Publication List | Merilä Lab

2024

Yi X, Wang D, Reid K, Feng X, Löytynoja A, Merilä J. Sex chromosome turnover in hybridizing stickleback lineages. Evolution Letters, in press.

Das S, Greenbaum E, Brecko J, Pauwels OSG, Ruane S, Pirro S, Merilä J. Resolving the Elapoidea (Serpentes) phylogeny: systematics of Psammodynastes and Buhoma with a description of a new Asian snake family. Scientific Reports, in press.

Merilä J, Lv L. Life history traits and climate change. In: Segoli M & Wanberg E (eds): Life History Evolution: Traits, Interactions, and Applications. Wiley.

Feng X, Merilä J, Löytynoja A. Secondary contact, introgressive hybridization and genome stabilization in sticklebacks. Molecular Biology and Evolution, in press. https://doi.org/10.1093/molbev/msae031

Fraimout A, Guillaume F, Li Z, Sillanpää M, Merilä J. Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing. Molecular Ecology, in press. https://doi.org/10.1111/mec.1729

Coll-Costa C, Dahms C, Kemppainen P, Alexandre CM, Ribeiro F, Zanella D, Zanella L, Merilä J, Momigliano P. Parallel evolution despite low genetic diversity in three-spined sticklebacks. Proceeding B: Biological Sciences, in press.

2023

Yi, X., Kemppainen, P., Reid, K., Chen, Y., Rastas, P., Fraimout, A., Merilä, J. Heterogeneous genomic architecture of skeletal armour traits in sticklebacks. (submitted) https://www.biorxiv.org/content/biorxiv/early/2023/05/31/2023.05.28.542672.full.pdf

Fraimout, A., Chen, Y., Reid, K. & Merilä, J. Divergent evolution of head morphology between marine and freshwater sticklebacks. (submitted) https://www.biorxiv.org/content/biorxiv/early/2023/07/15/2023.07.14.549115.full.pdf

Feng, X., Löytynoja, A. & Merilä, J. Estimating recent and historical effective population size of marine and freshwater sticklebacks. (submitted) https://www.biorxiv.org/content/10.1101/2023.05.22.541730v1.full.pdf

Wang, Y., Wang, Y., Cheng, X., Ding, Y., Wang, C., Merilä, J. & Guo, B. Prevalent introgression underlies convergent evolution in the diversification of Pungitius sticklebacks. Molecular Biology and Evolution 40(2):msad026.

Fraimout, A., Rastas, P., Lv, L. & Merilä, J. Inbreeding depression in an outbred stickleback population. Molecular Ecology 32:3440–3449.

Zhang, C., Reid, K., Sands, A. F., Fraimout, A., Schierup, M. H., & Merilä, J. (2023). De novo mutation rates in sticklebacks. Molecular Biology and Evolution, in press. bioRxiv, 2023-03. https://www.biorxiv.org/content/10.1101/2023.03.16.532904

Kivikoski M, Rastas P, Löytynoja A & J Merilä. Predicting recombination frequency from map distance. Heredity 130: 114–121. (Editor’s choice)

Kivikoski, M., Fraimout, A., Rastas, P., Löytynoja, A. & Merilä, J. Repeatability of crossover rate in wild sticklebacks. Biological Journal of the Linnean Society, 140: 74–84, https://doi.org/10.1093/biolinnean/blad032

Chen W, Chen H, Liao J, Tang M, Qin H; Zhao Z, Liu X, Wu Y, Jiang L, Zhang L, Fang B, Feng X, Zhang B, Reid K, Merilä J. Chromosome-level genome assembly of a high-altitude adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation. Frontiers in Zoology 20: https://doi.org/10.1186/s12983-022-00482-9

Das S, Greenbaum E, Shai M, Bauer AM, Burbrink FT, Raxworthy CJ, Weinell JL, Brown RM, Brecko J, Pauwels OSG, Rabibisoa N, Raselimanana AP & Merilä J. Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family. Molecular Phylogenetics and Evolution 180, 107700.

Chung MY, Merilä J, Kim Y, Mao K, López-Pujol J, Gi M & Chung MG. Neutral and adaptive genetic diversity in plants: an overview. Frontiers in Ecology & Evolution 11:1116814.

Liu C, Merilä J, Yang L & L Lv. Low-temperature nights delay the timing of breeding in a wild songbird. Journal of Avian Biology 2023:e03084.

Chung MY, Merilä J, Kim Y, Mao K, López-Pujol J, Chung MG. A review on QST–FST comparisons of seed plants: Insights for conservation. Ecology and Evolution, 13:e9926.

2022

Das S, Brecko J, Pauwels OSG, Merilä J. Cranial osteology of Hypoptophis (Aparallactinae: Atractaspididae: Caenophidia), with a discussion on the evolution of its fossorial adaptations. Journal of Morphology 283:510-538.

Dahms C, Kemppainen P, Zanella L, Zanella D, Carosi A, Merilä J, Momigliano P. Cast away in the Adriatic: Low degree of parallel genetic divergence in the Adriatic Sea sticklebacks. Molecular Ecology 31:1234-1253.

Cayela H, Lemaitre JF, Lena JP, Ronget V, …, Merilä J, ... Miller DAW. Sex-related differences in aging rate are associated with sex chromosome system in amphibians. Evolution 76:346-356.

Toli EA, Bounas A, Merilä J & K Sotiropoulos. Genetic diversity and detection of candidate loci associated with alternative morphotypes in a tailed amphibian. Biological Journal of the Linnean Society 137: 465-474

Fang B, Momigliano P, Kahilainen KK & J Merilä. Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation. Evolution 76: 1905-1913

Wang Y, Wang Y, Zaho Y, Kravchenko A, Merilä J, Guo B. Phylogenomics of Northeast Asian Pungitius sticklebacks. Diversity & Distributions 28: 2610-2621, https://doi.org/10.1111/ddi.13423

Fraimout A, Li Z, Sillanpää MJ & J Merilä. Age-dependent genetic architecture across ontogeny of body size in sticklebacks. Proceedings of the Royal Society B: Biological Sciences 289: 20220352

Merilä J. Human-induced evolution of salmon by means of unnatural selection. Proceedings of the National Academy of Sciences USA. 119: e22165226119

Feng X, Merilä J & A Löytynoja. Complex population history affects admixture analyses in nine‐spined sticklebacks. Molecular Ecology 31:5386-5401.

2021

Vatka E, Orell M, Rytkönen S, Merilä J. Effects of warming climate on evolutionary potential of reproductive timing in boreal passerines. Journal of Animal Ecology, 90:367-375.

Kemppainen P, Li Z, Yang J, Rastas P, Löytynoja A, Shikano T, Guo B, J Merilä. Genetic population structure constrains local adaptation and probability of parallel evolution in sticklebacks. Molecular Ecology 30: 1946-1961

Eriksson BK, C Yanos, S Bourlat, S Donadi, MC Fontaine, JP Hansen, E Jakubavičiūtė, K Kiragosyan, ME Maan, J Merilä, ÅN Austin, J Olsson, K Reiss, G Sundblad, U Bergström, JS Eklöf. The rise of the three-spined stickleback – eco-evolutionary consequences of a mesopredator release. Ecosphere 12:e03561

Momigliano P, Florin A-B & J Merilä. Biases in demographic modelling affect our understanding of the process of speciation. Molecular Biology and Evolution 38:2967-2985.

Kivikoski M, Rastas P, Löytynoja A & J. Merilä. Automated improvement of stickleback reference genome assemblies with Lep-Anchor software. Molecular Ecology Resources 21:2166-2176.

Fang B, Kemppainen P, Momigliano P, Merilä J. Population structure limits parallel evolution in sticklebacks. Molecular Biology and Evolution 38: 4205-4221.

Hirase S, Yamasaki YY, Sekino M, Nishisako M, Ikeda M, Hara M, Merilä J, K Kikuchi K. Genomic evidence for speciation with gene flow in broadcast spawning marine invertebrates. Molecular Biology and Evolution 38:4683-4699.

Long J, Liao W, Merilä J. Genomic evidence for adaptive differentiation among Microhyla fissipes populations and implications for conservation. Diversity & Distributions 28: 2665-2680, https://doi.org/10.1111/ddi.13433C

Cayela H, Lemaître J-F, Muths E, Mccaffery R, Fretey T, Schmidt BR, Grossenbacher K, Lenzi O, Hossack B, Lambert B, Elmberg J, Merilä J, Gippet J, Gaillard J-M, Pilliod DS. Thermal conditions predict intraspecific variation in senescence rate in frogs and toads. Proceedings of the National Academy of Sciences USA, 118 (49) e2112235118

2020

Wang Y, Zhao Y, Wang Y, Li Z, Guo B, Merilä J. Population transcriptomics reveals weak parallel genetic basis in repeated marine-freshwater divergence in nine-spined sticklebacks. Molecular Ecology 29:1642-1656.

Peng, L.Q., Tang, M., Liao, J.H., Liang, S.Y., Gan, L.T., Hua, K.J., Chen, Y., Li, H., Chen, W. & Merilä, J., 2020. Effects of temperature on growth and development of amphibian larvae across an altitudinal gradient in the Tibetan Plateau. Animal Biology 70:239-250.

Tibblin P, Hall M, Svensson A, Merilä J, Forsman A. Comparisons of background matching colour change in sticklebacks (G. aculeatus and P. pungitius) inform about sources of variation in phenotypic flexibility. Behavioural Ecology 31:950-959.

Fang B, Kemppainen P, Momigliano P, Merilä J. Heterogenous patterns of parallel evolution in sticklebacks. Nature Ecology & Evolution 4:1105-1115. bioRxiv 826412; doi: https://doi.org/10.1101/826412

Wei S, Li J, Li Z, Momigliano P, Fu C, Wu H, & J Merilä. The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in widespread amphibian Hyla annectans (Anura: Hylidae). Molecular Ecology 29:3667-3683.

De-La-Cruz IM, J Merilä, CM Flores-Ortiz, PL Valverde, J Núñez-Farfán. Genomic and chemical evidence for local adaptation in resistance to different herbivores in Datura stramonium. Evolution 74: 2629-2643.

Fang B, P Momigliano, M Matschuer, Merilä J. Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent. Molecular Phylogenetics and Evolution 142:106646

Cayuela H, Valenzuela-Sanchez A, Teulier L, Martínez-Solano I, Léna J-P, Merilä J, Muths E, Shine R, Quay L, Denoël M, Clobert J, Schmidt BR. Determinants and consequences of dispersal in vertebrates with complex life cycles: a review of pond-breeding amphibians. The Quarterly Review of Biology 95:1-36.

2019

Momigliano P, Jokinen H, Calboli F, Aro E, J Merilä. Cryptic temporal changes in stock composition explain the decline of a flounder (Platichthys spp.) assemblage. Evolutionary Applications 12:549-559.

Natri H.M, J. Merilä & T. Shikano. The evolution of sex determination associated with chromosomal inversion. Nature Communications 10: 145.

Morozov S, SJR McCairns & J. Merilä. FishResp: an r-package for filtering and analyzing raw data in aquatic respirometry. Conservation Physiology 7:coz003

Liang ZQ, Chen WT, Wang DQ, Zhang SH, Wang CR, He SP, Wu YA, He P, Xie J, Li CW, Merilä J. Phylogeographic patterns and conservation implications of the endangered Chinese giant salamander. Ecology and Evolution 7:3879-3890.

Sinai I, O Segev, G Weil, T Oron, J Merilä, AR Templeton, L Blaustein & L Blank. Do different types of peripheries and landscape characteristics influence genetic structure at the edge of species range? The fire salamander, Salamandra infraimmaculata in Northern Israel. Conservation Genetics 20:875-889.

Buechel SD, Noreikiene K, DeFaveri J, Toli E, Kolm N, Merilä J. Variation in sexual brain size dimorphism over the breeding cycle in the three-spined stickleback. Journal of Experimental Biology 22:194464

Radchuk V, T Reed, C Teplitsky, M van de Pol, A Charmantier, C Hassall, P Adamík, F Adriaensen, M Ahola, P Arcese, JM Avilés, J Balbontin, W Blanckenhorn, A Borras, S Burthe, J Clobert, N Dehnhard, F de Lope, AA Dhondt, NJ Dingemanse, H Doi, T Eeva, J Fickel, I Filella, F Fossøy, AE Goodenough, SJG Hall, B Hansson, M Harris, D Hasselquist, T Hickler, J Joshi, H Kharouba, J Gabriel Martínez, J-B Mihoub, JA Mills, M Molina Morales, A Moksnes, A Ozgul, D Parejo, P Pilard, M Poisbleau, F Rousset, M-O Rödel, D Scott, JC Senar, Constanti Stefanescu, BG Stokke, K Tamotsu, M Tarka, C Tarwater, K Thonicke, J Thorley, A Wilting, P Tryjanowski, J Merilä, B Sheldon, AP Møller, E Matthysen, F Janzen, S Dobson, ME Visser, SR Beissinger, A Courtiol, S Kramer-Schadt. Adaptive responses of animals to climate change: not universal, likely insufficient. Nature Communications 10:3109.

Jiang L, Pengb L, Youa Z, Zhanga M, Westc A, Ruana Q, Chen W & J Merilä. Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): sequence, structure and phylogenetic analyses. Ecology & Evolution 9:8813-8823.

Yurtseva A, Noreikiene K, Lajus D, Li Z, Alapassi T, IvanovaT, Ivanov M, Golovin P, Vesala & J Merilä. Aging three-spined sticklebacks (Gasterosteus aculeatus): comparison of estimates from three structures. Journal of Fish Biology 95:802-811.

Jokinen H, Momigliano P & J Merilä. From ecology to genetics and back: the tale of two flounder species in the Baltic Sea. ICES Journal of Marine Sciences 76:2267-2275.

Guo B, Fang B, Shikano T, Momigliano P, Wang C, Kravchenko A & J Merilä. A phylogenomic perspective to diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius. Molecular Ecology 28:4046-4064.

Li Z, Löytynoja A, Fraimout, Merilä J. Effects of marker type and filtering criteria on QST-FST comparisons. Royal Society Open Science 6: 190666.

Varadharajan S, P Rastas, A Löytynoja, M Matschiner, FCF Calboli, B Guo, AJ Nederbragt, KS Jakobsen, J Merilä. Genome sequencing of the nine-spined stickleback (Pungitius pungitius) provides insights into chromosome evolution. Genome Biology and Evolution 11:3291-3308.

2018

Gienapp P & J. Merilä. Evolutionary responses to climate change. Encyclopedia of the Anthropocene (DellaSala & Goldstein, eds). Reference Module in Earth Systems and Environmental Sciences, Elsevier. 2:51-59.

Noreikiene K, Kuparinen A & J Merilä. Age at maturation has sex and temperature specific effects on fish telomere length. Oecologia 184: 767-777.

Li Z, P Kemppainen, P Rastas, J Merilä. Linkage disequilibrium clustering‐based approach for association mapping with tightly linked genome‐wide data. Molecular Ecology Resources 18: 809-824.

Momigliano P, G.P.J. Denys, H Jokinen & J Merilä. Platichthys solemdali sp. Nov (Actinopterygii, Pleuronectiformes): A new flounder species from the Baltic Sea. Frontiers in Marine Science 5: 225.

Knytl M, L Kalous, K Rylková, L Choleva, J Merilä & P Ráb. Morphologically indistinguishable hybrid Carassius female with 156 chromosomes: A threat for the threatened crucian carp, C. carassius, L. PLoS One 13: e0190924

Bolotovskiy A, MA Levina, J DeFaveri, J Merilä & BA Levin. Heterochronic development of lateral plates in the three-spined stickleback induced by thyroid hormone level alterations. PLoS One 13: e0194040

Morozov S, Leinonen T, Merilä J & SJR McCairns. Morphology-physiology-performance and adaptation to a new environment: lessons from freshwater stickleback morphs. Ecology & Evolution 8: 1286-1299.

Fang B, J Merilä, F Ribero, C Alexandre & P. Momigliano Worldwide phylogeny of three-spined sticklebacks. Molecular Phylogeny and Evolution 127:613-625.

Jin L, P Yu, J Yang, J Merilä & W.B. Liao. Modulation of gene expression in liver of hibernating Asiatic toads (Bufo gargarizans). International Journal of Molecular Sciences 18:2363.

2017

Rodrigues, M., A.R. Bos, P. Schemri, R.F. Lima, P. Lymberakis, L. Parpal, M. Cento, S. Ruette, S.O. Ozkutrt, M. Santos-Reis, J. Merilä & C. Fernandes. Origin and introduction history of the least weasel (Mustela nivalis) on Mediterranean and Atlantic islands inferred from genetic data. Biological Invasions 19:399-421.

Merilä J, Eloranta A. Cannibalism facilitates gigantism in a nine-spined stickleback (Pungitius pungitius) population. Ecology of Freshwater Fishes 26:686-694.

Pritchard VL, Viitaniemi HM, McCairns SRJ, Merilä J, Nikinmaa M, Craig R. Primmer CR, Leder EH. Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus. G3, 7:165-178.

Li Z, Guo B, Yang J, Herczeg G, Gonda A, Balazs G, Shikano T, Calboli F, & Merilä J. Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach. Molecular Ecology 26:1557-1575.

Wang C, T Shikano, H Persat & J. Merilä. Phylogeography and historical introgression in smoothtail nine-spined sticklebacks (Pungitius laevis). Biological Journal of Linnean Society 121:340-354.

Toli E, Noreikiene K, DeFaveri J & J Merilä. Environmental enrichment, sexual dimorphism and brain size in sticklebacks. Ecology & Evolution 7:1691-1698.

Bancila R.C., D. Cogălniceanu, R. Plăiaşu, D. Roşioru & J. Merilä. Small-scale spatial and temporal variation of life history traits of common frogs (Rana temporaria) in sub-Arctic Finland. Polar Biology 40:1581-1592.

Hasan MM, DeFaveri J, Kuure S, Dash SN, Lehtonen S, Merilä J & RJS McCairns. Kidney morphology and candidate gene expression shows plasticity in sticklebacks adapted to divergent osmotic environments. Journal of Experimental Biology 220:2175-2186.

Momigliano P, Jokinen H, Fraimont A, Florin A-B, Norkko A & J Merilä. Extraordinarily rapid speciation in a marine fish. Proceedings of National Academy of Sciences USA, 114:6074-6079.

Sirén J, Ovaskainen O, Merilä J. Structure and stability of genetic variance-covariance matrices: A Bayesian sparse factor analysis of transcriptional variation in the three-spined stickleback. Molecular Ecology 26:5099-5113.

2016

Rastas P, Calboli F, Guo B, Shikano T, Merilä J. Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example. Genome Biology & Evolution 8:78-93.

Mills JA, Teplitsky C, Arroyo B, Charmantier A, Becker PH, Birkhead TR, Bize P, Blumstein DT, Bonenfant C, Boutin S, Bushuev A, Cam E, Cockburn A, Côté SD, Coulson JC, Daunt F, Dingemanse NJ, Doligez B, Drummond H, Espie RHM, Festa-Bianchet M, Frentiu F, Fitzpatrick JW, Furness RW, Gauthier G, Grant PR, Griesser M, Gustafsson L, Hansson B, Harris MP, Jiguet F, Kjellander P, Korpimäki E, Krebs CJ, Lens L, Linnell JDC, Low M, McAdam A, Margalida A, Merilä J, Møller AP, Nakagawa S, Nilsson J-Å, Nisbet ICT, van Noordwijk AJ, Oro D, Pärt T, Pelletier F, Potti J, Pujol B, Réale D, Rockwell RF, Ropert-Coudert Y, Roulin A, Thébaud C, Sedinger JS, Swenson E, Visser ME, Wanless S, Westneat DF, Wilson AJ, Zedrosser A. Solutions for archiving data in long-term studies - a reply to Whitlock et al. Trends in Ecology and Evolution31:85-87.

Guo B, Toli E & J Merilä. Complete mitochondrial genome of the nine-spined stickleback Pungitius pungitius (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA B: Resources 1:72-73.

Guo B, Shikano T, Wang C & J Merilä. Complete mitochondrial genome of the smooth-tailed nine-spined stickleback Pungitius laevis (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA B: Resources 1:70-71.

Guo B, Shikano T, Vukic J, Sanda R, Merilä J. Complete mitochondrial genome of the Ukrainian nine-spined stickleback Pungitius platygaster (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA B: Resources 1:68-69.

Shikano T, Guo B, Vukic J, Sanda R, Merilä J. Complete mitochondrial genome of the Greek nine-spined stickleback Pungitius hellenicus (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA B: Resources 1:66-67.

Shikano T, Guo B, Merilä J. Complete mitochondrial genome of the Shakhalin nine-spined stickleback Pungitius tymensis (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA B: Resources 1:74-75.

Howlader MH, Nair A, Merilä J. A new species of frog (Anura: Dicroglossidae) discovered from the densely populated mega city of Dhaka. PLoS One 11:e0149597.

Ab Ghani IN, Herczeg G, Merilä J. Effects of perceived predation risk and social environment on development of the three-spined stickleback morphology. Biological Journal of Linnean Society 118:520-535.

Merilä, J. & A.A. Hoffmann. Evolutionary impacts of climate change. Oxford Encyclopedia of Environmental Sciences. DOI: 10.1093/acrefore/9780199389414.013.136

Hoffmann AA, Merilä J, Kristensen T. Heritability and evolvability of fitness and non-fitness traits: lessons from livestock. Evolution 70:1770-1779.

Herczeg G, Ab Ghani IN, Merilä J. Plasticity of aggression: the effects of current and past predation risk, social environment and sex. Behavioural Ecology and Sociobiology 70: 179-187.

Rodrigues M., Bos, A.R., Hoath, R., P. Schembri, P. Lymberakis, M. Cento, L. Parpal, W. Ghawar, S. O. Ozkurt, M. Santos-Riaz, J. Merilä & C. Fernandes. Taxonomic status and origin of the Egyptian weasel (Mustela subpalmata) inferred from mitochondrial DNA. Genetica144:191-202.

Rodrigues N, Vuille Y, Brelsford A, Merilä J & N Perrin. The genetic contribution to sex determination and number of sex chromosomes vary among populations of common frogs (Rana temporaria). Heredity 117:25-32.

Von Hippel F, Trammell EM, Merilä J, Sanders MB, Schwarz T, Postlethwait JH, Titus TA, Buck CL & I Katsiaddaki. The ninespine stickleback as a model organism in artic ecotoxicology. Evolutionary Ecology Research 17: 487-504.

Guo B, Li Z & J Merilä. Population genomic evidence for adaptive differentiation in Baltic Sea herring. Molecular Ecology 25:2833-2852.

Calboli FC, Byström P, Merilä J A test for within lake niche differentiation in the nine-spined sticklebacks (Pungitius pungitius). Ecology & Evolution 14: 4753-4760.

Yang J., B. Guo, T. Shikano, X. Liu & J. Merilä. Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Scientific Reports 6:26632.

Guo, B., W.B. Liao & J. Merilä. Genome-wide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi. Molecular Ecology 25:3884-3900.

Toli, E., F. Calboli, T. Shikano & J. Merilä. A universal and reliable assay for molecular sex identification of three-spined sticklebacks (Gasterosteus aculeatus). Molecular Ecology Resources 16:1389-1400.

2015

Liao WB, Liu CW, Merilä J. Andrew meets Rensch: Sexual size dimorphism and the inverse of Rensch’s rule in Andrew’s toad (Bufo andrewsi). Oecologia 177:389-399.

Ab Ghani IN, Merilä J. Population divergence in compensatory growth responses and their costs in sticklebacks. Ecology & Evolution 5:7-23.

Howlader MH, Nair A, Gopalan SV, Merilä J. A new species of Euphlyctis (Anura: Dicroglossidae) from Barisal, Bangladesh. PLoS One 10: e0116666.

Leder E, McCairns SRJ, Leinonen T, Cano JM, Nikinmaa M, Primmer CR, Merilä J. The evolution and adaptive potential of transcriptional variation - signatures of selection and widespread heritability. Molecular Biology and Evolution 32:674-689.

Zanella L, DeFaveri J, Zanella D, Merilä J, Šanda R, Mrakovčić M. Morphological differentiation among Adriatic threespine stickleback populations: driven by predation? Biolological Journal of Linnean Society 115:219-240.

Howlader MH, Nair A, Gopalan SV, Merilä J. A new species of Microhyla (Anura: Microhylidae) from Nilphamari, Bangladesh. PLoS One 10:e0119825.

DeFaveri J, Merilä J. Temporal stability of genetic diversity and differentiation in the three-spined stickleback (Gasterosteus aculeatus). PLoS One 10: e0123891.

Guo, B., J. DeFaveri, G. Sotelo, A. Nair & J. Merilä. Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biology 13:19.

Merilä J. Factors influencing three-spined stickleback Gasterosteus aculeatus (Linneaus 1758) catch per unit effort. Journal of Applied Ichtyology 31:905-908.

Merilä J. Baiting improves CPUE in nine-spined stickleback (Pungitius pungitius) minnow trap fishery. Ecology & Evolution 17:3737-3742.

Norekeine, K., G. Herczeg, A. Gonda, G. Balazs, A. Husby & J. Merilä. Quantitative genetic analysis of brain size variation in sticklebacks: support for mosaic model of brain evolution. Proceedings of the Royal Society B: Biological Sciences 282: 20151008

Merilä J. Perplexing effects of phenotypic plasticity. Nature 525:326-327.

Mills JA, C Teplitsky, B Arroyo Lopez, A Charmantier, PH Becker, TR Birkhead, Pi Bize, DT Blumstein, C Bonenfant, S Boutin, A Bushuev, E Cam, A Cockburn, S Côté, F Daunt, N Dingemanse, B Doligez, H Drummond, RHM Espie, M Festa-Bianchet, F Frentiu, JW Fitzpatrick, RW Furness, D Garant, G Gauthier, Peter R. Grant, M Griesser, L Gustafsson, B Hansson, MP Harris, F Jiguet, P Kjellander, E Korpimäki, CJ Krebs, L Lens, JDC Linnell, M Low, A McAdam, A Margalida, J Merilä, AP Møller, S Nakagawa, J-Å Nilsson, ICT Nisbet, A van Noordwijk, D Oro, T Pärt, F Pelletier, J Potti, B Pujol, D Réale, RF Rockwell, Y Ropert-Coudert, A Roulin, JS Sedinger, JE Swenson, C Thébaud, ME Visser, S Wanless, DF Westneat, A Wilson & A Zedrosser. Archiving primary data: solutions for long-term studies. Trends in Ecology & Evolution 30:581-589.

Eloranta A, Knudsen R, Amundsen P-A, Merilä J. Consistent isotopic differences in Schistocephalus spp. parasites and their stickleback hosts. Diseases of Aquatic Organisms 115:121-128.

Shikano T, Marjamäki P, Järvinen A, Kahilainen K, Merilä J. Genetic variability and structuring of Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia. PLoS One 10: e0140344.

Liao WB, Lou SL, Zeng Y, Merilä J. Evolution of anuran brains: disentangling ecological and phylogenetic sources of variation. Journal of Evolutionary Biology 28:1986-1896.

Wang C, Shikano T, Persat H, Merilä J. Mitochondrial phylogeography and cryptic divergence in stickleback genus Pungitius. Journal of Biogeography 42: 2334-2348.

Budria A, DeFaveri J, Merilä J. Comparison of catch per unit effort among four minnow trap models in the three-spined stickleback (Gasterosteus aculeatus) fishery. Scientific Reports 5:18548.

Herczeg G, Gonda A, Balazs G, Norekeine K, Merilä J. Experimental demonstration of plasticity in adult brain. Frontiers in Zoology 12:38.

2014

Merilä J, Hendry AP. Climate change, adaptation, and phenotypic plasticity: the problem and the evidence. Evolutionary Applications 7:1-14.

Kuparinen A, Vinni M, Teacher A, Kähkönen K, Merilä J. Mechanism of hybridization between bream Ambramis brama and roach Rutilus rutilus in their native species range. Journal of Fish Biology 84: 237-242

Merilä J. Lakes and ponds as model systems to study parallel evolution. Journal of Limnology 73(s1): 29-41.

Karhunen M, Ovaskainen O, Herczeg G, Merilä J. Bringing habitat information into statistical tests of local adaptation in quantitative traits: a case study of nine-spined sticklebacks. Evolution 68:559-568.

DeFaveri J, Merilä J. Local adaptation to salinity in sticklebacks? Journal of Evolutionary Biology 27:290-302.

Blank L, Luoto M, Merilä J. Potential effects of climate change on the distribution of the common frog Rana temporaria at it’s northern range margin. Israel Journal of Ecology 59:130-140.

Teplitsky C, Robinson, Merilä J. Evolutionary potential and constraints in wild populations. In. Charmentier et al. (eds). Evolutionary Genetics in the Wild, Oxford Univ. Press. Pp. 190-208.

Liu J, Li M-H, Shikano T, T. Leinonen T, Cano JM, Merilä J. Identification of major and minor QTL for ecologically important morphological traits in three-spined sticklebacks (Gasterosteus aculeatus). G3: Genes, Genomes, Genetics 4:595-608.

Kershenbaum A, Blank L, Sinai I, Merilä J, Blaustein L, Templeton A. Landscape influences on dispersal behaviour: A theoretical model and empirical test using the fire salamander, Salamandra infraimmaculata. Oecologia, 175:509-520.

DeFaveri J, Shikano T, Merilä J. Geographic variation in age structure of nine-spined stickleback populations. PLoS One 9:e102660.

Gienapp P, Merilä J. Disentangling plastic and genetic changes in body mass of Siberian jays. Journal of Evolutionary Biology 27:1849-1858.

Herczeg G, Välimäki K., Gonda A, Merilä J. Evidence for sex-specific selection in brain: a case study of the nine-spined stickleback. Journal of Evolutionary Biology 27:1604-1612.

Ab Ghani IN, Merilä J. Cross-generational costs of compensatory growth responses sticklebacks. Oikos 123:1489-1498.

Rodrigues N, Patrelle C, Merilä J, Perrin N. Geographic variation in sex-chromosome differentiation in the common frog (Rana temporaria). Molecular Ecology 23:3409-3418.

Yang J, Li M-H, Shikano T, Merilä J. Genome-wide linkage disequilibrium in Fennoscandian sticklebacks. G3 4:1919-1929.

2013

Bruneaux M., S.E. Johnston, G. Herczeg, J. Merilä, C.R. Primmer & A. Vasemägi. Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified RAD tag approach. Molecular Ecology 22: 565-582.

Jaatinen, K., M. Öst, P. Gienapp & J. Merilä. Facultative sex allocation and sex-specific offspring survival in Barrow’s goldeneyes. Ethology 119: 146-155.

Aikio S., G. Herczeg, A. Kuparinen & J. Merilä. Optimal growth of nine-spined sticklebacks at different mortalities. Journal of Fish Biology 82: 318-331.

Leinonen, T., S. McCairns, R. O’Hara & J. Merilä. QST-FST comparisons: evolutionary and ecological insights from genomic heterogeneity. Nature Reviews in Genetics 14: 179-190.

Wang C., X. Hu, X. Xie, P. Liu, J. Merilä, Q. Zhang & M-H. Li. Isolation and characterization of 113 polymorphic microsatellite loci for the Tibetan frog (Nanorana parkeri) using next generation sequencing. Conservation Genetics Resources. doi:10.1007/s12686-013-9932-6

Corander, J., L. Cheng, K. Majander & J. Merilä. High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Molecular Ecology 22: 2931-2940.

Loehr J., G. Herczeg, T. Leinonen, A. Gonda, S. Van Dongen & J Merilä. Asymmetry in threespine stickleback lateral plates. Journal of Zoology 289: 279-284.

Ab Ghani, I.N, G. Herczeg, T. Leinonen & J. Merilä. Evidence for genetic differentiation in timing of maturation among nine-spined stickleback populations. Journal of Evolutionary Biology 26: 775-782.

Herczeg G., I. N. Ab Ghani & J. Merilä. Evolution of stickleback feeding activity: genetics of population divergence at different ontogenetic stages. Journal of Evolutionary Biology 26: 955-962.

Teacher A, P. Jonsson C., André, & J. Merilä. Oceanographic connectivity and environmental variation influence the genetic structure of Baltic Sea herring. Evolutionary Applications 6: 549-567.

DeFaveri, J., H. Viitanen, E. Leder & J. Merilä. Characterizing genic and non-genic molecular markers: comparison of microsatellites and SNPs. Molecular Ecology Resources 13: 377-392.

Nikinmaa M., R.J.S. McCairns, M.W. Nikinmaa, K.A. Vuori, M. Kanerva, T. Leinonen, C.R. Primmer, J. Merilä & E. Leder. Transcription and redox enzyme activities: comparison of equilibrium and nonequilibrium levels in the three-spined stickleback. Proceedings of the Royal Society, B 280:20122974.

Merilä J. Nine-spined stickleback (Pungitius pungitius): an emerging model for evolutionary biology research. Annals of New York Academy of Sciences (Year in Evolutionary Biology) 1289: 18-35.

Natri, H., T. Shikano & J. Merilä. Progressive recombination suppression and differentiation in recently evolved neo-sex chromosomes of threespine sticklebacks, Gasterosteus aculeatus. Molecular Biology and Evolution 30: 1131-1144.

Karhunen, M., J. Merilä, T. Leinonen, J.M. Cano Arias & O. Ovaskainen. driftsel: an R package for detecting signals of natural selection in quantitative traits. Molecular Ecology Resources 13: 746-754.

Merilä J., H.-K. Lakka & A. Eloranta. Large differenrences in catch per unit of effort between two minnow trap types. BMC Research Notes 6:151.

Blank, L., I. Sinai, S. Bar-David, N. Peleg, O. Segev, A. Sadeh, N.M. Kopelman, A.R. Templeton, J. Merilä & L. Blaustein. Genetic population structure of the endangered fire salamander (Salamandra infraimmaculata) at the southernmost extreme of its distribution. Animal Conservation 16: 412-421.

DeFaveri J., P. Sundström & J. Merilä. Heterogeneous genomic differentiation in marine threespine sticklebacks: adaptation along an environmental gradient. Evolution 67:2530-2546.

DeFaveri J. & J. Merilä. Evidence for adaptive phenotypic differentiation in the Baltic Sea sticklebacks. Journal of Evolutionary Biology 26: 1700-1715.

Gonda A., G. Herczeg & J. Merilä. B. Intraspecific brain size variation in the wild: a review. Ecology & Evolution 3: 2751-2764.

DeFaveri J., T. Shikano, J. Shimada, K. Kähkönen & J. Merilä. High degree of genetic differentiation in marine threespine sticklebacks (Gasterosteus aculeatus) - A targeted genome scan approach. Molecular Ecology 22: 4811-4828.

Shikano M, V.N. Laine, G. Herczeg, J. Vilkki & J. Merilä. Genetic architecture of parallel pelvic reduction in ninespine sticklebacks. G3: Genes, Genomes, Genetics 3: 1833-1842.

Saarikivi, J., T. Knopp, A. Granroth & J. Merilä. The role of golf courses in maintaining genetic connectivity between common frog (Rana temporia) populations in urban surroundings. Conservation Genetics 14: 1057-1064.

Savolainen, O., M. Lascoux & J. Merilä. Ecological genomics of local adaptation. Nature Reviews Genetics 14: 807-820.

Wennerström, L., L. Laikre, N. Ryman, F.M. Utter, N.I. Ab Ghani, C. Andre, J. DeFaveri, L. Kautsky, J. Merilä, N. Mikhailova, D. Johansson, R. Pereyra, A. Teacher, R. Wenne, A. Vasemagi, M. Zbavicka, K. Johannesson & C.R. Primmer. Genetic biodiversity in the Baltic Sea: species-specific patterns challenge management. Biodiversity & Conservation 22: 3045-3065.

Laine V., Shikano T., Herczeg G., Vilkki J. & Merilä J. Quantitative trait loci for growth and body size in the nine-spined stickleback Pungitius pungitius L. Molecular Ecology 22: 5861-5876.

DeFaveri J & J Merilä. Variation in age and size of Fennoscandian three-spined stickelbacks (Gasterosteus aculeatus). PLoS One 8: e80866

Laine V, T. Shikano, G. Herczeg, J. Vilkki & J. Merilä. QTL analysis of behavioral traits in nine-spined sticklebacks (Pungitius pungitius). Behavior Genetics 44:77-88.

Guo B, FJJ Chain, E Bornberg-Bauer, EH Leder & J Merilä. Genomic divergence between nine- and three-spined sticklebacks. BMC Genomics 14:756.

Ab Ghani, I.N., A. Kuparinen, T. Leinonen & J. Merilä. Population and sex-specific growth rate divergence between two nine-spined stickleback (Pungitius pungitius L) populations. Evolutionary Ecology Research 15: 793-808.