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Publications: Publications



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

Yi X, Kemppainen P, Reid K, Chen Y, Rastas P, Fraimout AMerilä, J. Heterogeneous genomic architecture of skeletal armour traits in sticklebacks. Journal of Evolutionary Biology, in press.


Wang XReid K, Dudgeon D, Merilä J. Ecological genetics of isolated loach populations indicate compromised adaptive potential. Heredity in press.


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


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.


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.

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



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.

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

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

Molecular Ecology 32: 3440-9.

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

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

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

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.

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

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


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

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

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

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

Toli EA ,  BounasA ,  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

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



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

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.

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.

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

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

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

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

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.

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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