Publications

Preprints

2018

Ojeda DI, Mattila T, Ruttink T, Kujala ST, Kärkkäinen K, Verta J-P,  Pyhäjärvi T (2018) Utilization of tissue ploidy level variation in de novo transcriptome assembly of Pinus sylvestris. biorXiv. 

Articles in refereed scientific journals

2019

Pyhäjärvi T, Kujala S, Savolainen O (2019) 275 years of forestry meets genomics in Pinus sylvestris. Evolutionary Applications. Accepted.

2017

Mattila TM, Tyrmi J, Pyhäjärvi T, Savolainen O (2017) Genome-wide analysis of colonization history and concomitant selection in Arabidopsis lyrata. Molecular Biology and Evolution. 34: 2665-2677 HTML

2016

Niskanen AK, Kennedy LJ, Lohi H, Aspi J, Pyhäjärvi T (2016) No evidence of prenatal diversifying selection at locus or supertype levels in the dog MHC class II loci. Canine Genetics and Epidemiology 3: 9. HTML

2015 

Heikkinen ME, Ruokonen M, Alexander M, Aspi J, Pyhäjärvi T, Searle JB (2015) Relationship between wild greylag and European domestic geese based on mitochondrial DNA. Animal genetics 46:485-497. HTML

Vann L, Kono T, Pyhäjärvi T, Hufford MB, Ross-Ibarra J (2015) Natural variation in teosinte at the domestication locus teosinte branched1 (tb1). PeerJ 3, e900. HTML 

2014

Toivainen T, Pyhäjärvi T, Niittyvuopio A, Savolainen O (2014) A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata . Molecular Ecology 23:1040-1052. HTML.

Niskanen AK, Kennedy LJ, Ruokonen M, Kojola I, Lohi H, Isomursu , Jansson E,Pyhäjärvi T, Aspi J (2014) Balancing selection and heterozygote advantage in MHC loci of the bottlenecked Finnish wolf population. Molecular Ecology 23:875-889. . Covered by the molecularecologist.com. 

2013

Pyhäjärvi T, Hufford MB, Mezmouk S, Ross-Ibarra J (2013) Complex patterns of local adaptation in teosinte. Genome Biology and Evolution 5:1594:1609. HTML Cover illustration

Hufford MB, Lubinsky P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J (2013) The genomic signature of crop-wild introgression in maize. PLoS Genetics 9(5): e1003477. HTML

Kanizay LB, Pyhäjärvi T, Lowry EG, Hufford MB, Peterson DG, Ross-Ibarra J, Dawe RK (2013) Diversity and abundance of the Abnormal chromosome 10 meiotic drive complex in Zea mays. Heredity 110: 570-577. HTML

2012

Hufford MB, Bilinski P, Pyhäjärvi T, Ross-Ibarra J (2012) Teosinte as a model system for population and ecological genomics. Trends in Genetics. 28:606-615. HTML

Pyhäjärvi T, Aalto E & Savolainen O (2012) Timescales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae). American Journal of Botany. 99:1314-1322 HTML

Hufford MB,* Xun X*, van Heerwaarden J*, Pyhäjärvi T*, Chia J-M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler S, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (2012) Comparative population genomics of maize domestication and improvement. Nature Genetics 44: 808-811. HTML 
* equal contribution

Chia J-M, Song C, Bradbury P, Costich D, de Leon N, Doebley JC, Elshire RJ, Gaut BS, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon M, Tian F, Wang J, Xu X, Zhang Z, Kaeppler S, Ross-Ibarra J, McMullen M, Buckler ES, Zhang G, Xu Y, Ware D (2012) Capturing extant variation from a genome in flux: maize HapMap II. Nature Genetics 44: 803-807. HTML

Fang Z, Pyhäjärvi T, Weber AL, Dawe RK, Glaubitz JC, JS G, Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J (2012) Megabase-scale inversion polymorphism in the wild ancestor of maize. Genetics 191: 883--894. HTML

2011

Savolainen O, Kujala ST, Sokol C, Pyhäjärvi T, Avia K, Knürr T, Kärkkäinen K & Hicks S (2011) Adaptive Potential of Northernmost Tree Populations to Climate Change, with Emphasis on Scots Pine (Pinus sylvestris L.). Journal of Heredity HTML

Pyhäjärvi T*, Kujala ST* & Savolainen O (2011) Revisiting protein heterozygosity in plants - nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris. Tree Genetics & Genomes 7: 385-397.HTML 
* equal contribution

2009

Palmé A, Pyhäjärvi T, Wachowiak W & Savolainen O (2009) Selection on nuclear genes in a Pinus phylogeny. Molecular Biology & Evolution 26(4): 893-905. HTML

2008

Lascoux M, Pyhäjärvi T, Källman T & Savolainen O (2008) 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. HTML

Pyhäjärvi T, Salmela MJ & Savolainen O (2008) Colonization routes of Pinus sylvestris inferred from distribution of mitochondrial DNA variation. Tree Genetics & Genomes 4: 247-254. HTML

2007

Pyhäjärvi T, García-Gil RM, Knürr T, Mikkonen M, Wachowiak W & Savolainen O (2007) Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177: 1713-1724. HTML

Savolainen O & Pyhäjärvi T (2007) Genomic diversity in forest trees. Current Opinion in Plant Biology 10: 162-167. HTML

Savolainen O, Pyhäjärvi T & Knürr T (2007) Gene flow and local adaptation in forest trees. Annual Review of Ecology Evolution, & Systematics 38: 595-619. HTML