Dr. P.G. (Patrick) Meirmans
Universitair Docent Populatiegenetica van Planten
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Institute for Biodiversity and Ecosystem Dynamics
Bezoekadres
- Science Park 904
- Kamernummer: C3.212
Postadres
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Postbus 94240
1090 GE Amsterdam
Contactgegevens
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Research
At its most elementary, evolution is a shift in allele frequencies. Therefore, we can learn a lot about evolution by investigating the drivers that determine the distribution of genetic diversity. My main research interest is how we can use population genetic data to say something about evolutionary and demographic processes. Ultimately, I want to know which processes, including migration, selection, drift, but also anthropogenic disturbance, determine the distribution of genetic information in space. I do this both empirically and theoretically, but my main strength lies in the analysis of genetic data. Some of my main topics are:
Testing statistical methodology
Genetic data can provide very powerful tools for addressing evolutionary and ecological questions. However, the statistical methods used often have biases and implicit assumptions that are not well understood. I use simulations to test the performance of widely-used statistical methods to see when they return the expected outcomes, and when they are biased. I then provide recommendations for their use, which hopefully leads to more robust inferences in the whole field.
Polyploidy
Polyploids do strange things: they have many peculiarities in their genetic system that can make them quite different from diploids. This also means that the statistical and molecular tools that are used for diploids do not apply for polyploids. I study how polyploidy affects the distribution of genetic diversity and how genetic data analysis can be adapted for polyploid systems.
GenoDive Software development
I have developed a widely-used program for genetic data analysis: GenoDive. GenoDive includes some methods that I have developed myself that are not implemented in any other program, such as AMOVA-based clustering and clone assignment. GenoDive can also handle polyploid data up to hexadecaploids. In addition, I have developed Marlin, a program for performing spatially-explicit simulations. Both GenoDive and Marlin are under constant development.
Application to conservation biology, ecological risk assessment, and climate change
Besides being very informative about the process of evolution, the study of genetic diversity has practical applications in a wide variety of fields. I use population genetics to get insights about the conservation of endangered species, both plants and animals. I have also used population genetics to answer questions around the introduction of genetically modified crops. Ultimately, the genetic diversity of populations drives their adaptation to current and future threats such as climate change and habitat loss.
Additional topics
Plant mating systems, hybridization, evolution of sex, invasive species
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Publicaties
2020
Meirmans, P. G. (2020). GenoDive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids. Molecular Ecology Resources, 20(4), 1126-1131. Advance online publication. https://doi.org/10.1111/1755-0998.13145 [details]
2018
- Meirmans, P. G., Liu, S., & van Tienderen, P. H. (2018). The Analysis of Polyploid Genetic Data. Journal of Heredity, 109(3), 283-296. Advance online publication. https://doi.org/10.1093/jhered/esy006 [details]
2015
- Meirmans, P. G. (2015). Seven common mistakes in population genetics and how to avoid them. Molecular Ecology, 24(13), 3223-3231. Advance online publication. https://doi.org/10.1111/mec.13243 [details]
2012
- Meirmans, P. G. (2012). The trouble with isolation by distance. Molecular Ecology, 21(12), 2839-2846. https://doi.org/10.1111/j.1365-294X.2012.05578.x [details]
2023
- Meirmans, P. G. (2023). Analyzing Autopolyploid Genetic Data Using GenoDive. In Y. Van de Peer (Ed.), Polyploidy : Methods and Protocols (pp. 261-277). (Methods in molecular biology; Vol. 2545). Humana Press. https://doi.org/10.1007/978-1-0716-2561-3_14
2022
- López-Delgado, J., & Meirmans, P. G. (2022). History or demography? Determining the drivers of genetic variation in North American plants. Molecular Ecology, 31(7), 1951-1962. Advance online publication. https://doi.org/10.1111/mec.16230 [details]
- Varela-Álvarez, E., Meirmans, P. G., Guiry, M. D., & Serrão, E. A. (2022). Biogeographic Population Structure of Chimeric Blades of Porphyra in the Northeast Atlantic Reveals Southern Rich Gene Pools, Introgression and Cryptic Plasticity. Frontiers in Plant Science, 13, Article 818368. https://doi.org/10.3389/fpls.2022.818368
2021
- Meirmans, P. G. (2021). Niche divergence contributes to geographical parthenogenesis in two dandelion taxa. Journal of Evolutionary Biology, 34(7), 1071-1086. https://doi.org/10.1111/jeb.13794 [details]
- Varela-Álvarez, E., Loureiro, J., Meirmans, P. G., Castro, M., & Serrão, E. A. (2021). Genomes Vary in Size and Spatial Patterns Within Chimeric Blades of Porphyra spp. Frontiers in Marine Science, 8, Article 628183. https://doi.org/10.3389/fmars.2021.628183 [details]
2020
- Meirmans, P. G. (2020). GenoDive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids. Molecular Ecology Resources, 20(4), 1126-1131. Advance online publication. https://doi.org/10.1111/1755-0998.13145 [details]
2019
- Meirmans, P. G. (2019). Hardy-weinberg equilibrium. In B. Fath (Ed.), Encyclopedia of Ecology (2nd ed., Vol. 3, pp. 118-126). (Reference Module in Earth Systems and Environmental Sciences). Elsevier. https://doi.org/10.1016/B978-0-12-409548-9.10555-X [details]
- Meirmans, S., & Meirmans, P. G. (2019). The Queen of Problems in Evolutionary Biology. In Encyclopedia of life sciences Wiley. https://doi.org/10.1002/9780470015902.a0028485 [details]
- Stift, M., Kolar, F., & Meirmans, P. G. (2019). STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations. Heredity, 123(4), 429-441. https://doi.org/10.1038/s41437-019-0247-6 [details]
2018
- Barmentlo, S. H., Meirmans, P. G., Luijten, S. H., Triest, L., & Oostermeijer, J. G. B. (2018). Outbreeding depression and breeding system evolution in small, remnant populations of Primula vulgaris: consequences for genetic rescue. Conservation Genetics, 19(3), 545-554. Advance online publication. https://doi.org/10.1007/s10592-017-1031-x [details]
- Meirmans, P. G. (2018). Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset. Heredity, 122, 276-287. https://doi.org/10.1038/s41437-018-0124-8 [details]
- Meirmans, P. G., & Liu, S. (2018). Analysis of Molecular Variance (AMOVA) for Autopolyploids. Frontiers in Ecology and Evolution, 6, Article 66. https://doi.org/10.3389/fevo.2018.00066 [details]
- Meirmans, P. G., Liu, S., & van Tienderen, P. H. (2018). The Analysis of Polyploid Genetic Data. Journal of Heredity, 109(3), 283-296. Advance online publication. https://doi.org/10.1093/jhered/esy006 [details]
- Neiman, M., Meirmans, P. G., Schwander, T., & Meirmans, S. (2018). Sex in the wild: How and why field‐based studies contribute to solving the problem of sex. Evolution, 72(6), 1194-1203. https://doi.org/10.1111/evo.13485 [details]
- van den Burg, M. P., Meirmans, P. G., Van Wagensveld, T. P., Kluskens, B., Madden, H., Welch, M. E., & Breeuwer, J. A. J. (2018). The Lesser Antillean Iguana (Iguana delicatissima) on St. Eustatius: Genetically Depauperate and Threatened by Ongoing Hybridization. Journal of Heredity, 109(4), 426-437. https://doi.org/10.1093/jhered/esy008 [details]
2017
- Christie, M. R., Meirmans, P. G., Gaggiotti, O. E., Toonen, R. J., & White, C. (2017). Disentangling the relative merits and disadvantages of parentage analysis and assignment tests for inferring population connectivity. ICES Journal of Marine Science, 74(6), 1749-1762. https://doi.org/10.1093/icesjms/fsx044 [details]
- D'Andrea, L., Meirmans, P., van de Wiel, C., Guadagnuolo, R., van Treuren, R., Kozlowski, G., den Nijs, H., & Felber, F. (2017). Molecular biogeography of prickly lettuce (Lactuca serriola L.) shows traces of recent range expansion. Journal of Heredity, 108(2), 194-206. Advance online publication. https://doi.org/10.1093/jhered/esw078 [details]
- Meirmans, P. G., Godbout, J., Lamothe, M., Thompson, S. L., & Isabel, N. (2017). History rather than hybridization determines population structure and adaptation in Populus balsamifera. Journal of Evolutionary Biology, 30(11), 2044-2058. https://doi.org/10.1111/jeb.13174 [details]
2016
- Nadeau, S., Meirmans, P. G., Aitken, S. N., Ritland, K., & Isabel, N. (2016). The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines. Ecology and Evolution, 6(24), 8649-8664. https://doi.org/10.1002/ece3.2550 [details]
2015
- Luijten, S. H., Shidlo, N. S., Meirmans, P. G., & de Jong, T. J. (2015). Hybridisation and introgression between Brassica napus and B. rapa in the Netherlands. Plant Biology, 17(1), 262-267. Advance online publication. https://doi.org/10.1111/plb.12197 [details]
- Meirmans, P. G. (2015). Seven common mistakes in population genetics and how to avoid them. Molecular Ecology, 24(13), 3223-3231. Advance online publication. https://doi.org/10.1111/mec.13243 [details]
2014
- Hidding, B., Meirmans, P. G., Klaassen, M., de Boer, T., Ouborg, N. J., Wagemaker, C. A. M., & Nolet, B. A. (2014). The effect of herbivores on genotypic diversity in a clonal aquatic plant. Oikos, 123(9), 1112-1120. Advance online publication. https://doi.org/10.1111/oik.01136 [details]
- Meirmans, P. G. (2014). Nonconvergence in Bayesian estimation of migration rates. Molecular Ecology Resources, 14(4), 726-733. https://doi.org/10.1111/1755-0998.12216 [details]
- Meirmans, P. G., Gros-Louis, M. C., Lamothe, M., Perron, M., Bousquet, J., & Isabel, N. (2014). Rates of spontaneous hybridization and hybrid recruitment in co-existing exotic and native mature larch populations. Tree Genetics & Genomes, 10(4), 965-975. Advance online publication. https://doi.org/10.1007/s11295-014-0735-z [details]
2013
- Ellstrand, N. C., Meirmans, P., Rong, J., Bartsch, D., Ghosh, A., de Jong, T. J., Haccou, P., Lu, B-R., Snow, A. A., Stewart, C. N., Strasburg, J. L., van Tienderen, P. H., Vrieling, K., & Hooftman, D. A. P. (2013). Introgression of Crop Alleles into Wild or Weedy Populations. Annual Review of Ecology, Evolution, and Systematics, 44, 325-345. Advance online publication. https://doi.org/10.1146/annurev-ecolsys-110512-135840 [details]
- Meirmans, P. G., & van Tienderen, P. H. (2013). The effects of inheritance in tetraploids on genetic diversity and population divergence. Heredity, 110(2), 131-137. https://doi.org/10.1038/hdy.2012.80 [details]
- Rong, J., Xu, S., Meirmans, P. G., & Vrieling, K. (2013). Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression. Annals of Botany, 112(7), 1361-1370. Advance online publication. https://doi.org/10.1093/aob/mct208 [details]
2012
- Ghosh, A., Meirmans, P. G., & Haccou, P. (2012). Quantifying introgression risk with realistic population genetics. Proceedings of the Royal Society B-Biological Sciences, 279(1748), 4747-4754. Advance online publication. https://doi.org/10.1098/rspb.2012.1907 [details]
- Meirmans, P. G. (2012). AMOVA-based clustering of population genetic data. Journal of Heredity, 103(5), 744-750. Advance online publication. https://doi.org/10.1093/jhered/ess047 [details]
- Meirmans, P. G. (2012). The trouble with isolation by distance. Molecular Ecology, 21(12), 2839-2846. https://doi.org/10.1111/j.1365-294X.2012.05578.x [details]
- Meirmans, S., Meirmans, P. G., & Kirkendall, L. R. (2012). The costs of sex: facing real-world complexities. The Quarterly Review of Biology, 87(1), 19-40. https://doi.org/10.1086/663945 [details]
- van Hengstum, T., Lachmuth, S., Oostermeijer, J. G. B., den Nijs, J. C. M., Meirmans, P. G., & van Tienderen, P. H. (2012). Human-induced hybridization among congeneric endemic plants on Tenerife, Canary Islands. Plant Systematics and Evolution, 298(6), 1119-1131. https://doi.org/10.1007/s00606-012-0624-6 [details]
2011
- Meirmans, P. G. (2011). MARLIN, software to create, run, and analyse spatially realistic simulations. Molecular Ecology Resources, 11(1), 146-150. https://doi.org/10.1111/j.1755-0998.2010.02888.x [details]
- Meirmans, P. G., & Hedrick, P. W. (2011). Assessing population structure: FST and related measures. Molecular Ecology Resources, 11(1), 5-18. https://doi.org/10.1111/j.1755-0998.2010.02927.x [details]
- Meirmans, P. G., Goudet, J., & Gaggiotti, O. E. (2011). Ecology and life history affect different aspects of the population structure of 27 high-alpine plants. Molecular Ecology, 20, 3144-3155. https://doi.org/10.1111/j.1365-294X.2011.05164.x [details]
- Pelgas, B., Bousquet, J., Meirmans, P. G., Ritland, K., & Isabel, N. (2011). QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. BMC Genomics, 12, 145. https://doi.org/10.1186/1471-2164-12-145 [details]
2010
- Meirmans, P. G., Lamothe, M., Gros-Louis, M. C., Khasa, D., Périnet, P., Bousquet, J., & Isabel, N. (2010). Complex patterns of hybridization between exotic and native North American poplar species. American Journal of Botany, 97(10), 1688-1697. https://doi.org/10.3732/ajb.0900271 [details]
- Thompson, S. L., Lamothe, M., Meirmans, P. G., Périnet, P., & Isabel, N. (2010). Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars. Molecular Ecology, 19(1), 132-145. https://doi.org/10.1111/j.1365-294X.2009.04442.x [details]
2009
- Meirmans, P. G., Bousquet, J., & Isabel, N. (2009). A metapopulation model for the introgression from Genetically Modified Plants into their wild relatives. Evolutionary Applications, 2(2), 160-171. https://doi.org/10.1111/j.1752-4571.2008.00050.x
- Neiman, M., Meirmans, S., & Meirmans, P. G. (2009). What can asexual lineage age tell us about the maintenance of sex? Annals of the New York Academy of Sciences, 1168(1), 185-200. https://doi.org/10.1111/j.1749-6632.2009.04572.x [details]
2007
- Meirmans, P. G., Lamothe, M., Périnet, P., & Isabel, N. (2007). Species-specific single nucleotide polymorphism markers for detecting hybridization and introgression in poplar. Canadian Journal of Botany, 85, 1082-1091. https://doi.org/10.1139/B07-069
2006
- Lamothe, M., Meirmans, P. G., & Isabel, N. (2006). A set of polymorphic EST-derived markers for Picea species. Molecular Ecology Notes, 6, 237-240. https://doi.org/10.1111/j.1471-8286.2005.01205.x
- Meirmans, P. G. (2006). Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution, 60, 2399-2402. https://doi.org/10.1111/j.0014-3820.2006.tb01874.x
- Meirmans, P. G., den Nijs, J. C. M., & van Tienderen, P. H. (2006). Male sterility in triploid dandelions: asexual females vs asexual hermaphrodites. Heredity, 96, 45-52. https://doi.org/10.1038/sj.hdy.6800750
2004
- Meirmans, P. G., & van Tienderen, P. H. (2004). GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794. https://doi.org/10.1111/j.1471-8286.2004.00770.x [details]
- van der Hulst, R. G. M., Meirmans, P. G., van Tienderen, P. H., & van Damme, J. M. M. (2004). Nuclear-cytoplasmic male-sterility in diploid dandelions. Heredity, 93, 43-50. https://doi.org/10.1038/sj.hdy.6800478 [details]
2003
- Meirmans, P. G., Vlot, E. C., den Nijs, J. C. M., & Menken, S. B. J. (2003). Spatial ecological and genetic structure of a mixed population of sexual diploid and apomictic triploid dandelions. Journal of Evolutionary Biology, 16(2), 343-352. https://doi.org/10.1046/j.1420-9101.2003.00515.x [details]
1999
- Meirmans, P. G., Calame, F. G., Bretagnolle, F., Felber, F., & den Nijs, J. C. M. (1999). Anthropogenic disturbance and habitat differentiation between sexual diploid and apomictic triploid Taraxacum sect. Ruderalia. Folia Geobotanica, 34, 451-469. [details]
1998
- de Roos, A. M., Sabelis, M. W., van der Geest, L., van Breemen, M., Geerts, R., Groeneveld, B., ... Vlaar, M. (1998). Genetisch gemodificeerde organismen. Risico's voor ecosystemen en biodiversiteit? Landschap, 15, 157-168. [details]
Andere
- Meirmans, P. (organiser), Kolar, F. (organiser) & Stift, M. (participant) (2-12-2018 - 7-12-2018). Population genetics of polyploids, from theory to practice, Drøbak. Polyploidy is widespread and frequent in plants (including many crops), but also occurs in animals such as fish and amphibians. However, our (…) (organising a conference, workshop, ...).
- Kolar, F. (organiser), Meirmans, P. (organiser) & Stift, M. (organiser) (23-1-2017 - 25-1-2017). Population genetics of polyploids, Prague. Course aimed at PhD course and young scientists on the analysis of polyploid genetic data. (organising a conference, workshop, ...).
2020
- Pelgas, B., Bousquet, J., Meirmans, P. G., Ritland, K. & Isabel, N. (2020). Additional file of QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. Figshare. https://doi.org/10.6084/m9.figshare.12879146.v2
- Pelgas, B., Bousquet, J., Meirmans, P. G., Ritland, K. & Isabel, N. (2020). Additional file 1 of QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. Figshare. https://doi.org/10.6084/m9.figshare.12879152.v1
2019
- Meirmans, P. G., Stift, M. & Kolář, F. (2019). Data from: STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations. DRYAD. https://doi.org/10.5061/dryad.6g635f6
2018
- Meirmans, P. G. (2018). Data from: Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset. DRYAD. https://doi.org/10.5061/dryad.nh4366s
2016
- Van De Wiel, C., Guadagnuolo, R., den Nijs, H., Van Treuren, R., Felber, F., D'Andrea, L., Meirmans, P. & Kozlowski, G. (2016). Data from: Molecular biogeography of prickly lettuce (Lactuca serriola L.) shows traces of recent range expansion. DRYAD. https://doi.org/10.5061/dryad.tb2tv
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Nevenwerkzaamheden
- Geen nevenwerkzaamheden
Meirmans, P. G. (2020). GenoDive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids. Molecular Ecology Resources, 20(4), 1126-1131. Advance online publication.