--- _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' ...