List of Publications

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List of Publications

Selected publications have been annotated with a short summary highlighting my contribution

* Indicates shared first-authorship

Yi X, Kemppainen P, Reid K, Chen Y, Rastas R, Fraimout A, Merilä J. (2024) Heterogeneous genomic architecture of skeletal armour traits in sticklebacks, Journal of Evolutionary Biology, Volume 37, Issue 9, September 2024, Pages 995–1008

Yi X*, Kemppainen P*, Merilä J. 2024. SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering. Mol. Ecol. Resour. 24:e13985. Introduces a novel linkage disequilibrium network-analytical approach to detect sex determining regions in population genomic data when the sex-identity of individuals is unknown. This method was invented and initially implemented by me, but most of the analyses and writing was nevertheless carried out by the Yi X.

Kemppainen P, Schembri R, Momigliano P (2024) Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data, Molecular Biology and Evolution, Volume 41, Issue 5, May 2024. This challenges with the widely used ψ statistic of Peter and Slatkin (2013, 2015); testing this method on simulated data (SLiM), showed that boundary effects in continuous and finite populations create similar asymmetries in the site frequency spectra (that ψ estimates) as range extensions, creating high false positive rates. We showed that boundary effect is inversely proportional to the overall levels of genetic structuring in the data and introduce ɛ=|ψ|/FST that accounts for this. We conclude that a true signature of range expansion requires that the overall strength of ψ is at least 50% of the mean pairwise FST in the data. We show that the majority of previous studies with significant signatures of range expansions likely are false positives.

Coll-Costa C, Dahms C, Kemppainen P, Alexandre CM, Ribeiro F, Zanella D, Zanella L, Merilä J, Momigliano P. (2024) Parallel evolution despite low genetic diversity in three-spined sticklebacksProc. R. Soc. B.29120232617. I helped to analyses the data using LDna.

Toli EA, Kemppainen P, Bounas A, Sotiropoulos K. (2024) Genetic insight into a polygenic trait using a novel genome-wide association approach in a wild amphibian population. Mol Ecol. 2024 May;33(9):e17344. Due to the small numbers of individuals as well as loci in this study, I introduced a method where not only the significant SNPs from a GWAS, but also those in high LD with them, were used to blast against a reference genome to increase the chances of identifying candidate regions.I was approached by the author of this study (after recommendations from a colleague) to help analyzing this data. 

Dahms C, Kemppainen P, Zanella LN, Zanella D, Carosi A, Merilä J & Momigliano P (2021). Cast Away in the Adriatic: Low Degree of Parallel Genetic Divergence in Three-Spined Sticklebacks. Mol Ecol. 2021 Nov 29. doi: 10.1111/mec.16295. I helped with the LDna analyses.

Guzmán NV, Kemppainen P, Monti D, Castillo E, Rodriguero MS, Sanchez-Restrepo AF, Cigliano MM & Confalonieri VA (2021). Chromosomal inversions as drivers of ecological adaptation and diversification in a grasshopper species complex. Mol Ecol. 2021 Dec 4. doi: 10.1111/mec.16305.  I was approached by the author after a reviewer on a previous version of this manuscript suggested to get in contact with me for using LDna on the data to study inversions polymorphism. Subsequently I helped with the LDna analyses.

Fang B*, Kemppainen P*, Momigliano P & Merilä J (2021). Population structure limits parallel evolution in sticklebacks. Molecular Biology and Evolution, 38(10), msab144. doi: 10.1093/ molbev/msab144. This is one of the few comparative studies that explicitly compares levels of genetic parallelism – and the geographic extent thereof – between two closely related, but widely contrasting species with respect to population demographics. For the first time LDna was used for complexity reduction prior to a genome scan (EMMAX treating ecotype as a binary trait) in population genomic data to significantly increase statistical power to detect genomic regions under selection. This was necessary since no single SNP analyses were able to detect any outlier regions, due to the small and complex data sets from a geographic region where parallelism is weak (Northern Fennoscandia). In contrast, LDna identified similar regions under selection as previous studies that had access to larger data sets from geographic regions where parallelism is much more prevalent (the Eastern Pacific). Includes simulations.

Nygaard M, Kemppainen P, Speed JDM, Elven R, Flatberg KI, Galten LP, … Bendiksby M. (2021). Combining population genomics and ecological niche modeling to assess taxon limits between Carex jemtlandica and C. lepidocarpa. Journal of Systematics and Evolution, 59(4), 627–641. doi: 10.1111/jse.12743. Here I assisted with general population genomic analyses.

Kemppainen P, Li Z, Rastas P, Löytynoja A. Fang B, Yang J, … Merilä J (2021). Genetic population structure constrains local adaptation in sticklebacks. Molecular Ecology. doi: 10.1111/mec.15808 This compared the genetic architectures of armor morphology in three and nine-spines sticklebacks using QTL-mapping (four-way single mapping) and simulations showing that parallelism is highly restricted when population structuring is strong. I also found emprical evidence of potential epistatic interactions responsible for armor morphology. Includes simulations.

Galindo J, Carvalho J, Sotelo G, Duvetorp M, Costa D, Kemppainen P, … Faria R (2021) Genetic and morphological divergence between Littorina fabalis ecotypes in Northern Europe. Journal of Evolutionary Biology, 34(1), 97–113. doi: 10.1111/jeb.13705 Kemppainen P*, Fang B, Momigliano P, Feng X, & Merilä J (2020). On the causes of geographically heterogeneous parallel evolution in sticklebacks. Nature Ecology & Evolution, 4(8), 1105–1115. doi: 10.1038/s41559-020-1222-6

Fang B*, Kemppainen P*, Momigliano P, Feng X, & Merilä J (2020). On the causes of geographically heterogeneous parallel evolution in sticklebacks. Nature Ecology & Evolution, 4(8), 1105–1115. doi: 10.1038/s41559-020-1222-6. The idea behind this study directly descends from the my seminal paper on LDna (Kemppainen et al. 2015, see below). In the seminal study we identified a large cluster of highly correlated SNPs (~2% of the data) that specifically separated Eastern Pacific freshwater individuals in three-spined sticklebacks from all remaining individuals that comprised marine individuals from the Eastern Pacific as well as both marine and freshwater individuals from Northern Fennoscandia. Despite that the Eastern Pacific three-spiked stickleback is one of the most iconic examples of genetic parallelism caused by local adaptation, we demonstrate that Northern Fennoscandia has much lower levels of parallelism, and suggest that the Eastern Pacific could be the exception, rather than the rule. We hypothesized that the high level of parallelism in the Eastern Pacific might instead be the result of secondary contact between allopatric marine and freshwater adapted ecotypes. Subsequent studies have found support for this hypothesis. Includes simulations.

Kemppainen P, Husby A. (2018a). Accounting for heteroscedasticity and censoring in chromosome partitioning analyses. Evolution Letters 0-0: 1–11. A significant  linear regression between the proportion phenotypic variance explained (PVE) by a chromosome and chromosome size was generally considered as evidence of polygenic genetic architecture. Here we show that since PVE is censored to a minimum value of 0 AND the estimates are heteroscedastic (variance increases with chromosome size) this approach is highly prone to false positives. We suggest two alternative approaches to account for this bias, one based on weighted regression, the other based on permutation. Includes simulations.

Kemppainen P & Husby A. (2018b). Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation, sample size, heritability and effect size distribution. Molecular Ecology Resources,18:4. This was published at the same time as the heteroscedasticity study (see above), and demonstrated that, besides polygenic genetic architecture, multitude other factors can also cause correlations between PVE and chromosome size. Includes simulations.

Lundregan S, Hagen IJ, Gohli J, Niskanen AK, Kemppainen P, … Jensen J (2018) Investigating the Genetic Architecture of Bill Morphology in a Free-Living House Sparrow Metapopulation Using a 200K SNP Array. Molecular Ecology, 27:17. This study used the method I developed in Kemppanen & Husby (2018a) to account for heteroscedasticiy in chromosome partitioning analyses.

Kemppainen P*, Li Z*, Rastas P, and Merilä M (2018). Linkage disequilibrium clustering-based approach for association mapping with tightly linked genomewide data. Molecular Ecology Resources, 18:4. This study is the first to introduce Linkage Disequilibrium network analyses as a means to reduce complexity in data in GWAS and QTL-mapping. This approach was developed further in both Kemppainen et al. (2021) and Fang et al. (2021) and is a natural extension of the seminal paper on LDna (Kemppainen et al. 2015)

Yousefi N, Hassel K, Flatberg KI, Kemppainen P, Trucchi E, Shaw AJ, Kyrkjeeide M, Szövényi P, Stenøien HK (2017). Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum Brid. American Journal of Botany 104:7

Silva CNS, McFarlane SE, Hagen IJ, Billing AM, Kvalnes T, Kemppainen P, et al. (2017). Insights into the genetic architecture of morphological and sexually selected traits in two passerine bird species. Heredity 119 197-205. This study used the method I developed in Kemppanen & Husby (2018a) to account for heteroscedasticity in chromosome partitioning analyses.

Kemppainen P, Rønning B, Kvalnes T et al. (2016) Controlling for P-value inflation in allele frequency change in experimental evolution and artificial selection experiments. Molecular Ecology Resources 17:4 770–782. Previously a permutation test were used to test for allele frequency differences before and after selection in artificial selection experiments. Here we demonstrate that this is equivalent to using a simple linear regression using survival as a binary trait which we know are highly prone to false positives in genome wide association studies (GWAS). We thus demonstrate that accounting for relatedness using existing GWAS methods also reduce false positives in testing for allele frequency changes before and after selection in artificial selection experiments.

Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, et al. (2015) Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 2015;347: 1258522. doi:10.1126/science.1258522 

Kemppainen P, Knight CG, Sarma DK, Hlaing T, Prakash A, Maung Maung YN, et al. (2015) Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. Molecular Ecology Resources. 15:5 1031–1045. This is the seminal paper on LDna that much of my subsequent work is based on. The initial idea was to use fluorescence in situ hybridization to study inversion polymorphism in a malaria mosquito. However, after understanding that inversions leave strong signatures of LD in population genomic data, I introduce a network analytical approach to study LD. In addition de novo detection of invasions polymorphism in population genomic data (even in the absence of a reference genome or linkage map), LDna has subsequently also been used for complexity reduction prior to GWAS, QTL-mapping and outlier analyses, as well as for de novo identification of sex determining regions (in the absence of sex identity information in the data).

Butlin RK, Saura M, Charrier G, Jackson B, André C, Caballero A, Coyne J A, Galindo J, Grahame JW, Hollander J, Kemppainen P, Martínez-Fernández M, Panova M, Quesada H, Johannesson K and Rolán-Alvarez E (2013). Parallel Evolution of Local Adaptation and Reproductive Isolation in the Face of Gene Flow. Evolution 68-4: 935–949

Surendran S N, Sarma D K, Jude P J, Kemppainen P, Kanthakumaran N, Gajapathy K et al. (2013). Molecular characterization and identification of members of the Anopheles subpictus complex in Sri Lanka. Malaria journal, 12(1), 304. doi:10.1186/1475-2875-12-304

Johannesson K, Panova M, Kemppainen P, André C, Rolán-Alvarez E and Butlin RK. Repeated evolution of reproductive isolation in a marine snail: unveiling mechanisms of speciation. Phil. Trans. R. Soc. B (2010) 365, 1735-1747.

Kemppainen P, Lindskog T, Butlin RK, Johannesson K (2010). Intron sequences of arginine kinase in an intertidal snail suggest an ecotype-specific selective sweep and a gene duplication. 106(5): 808–816

Kemppainen P, Panova M, Hollander J, Johannesson K (2009). Complete lack of mitochondrial divergence between two species of NE Atlantic marine intertidal gastropods. J. Evol. Biol. 22 2000–2011

Bierne N, Tanguy A, Faure M, Faure B, David E, Boutet I, Boon E, Quere N, Plouviez S, Kemppainen P, Jollivet D, Moraga D, Boudry P, David, P (2007). Mark–recapture cloning: a straightforward and cost effective cloning method for population genetics of single copy nuclear DNA sequences in diploids. Molecular Ecology Notes 7 (4): 562-566

Kemppainen P, Van Nes S, Ceder C, Johannesson K (2005). Refuge function of marine algae complicates selection in an intertidal snail. Oecologia 142: 402-411