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Publications: Publications
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QUANTITATIVE AND POPULATION GENOMICS

2023

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.

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 . Rate of 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

2022

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

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.

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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