​2024

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Wang X, Reid K, Wang D, Wang H, Dudgeon D, Merilä J. Chromosome-level haplotype-resolved genome of the tropical loach (Oronectes playtycephalus). Scientific Data, in press.

 

Yi, X., Kemppainen, P., Reid, K., Chen, Y., Rastas, P., Fraimout, A., & Merilä, J. Heterogeneous genomic architecture of skeletal armour traits in sticklebacks. Journal of Evolutionary Biology, 37, 9, 995–1008. bioRxiv, 2023-05.

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Yi X, Merilä J, Kemppainen P. SLRfinder: a method to detect candidate sex-linked regions with linkage disequilibrium clustering. Molecular Ecology Resources 24:e13985

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Yi X, Kemppainen P, Reid K, Chen Y, Rastas P, Fraimout A, Merilä, J. Heterogeneous genomic architecture of skeletal armour traits in sticklebacks. Journal of Evolutionary Biology 37:995-1008.

 

Wang X, Reid K, Dudgeon D, Merilä J. Ecological genetics of isolated loach populations indicate compromised adaptive potential. Heredity 133: 88–98.

 

Yi X, Wang D, Reid K, Feng X, Löytynoja A, Merilä J. Sex chromosome turnover in hybridizing stickleback lineages. Evolution Letters 8:658-668.

 

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 291: 20232617

 

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 33: e17299. https://doi.org/10.1111/mec.17299

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Feng X, Merilä J ,  Löytynoja A. Secondary contact, introgressive hybridization and genome stabilization in sticklebacks. Molecular Biology and Evolution 41(2):msae031

 

2023

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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.

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Zhang C, Reid K, Sands A, Fraimout A, Schierup M, Merilä J . De novo Mutation rates in sticklebacks

Molecular Biology and Evolution 40 (9), msad192

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Fraimout A, Rastas P, L Lv, Merilä J. Inbreeding depression in an outbred stickleback population

Molecular Ecology 32: 3440-9.

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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

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

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Chung MY,  Merilä J,  Li J,  Mao K,  López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Frontiers in Ecology and Evolution 11, 1116814

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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.

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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 R, 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 (1), 1-12

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Kivikoski M, Rastas P , Löytynoja A , Merilä J . Predicting recombination frequency from map distance. Heredity 130, 114–121

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2022

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Feng X,  Merilä J, Löytynoja A. Complex population history affects admixture analyses in nine‐spined sticklebacks. Molecular Ecology 31 (20), 5386-5401.

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Fraimout A,  Li Z,  Sillanpää MJ,  Merilä J. Age-dependent genetic architecture across ontogeny of body size in sticklebacks. Proceedings of the Royal Society B 289 (1975), 20220352

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Wang Y, Wang Y, Zhao Y,  Kravchenko A,  Merilä J, Guo B. Phylogenomics of Northeast Asian Pungitius sticklebacks. Diversity and Distributions 28 (12), 2610-2621

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Fang B,  Momigliano P,  Kahilainen KK,  Merilä J. Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation. Evolution 76 (8), 1905-1913

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Toli EA,  Bounas A,  Merilä J, Sotiropoulos K. Genetic diversity and detection of candidate loci associated with alternative morphotypes in a tailed amphibian. Biological Journal of the Linnean Society 137 (3), 465-474

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Dahms C,  Kemppainen P,  Zanella L,  Zanella D, Carosi A,   Merilä J,   Momigliano P. Cast away in the Adriatic: Low degree of parallel genetic differentiation in three‐spined sticklebacks. Molecular Ecology 31 (4), 1234-1253

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2021

 

Fang, B., Kemppainen, P., Momigliano, P., & Merilä, J. (2021). Population structure limits parallel evolution in sticklebacks. Molecular biology and evolution, 38(10), 4205-4221.

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Momigliano, P., Florin, A. B., & Merilä, J. (2021). Biases in demographic modeling affect our understanding of recent divergence. Molecular Biology and Evolution, 38(7), 2967-2985.

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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, 30(9), 1946-1961.

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Feng, X., Merilä, J., & Löytynoja, A. (2021). Detailed phylogeographic analysis of sticklebacks exposes challenges in genetic studies of admixed populations. bioRxiv.

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Fraimout et al. 2021. Age-dependent genetic architecture underlines similar heritability of body size in sticklebacks. bioRxiv

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Fraimout et al. 2021. Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing among full-sibs. bioRxiv. 

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Long,  J ., Liao W., Merilä J. Genomic evidence for adaptive differentiation among Microhyla fissipes populations: Implications for conservation. Diversity and Distributions 28:2665-2680.

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

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

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