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Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata

Molecular Ecology 26 (13), 3484-3496 T Hämälä, TM Mattila, PH Leinonen, H Kuittinen, O Savolainen

Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis

Heredity 118 (5), 413-423 ST Kujala, T Knürr, K Kärkkäinen, DB Neale, MJ Sillanpää, O Savolainen

Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions

Heredity 118, 211–220 Y Zhou, L Duvaux, G Ren, L Zhang, O Savolainen, J Liu


Genomics: Geography matters for Arabidopsis

Nature 537, 314-315 O Savolainen, M Lascoux

Selection for population‐specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post‐glacial colonization

Molecular ecology 25 (581-597). Mattila T.M., Aalto, E.A., Toivainen, T., Niittyvuopio, A.,Piltonen, S.,Kuittinen, H. and Savolainen, O.


A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata

Molecular Ecology 23 (1040-1052). Toivainen, T., Niittyvuopio, A., Pyhäjärvi, T. and Savolainen, O.

Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris)

New Phytologist. DOI: 10.1111/nph.12901. Avia, K., Kärkkäinen, K., Lagercrantz, U. and Savolainen, O.

Climatic adaptation and ecological divergence between two closely related pine species in Southeast China

Molecular Ecology 23 (3504-3522). Zhou, Y. F., Zhang, L.Liu, J. Q., Wu, G.and Savolainen, O.

Evolutionary conservation of cold-induced antisense RNAs of FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives

Nature Communications  5 (4457). Castaings, L., Bergonzi, S. Albani, M.C., Kemi, U. Savolainen, O and Coupland, G.


Cytoplasmic Male Sterility Contributes to Hybrid Incompatibility Between Subspecies of Arabidopsis lyrata

G3 Genes, Genomes, Genetics 3 (1727-1740). Aalto, E. A., Koelewijn, H. P. and Savolainen, O.

Ecological genomics of local adaptation

Nature Reviews Genetics 14 (807-820) .Savolainen, O., Lascoux, M. Merilä, J.

Potential for evolutionary responses to climate change - evidence from tree populations.

Global Change Biology 19 (1645-1661). Alberto, F., Aitken, S. N., Alia, R., González-Martínez, S. C., Hänninen, H. Kremer, A. Lefèvre, F. Lenormand, T., Whetten, R.Yeaman, S., Savolainen, O.

Investigating incipient speciation in Arabidopsis lyrata from transmission ratio distortion.

Genetics 194 (697- 708). Leppälä, J., Bokma, F.  Savolainen, O

Complex genetic effects on early vegetative development shape resource allocation differences between Arabidopsis lyrata populations.

Genetics 195 (1087-1102). (Remington DL, Leinonen PH, Leppälä J & Savolainen O)

Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata.

New Phytologist 197 (323-335). (Kemi U, Niittyvuopio A, Toivainen T, Pasanen A, Quilot-Turion B, Holm K, Lagercrantz U, Savolainen O & Kuittinen H)

Genetic basis of local adaptation and flowering time variation in Arabidopsis lyrata.
Molecular Ecology 22 (709-723). (Leinonen PH, Remington DL, Leppälä J & Savolainen O)

Genetic changes in flowering and morphology in response to adaptation to a high-latitude environment in Arabidopsis lyrata.
Annals of Botany 111 (957-968). (Quilot-Turion B, Leppälä J, Leinonen PH, Waldmann P, Savolainen O & Kuittinen H) 


Towards decoding the conifer giga-genomes.

Plant Mol. Biol. 80:555-569  Mackay, J.,Dean, J.,  Plomion, C., Peterson, D, Canovas, F., Pavy, N., Ingvarsson, P., Savolainen, O., Fluch, S, Vinceti, B., Abarca, D., Díaz-Sala, C., Cervera, M. T. 2012. 

Sequence variation patterns along a latitudinal cline in Scots pine (Pinus sylvestris): signs of clinal adaptation?
Tree Genetics & Genomics. 2012, DOI: 10.1007/s11295-012-0532-5. (Kujala ST & Savolainen O)

Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae).
Am J Bot. 2012 Aug;99(8):1314-22. (Pyhäjärvi T, Aalto EA & Savolainen O)


The genomic basis of local climatic adaptation.
Science 334 (49-50) (Savolainen O)

Adaptive potential of northernmost tree populations to climate change, with emphasis on Scots Pine (Pinus sylvestris L.).
Journal of Heredity (Savolainen O, Kujala ST, Sokol C, Pyhäjärvi T, Avia K, Knürr T, Kärkkäinen K & Hicks S)

Arabidopsis lyrata genetics.
Genetics and genomics of Brassicaceae: Crops and models 9 (347-372) (Savolainen O & Kuittinen H)

Local adaptation, phenotypic differentiation and hybrid fitness in diverged natural populations of Arabidopsis lyrata.
Evolution 65 (90-107) (Leinonen PH, Remington DL & Savolainen O)

Revisiting protein heterozygosity in plants - nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris.
Tree Genetics & Genomes 7 (85-397) (Pyhäjärvi T, Kujala ST & Savolainen O)

Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.).
Molecular Ecology 20 (1729-1743) (Wachowiak W, Palmé AE. & Savolainen O)

Nuclear cytoplasmic interactions reduce male fertility in hybrids of Arabidopsis lyrata subspecies.
Evolution 65 (2959-2972) (Leppälä J & Savolainen O)

Forest Ecosystem genomics and adaptation: EVOLTREE conference report. 

Tree Genetics & Genomes. (Kremer, A., Vinceti, B., Alia, R., Burczyk, J., Cavers, S., Degen, B., Finkeldey, R., Fluch, S., Gömöry, D., Gugerli, F., Koelewijn, H.P., Koskela, J., Lefèvre, F., Morgante, M., Mueller-Starck, G., Plomion, C., Taylor, G., Turok, J., Savolainen, O., Ziegenhagen, B., 2011.) 


Cryptic population genetic structure: the number of inferred clusters depends on sample size.
Molecular Ecology Resources 10 (314-323) (Fogelqvist J, Niittyvuopio A, Ågren J, Savolainen O & Lascoux M)

Increased mortality can promote adaptation of forest trees to climate change.
Forest Ecology and Management 259 (1003-1008) (Kuparinen A, Savolainen O & Schurr F)

Investigating the effects of topography and clonality on genetic structuring within a large Norwegian population of Arabidopsis lyrata.
Annals of Botany 106 (243-254) (Lundemo S, Stenøien H & Savolainen O)


Search for nucleotide patterns of local adaptation in dehydrins and other cold related candidate genes in Scots pine (Pinus sylvestris L.).
Tree Genetics & Genomes 5 (117-132) (Wachowiak W, Balk P & Savolainen O)

The allopolyploid Arabidopsis kamchatica originated from multiple individuals of A. lyrata and A. halleri.
Molecular Ecology 18 (4024-4048) (Shimizu-Inatsugi R, Lihová J Ishiyama H, Kudoh H, Marhold K, Savolainen O, Watanabe K, Yakubov VV & Shimizu KK)

Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae).
American Journal of Botany 96 (1129-1137) (Leinonen PH, Sandring S, Quilot B, Clauss MJ, Mitchell-Olds, T, Ågren, J & Savolainen, O)

Selection on nuclear genes in a Pinus phylogeny.
Molecular Biology & Evolution 26 (893-905) (Palmé A, Pyhäjärvi T, Wachowiak W & Savolainen O)


Genome wide effects of post-glacial colonization in Arabidopsis lyrata.
Heredity 100 (47-58) (Muller H, Leppälä J & Savolainen O)

Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus.
Heredity 100 (71-78) (Leppälä J, Bechsgaard J, Schierup M & Savolainen O)

Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps.
Molecular Biology and Evolution 25 (2567-2577) (Palmé A, Wright M & Savolainen O)

Natural variation in Arabidopsis lyrata vernalization requirement conferred by a FRIGIDA indel polymorphism.
Molecular Biology and Evolution 25 (319-329) (Kuittinen H, Niittyvuopio A, Rinne P & Savolainen O)

Past demography in forest trees: what can we learn from nuclear DNA sequences that we do not already know?
Plant Ecology & Diversity 1 (209-215). (Lascoux M, Pyhäjärvi T, Källman T & Savolainen O)

Colonization routes of Pinus sylvestris inferred from distribution of mitochondrial DNA variation.
Tree Genetics and Genomes 4 (247-254) (Pyhäjärvi T, Salmela MJ & Savolainen O)


Gene flow and local adaptation in forest trees.
Annual Review of Ecology, Evolution and Systematics 38 (595-619) (Savolainen O, Pyhäjärvi T & Knürr T)

Genetic variation of growth rhythm in the limits of a latitudinal cline in Scots pine.
Canadian Journal of Forest Research 37 (540-551) (Notivol E, Garcia-Gil MR, Alia R & Savolainen O)

Genomic diversity in forest trees.
Current Opinion in Plant Biology 10(2) (162-167) (Savolainen O & Pyhäjärvi T)

Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations.
Genetics 177 (1713-1724) (Pyhäjärvi T, Garcia-Gil MR, Knürr T, Mikkonen M, Wachowiak W & Savolainen O)

Selection on flowering time and floral display in an alpine and a lowland population of Arabidopsis lyrata.
Journal of Evolutionary Biology 20 (558-567) (Sandring S, Riihimäki M, Savolainen O & Ågren J)


Comparative gene mapping in Arabidopsis lyrata chromosomes 1 and 2 and the corresponding A. thaliana chromosome 1: recombination rates, rearrangements and centromere location.
Genetical Research 87 (79-85) (Hansson B, Kawabe A, Preuss S, Kuittinen H & Charlesworth D)

Natural variation in MAM within and between populations of Arabidopsis lyrata determines glucosinolate phenotype.
Genetics 173 (1629-1636) (Heidel AJ, Clauss M, Kroymann J, Savolainen O & Mitchell-Olds O)

Analysis of microsatellite variation in Pinus radiata reveals effects of genetic drift but no recent bottlenecks.
Journal of Evolutionary Biology 19 (167-175) (Karhu A, Vogl C, Moran GF, Bell JC & Savolainen O)


Studying genetics of adaptive variation in model organisms: flowering time variation in Arabidopsis lyrata.
Genetica 123 (63-74) (Riihimäki M, Podolsky R, Kuittinen H, Koelewijn, H & Savolainen O)

Analysis of microsatellite variation in Pinus radiata reveals effects of genetic drift but no recent bottlenecks.
Journal of Evolutionary Biology 19 (167-175) (Karhu A, Vogl C, Moran GF, Bell JC & Savolainen O)

Genetic variability in natural populations of Arabidopsis thaliana in northern Europe.
Molecular Ecology 14 (137-148) (Stenoien HK, Fenster CB, Tonteri A & Savolainen O)


Environmental and genetic effects on flowering differences between Northern and Southern populations of Arabidopsis lyrata (Brassicaceae).
American Journal of Botany 91 (1036-1045) (Riihimäki MA & Savolainen O)

Genetic variation in cessation of growth and frost hardiness and consequences for adaptation of Pinus sylvestris to climatic changes.
Forest Ecology and Management 197 (79-89) (Savolainen O, Bokma F, Garcia-Gil R. & Repo T)

Comparing the linkage maps of the close relatives Arabidopsis lyrata and Arabidopsis thaliana.
Genetics 168 (1575-1584) (Kuittinen H, de Haan AA, Vogl C, Oikarinen S, Leppälä J, Koch M, Mitchell-Olds T, Langley C & Savolainen O)

Association genetics in conifers.
Trends in Plant Science 9 (325-330) (Neale D & Savolainen O)


Studying genetics of adaptive variation in model organisms: flowering time variation in Arabidopsis lyrata.
Genetica 123 (63-74) (Riihimäki M, Podolsky R, Kuittinen H, Koelewijn H & Savolainen O)

Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris.
Molecular Ecology 12 (1195-1206) (García MR, Mikkonen M & Savolainen O)

DNA sequence variation in BpMADS2 gene in two populations of Betula pendula.
Molecular Ecology 12 (369-384) (Järvinen P, Lemmetyinen J, Savolainen O & T. Sopanen T)

Comparing EST based genetic maps between Pinus sylvestris and P. taeda.
Theoretical Applied Genetics 107 (667-678) (Komulainen P, Brown GR, Mikkonen M, Karhu A, García MR, O'Malley D, Lee B, Neale DB & Savolainen O)


Quantifying latitudinal clines in natural populations of Arabidopsis thaliana (Brassicaceae).
American Journal of Botany 89 (1604-1608) (Stenøien H, Fenster C, Kuittinen H & Savolainen O)

High resolution analysis of mating systems: inbreeding in natural populations of Pinus radiata.
Journal of Evolutionary Biology 15 (433-439) (Vogl C, Karhu A, Moran GF & Savolainen O)

Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris.
Molecular Biology and Evolution 19 (179-188) (Dvornyk V, Sirviö A, Mikkonen M & Savolainen O)

Primers for 22 candidate genes for ecological adaptations in Brassicaceae.
Molecular Ecology Notes 2 (258-262) (Kuittinen H, Aguadé M, Charlesworth D, De Haan A, Lauga B, Mitchell-Olds T, Oikarinen S, Ramos-Onsins S, Stranger B, van Tienderen P & Savolainen O)


Genetic composition and diploid hybrid speciation of a high mountain pine, Pinus densata, native to the Tibetan plateau.
Genetics 159 (337-346) (Wang XR, Szmidt AE & Savolainen O)


Genetic basis of climatic adaptation in Scots pine by Baysesian QTL analysis.
Genetics 156 (1309-1322) (Hurme P, Sillanpää MJ, Arjas E, Repo T & Savolainen O)

Contrasting patterns of variation at the alcoholdehydrogenase locus of the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana.
Molecular Biology and Evolution 17 (645-655) (Savolainen O, Langley CH, Lazzaro B & Fréville H)

Rapid extension of microsatellites in pines.
Molecular Biology and Evolution 17 (259-265) (Karhu A, Dieterich JH & Savolainen O)


Genetic basis of inbreeding depression in Arabis petraea.
Evolution 53 (1354-1365) (Kärkkäinen K, Kuittinen H, van Treuren R, Vogl C, Oikarinen S & Savolainen O) 

Magnitude and timing of inbreeding depression in Scots pine (Pinus sylvestris L.).
Evolution 53 (758-768) (Koelewijn H, Koski V & Savolainen O)

Why do plants abort so many developing seeds: bad offspring or bad maternal genotypes?
Evolutionary Ecology 13 (305-317) (Kärkkäinen K, Koski V & Savolainen O)

Post-glacial colonization, drift, local selection and conservation value of population: a northern perspective.
Hereditas 130 (229-238) (Pamilo P & Savolainen O)

Deleterious mutations can reduce differentiation in small, subdivided populations.
Hereditas 130 (257-264) (Pamilo P, Pálsson P & Savolainen O)

Factors influencing the extent of inbreeding depression: an example from Scots pine.
Heredity 82 (441-450) (Hedrick PW, Savolainen O & Kärkkäinen K)

Developing SSCP markers for comparative mapping and QTL characterization.
Molecular Breeding 5 (21-31) (Plomion C, Hurme P, Frigerio JM, Ridolphi M, Pot D, Pionneau C, Avila C, Gallardo F, David H, Neutelings G, Campbell M, Canova FM, Savolainen O & Kremer A)

Comparison of homology and linkage of RAPD markers between individual trees of Scots Pine (Pinus sylvestris).
Molecular Ecology 8 (15-22) (Hurme P & Savolainen O)


Climatic adaptation of bud set and frost hardiness in Scots pine (Pinus sylvestris L.).
Canadian Journal of Forest Research 27 (716-523) (Hurme P, Repo T, Pääkkönen T & Savolainen O)

Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana.
Heredity 79 (144-152) (Kuittinen H, Mattila A & Savolainen O)

Evolution of microsatellites in Arabis petraea and Arabis lyrata, outcrossing relatives of Arabidopsis thaliana.
Molecular Biology and Evolution 14 (220-229) (R. Van Treuren, Kuittinen H, Kärkkäinen K, Baena-Gonzalez E & Savolainen O) 

Genetic basis of flowering time adaptation in Arabidopsis thaliana.
Theoretical Applied Genetics 95 (573-583) (Kuittinen H, Sillanpää M & Savolainen O)


Genetic variation in populations of the arctic perennial Pedicularis dasyantha (Scrophulariaceae), on Svalbard, Norway.
American Journal of Botany 83 (1379-1385) (Odasz AM & Savolainen O)

Genotype by environment interaction is not sufficient to maintain variation: Levene and the leaf hopper.
American Naturalist 148 (930-936) (Prout T & Savolainen O)

Geographical variation in the inbreeding depression of Scots pine.
Evolution 50 (111-119) (Kärkkäinen K, Koski K & Savolainen O)

Inbreeding depression in conifers: implications for using selfing as a breeding strategy.
Forest Science 42 (102-117) (Williams CG & Savolainen O)

Do molecular markers predict patterns of adaptive variation?
Theoretical Applied Genetics 93 (215-221) (Karhu A, Hurme P, Karjalainen M, Karvonen P, Kärkkäinen K, Neale DB & Savolainen O)


Heterozygosity and fitness: no association in Scots pine.
Genetics 140 (755-766) (Savolainen O & Hedrick PW)


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