 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: Daniel
full_name: Escobar-Camacho, Daniel
last_name: Escobar-Camacho
- first_name: Sri Pratima
full_name: Nandamuri, Sri Pratima
last_name: Nandamuri
- first_name: Frances E.
full_name: Clark, Frances E.
last_name: Clark
- first_name: Brendan
full_name: Joyce, Brendan
last_name: Joyce
- first_name: Matthew A.
full_name: Conte, Matthew A.
last_name: Conte
- first_name: Thomas D.
full_name: Kocher, Thomas D.
last_name: Kocher
- first_name: Karen L.
full_name: Carleton, Karen L.
last_name: Carleton
citation:
ama: Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin
expression and common housekeeping genes necessitates comprehensive normalization
methods for quantitative real-time PCR analyses. Molecular Ecology Resources.
2019;19(6):1447-1460. doi:10.1111/1755-0998.13062
apa: Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri,
S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression
and common housekeeping genes necessitates comprehensive normalization methods
for quantitative real-time PCR analyses. Molecular Ecology Resources. Wiley.
https://doi.org/10.1111/1755-0998.13062
chicago: Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel
Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew
A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin
Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization
Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources.
Wiley, 2019. https://doi.org/10.1111/1755-0998.13062.
ieee: M. R. Yourick et al., “Diurnal variation in opsin expression and common
housekeeping genes necessitates comprehensive normalization methods for quantitative
real-time PCR analyses,” Molecular Ecology Resources, vol. 19, no. 6. Wiley,
pp. 1447–1460, 2019.
ista: Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP,
Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in
opsin expression and common housekeeping genes necessitates comprehensive normalization
methods for quantitative real-time PCR analyses. Molecular Ecology Resources.
19(6), 1447–1460.
mla: Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common
Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative
Real-Time PCR Analyses.” Molecular Ecology Resources, vol. 19, no. 6, Wiley,
2019, pp. 1447–60, doi:10.1111/1755-0998.13062.
short: M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri,
F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology
Resources 19 (2019) 1447–1460.
date_created: 2019-08-18T22:00:41Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-29T07:10:44Z
day: '01'
department:
- _id: BeVi
doi: 10.1111/1755-0998.13062
external_id:
isi:
- '000480196800001'
pmid:
- '31325910'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727
month: '11'
oa: 1
oa_version: Submitted Version
page: 1447-1460
pmid: 1
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- 1755-0998
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diurnal variation in opsin expression and common housekeeping genes necessitates
comprehensive normalization methods for quantitative real-time PCR analyses
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2019'
...