Publications

Pre-prints

• Wang, X. Ingvarsson PK. Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome.
• Panahabadi, R., McKee, L.S., Ahmadikhah, A., Ingvarsson, P.K., Farrokhi, N. (2021) Rice (Oryza Sativa L.) whole-grain genome-wide association study for neutral sugar content.
• Shang, H., Rendón-Anaya, M., Paun, O., Field, D., Hess, J. Vogl, V., Liu, J., Ingvarsson, P.K., Lexer, C., Leroy, T. (2021) Conserved genomic landscapes of differentiation across Populus speciation continuum.

2022

• Liu, S., Zhang, L., Sang, Y., Lai, Q., Zhang, X., Jia, C., Long, Z., Wu, J., Ma, T., Mao, K., Street, N.R., Ingvarsson, P.K., Liu, J., Wang, J., (2022) Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome.
• Rönnberg-Wästljung, A-C., Adler, A., Karacic, A., Liepins, K., Richards, T.J., Ingvarsson, P.K., Weih, M. (2022) Phenotypic plasticity in Populus trichocarpa clones across environments in the Nordic-Baltic region.
• Tan, B., Ingvarsson, P.K. (2022) Integrating genome-wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus.
• Chen, P., Song, Y., Liu, X., Xiao, L., Bua, C., Liu, P., Zhao, L., Ingvarsson, P.K., Wu, H.X., El-Kassaby, Y.A. and Zhang, D. (2022) LncRNA PMAT–PtoMYB46 module represses PtoMATE and PtoARF2 promoting Pb²⁺ uptake and plant growth in poplar.
• Tariq, R., Hussain, A., Tariq, A., Hayder Bin Khalid, M., Khan, I., Basim,H. Ingvarsson, P.K. (2022) Genome-wide analyses of the mung bean NAC gene family reveals orthologs, co-expression networking and expression profiling under abiotic and biotic stresses.
• Tian, Y., Liu, S., Ingvarsson, P.K., Zhao, D., Wang, L., Abuduhamiti, B., Wu, Z., Zhang, J., Wang, Z. (2022) Genomic analyses reveal natural selection on reproduction related genes between two closely related Populus (Salicaceae) species.
• Sang, Y., Long, Z., Dan, X., Feng, J., Shi, T., Jia, C., Zhang, X., Lai, Q., Yang, G., Zhang, H., Xu, X., Liu, H., Jiang, Y., Ingvarsson, P.K., Liu, J., Mao, K., Wang, J. (2022) Genomic insights into local adaptation and future climate change vulnerability of a keystone forest tree species in East Asia.
• Rahimi, Y., Khahani, B., Jamali, A., Alipour, H., Bihamta, M.R., Ingvarsson, P.K. (2002) GWAS to identify genomic loci associated with early vigour in bread wheat under simulated water deficit complemented with QTL meta-analysis.
• Javid, S., Bihamta, M.R., Omidi, M., Abbasi, A.R., Alipour, H. Ingvarsson, P. K. (2022) Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.).

2021

• Bernhardsson, C., Zan, Y., Chen, Z., Ingvarsson, P.K., Wu, H.X. (2021) Development of a highly efficient 50K SNP genotyping array for the large and complex genome of Norway spruce (Picea abies Karst) by whole genome re‐sequencing and its transferability to other spruce species.
• Song, Y., Chen, P., Xuan, A., Bu, C., Liu, P., Ingvarsson, P.K., El-Kassaby, Y, Zhang, D. (2021) Integration of genome-wide association studies and co-expression networks reveal roles of PtoWRKY42-PtoUGT76C1-1 in trans-zeatin metabolism and cytokinin sensitivity in poplar. 
• Apuli, R-P., Richards, T., Rendón-Anaya, M., Karacic, A., Wästljung-Rönnberg, A-C., Ingvarsson, P.K. (2021) The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray).
• Capador, H., Bernhardsson, C., Milesi, P. Lundén, K., Vos, I., Wu, H.X., Ingvarsson, P.K., Stenlid, J., Elfstrand, M. (2021) Killing two enemies with one stone?: Genomics of resistance to two sympatric pathogens in Norway spruce.
• Rahimi, Y., Ingvarsson, P.K., Bihamta, M.R., Alipour, H., Taleei, A., Khoshnoodi S., Abadi, J. (2021) Characterization of dynamic regulatory gene and protein networks in wheat roots upon perceiving water deficit through comparative transcriptomics survey.
• Rendón-Anaya, M., Wilson, J., Sveinsson, S., Fedorkov, A., Cottrell, J., Bailey, M.E.S., Ruņģis, D., Lexer, C., Jansson, S., Robinson, K.M., Street, N.R., Ingvarsson, P.K. (2021) Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula).
• Panahabadi, R., Ahmadikhah, A., McKee, L.S., Ingvarsson, P.K., Farrokhi, N. (2021) Genome-wide association mapping of mixed linkage (1,3;1,4)-β-glucan and starch content in rice whole grain.
• Fataftah, N., Bag, P., André, D., Lihavainen, J., Zhang, B., Ingvarsson, P.K., Nilsson, O., Jansson, S., (2021) GIGANTEA gene expression influence leaf senescence in Populus in two different ways.
• Hallingbäck, H.R., Puscholt, P., Ingvarsson, P.K., Rönnberg-Wästljung, A-C., Berlin, S. (2021) Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.
• Liang, Y-Y., Shi, Y., Yuan, S., Zhou, B-F., Chen, X-Y., An, Q-Q., Ingvarsson, P.K., Plomion, C., Wang, B. (2021) Linked selection shapes the landscape of genomic variation in three oak species.
• Panahabadi, R., Ahmadikhah, A., McKee, L.S., Ingvarsson, P.K., Farrokhi, N. (2021) Genome-wide association study (GWAS) for lignocellulosic compounds and fermentable sugars in rice straw.

2020

• Apuli, R-P., Bernhardsson, C., Schiffthaler, B., Robinson, K.M., Jansson, S., Street, N.R., Ingvarsson, P.K. (2020) Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European aspen (Populus tremula).
• Wang, X., Bernhardsson, C., Ingvarsson, P.K. (2020) Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies).
• Wang J, Street NR, Park E-J, Liu J, Ingvarsson PK. 2020. Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.
• Ingvarsson PK, Bernhardsson C. (2020) Genome-wide signatures of environmental adaptation in European aspen (Populus tremula) under current and future climate conditions.
• Thistlethwaite, F.R., Gamal El-Dien, O., Ratcliffe, B. Klápště, J., Porth, I., Chen, C., Stoehr, M.U., Ingvarsson, P.K., El-Kassaby, Y.A. (2020) Linkage disequilibrium vs. pedigree: genomic selection prediction accuracy in conifer species.
• Müller, N.A., Kersten, B., Leite Montalvão, A.P., Mähler, N., Bernhardsson, C., Bräutigam, K., Carracedo Lorenzo, Z., Hoenicka, H., Kumar, V., Mader, M., Pakull, B., Robinson, K., Sabatti, M., Vettori, C., Ingvarsson, P.K., Cronk, Q., Street, N.R., Fladung, M. (2020) A single gene underlies the dynamic evolution of poplar sex determination.
•  Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P.K., Liu, J., Lexer, C. (2020) Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group.
  Skytte af Sätra, J., Troggio, M, Odilbekov, F., Hjalmarsson, I., Ingvarsson, P.K., Garkava-Gustavsson, L. (2020) Genetic structure of the Swedish central collection of local apple cultivars.
• Bernhardsson C, Wang X, Eklöf H, Ingvarsson PK. 2020. Variant calling using NGS and sequence capture data for population and evolutionary genomic inferences in Norway Spruce (Picea abies).
•  Richards, T.J., Karacic, A., Apuli, R-P, Weih, M., Ingvarsson, P.K., Rönnberg-Wästljung, A-C. (2020) Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. & Gray).
• Eklöf, H., Bernhardsson, C., Ingvarsson, P.K. (2020) Comparing the effectiveness of exome capture probes, genotyping by sequencing and whole-genome re-sequencing for assessing genetic diversity in natural and managed stands of Picea abies.

2019

• Xie, J., Li, Y., Liu, X., Zhao, Y., Li, B., Ingvarsson, P.K., Zhang, D. (2019) Evolutionary origins of pseudogenes and their association with regulatory sequences in plants.
•  Bernhardsson C, Vidalis A, Wang X, Scofield DG, Shiffthaler B, Baison J, Street NR, Rosario Garcia-Gíl MR, Ingvarsson PK. (2019) An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce (Picea abies).
• Baison J, Vidalis A, Zhou L, Chen Z-Q, Li Z, Sillanpää MJ, Bernhardsson C, Scofield DG, Forsberg N, Olsson L, Karlsson B, Wu HX, Ingvarsson PK, Lundqvist SO, Niittylä T, Garcia-Gíl MR. (2019) Association mapping identified novel candidate loci affecting wood formation in Norway spruce.
• Barker, H., Riehl, J.F., Bernhardsson, C., Rubert-Nason, K., Holeski, L, Ingvarsson, P.K, Lindroth, R.L. (2019) Linking plant genes to insect communities: identifying the genetic bases of plant traits and community composition.
• Rahimi, Y., Reza Bihamta, M., Taleei, A., Alipour, H., Ingvarsson, P.K. (2019) Applying an artificial neural network approach for drought tolerance screening among Iranian wheat landraces and cultivars grown under normal and rain-fed conditions.
• Ma, X-F., Qian, C., Yan, X., Shi, Y., Yin, H., Chang, Y., Chen, J., Ingvarsson, P.K., Nevo, E. (2019) Adaptive signals of flowering time pathways in wild barley from Israel over 28 generations.
• Rosvall, O., Bradshaw, R.H.W., Egertsdotter, U., Ingvarsson, P.K., Wu, H. (2019) Using clones in Swedish forestry: introduction.
•  Ingvarsson, P.K. and Dahlberg, H. (2019) The effects of clonal forestry on genetic diversity in wild and domesticated stands of forest trees.
•  Bradshaw, R.H.W, Ingvarsson, P.K., Rosvall, O. (2019) The ecological consequences of using clones in forestry. 
•  Rosvall, O., Bradshaw, R.H.W., Egertsdotter, U., Ingvarsson, P.K., Mullin, T.J., Wu, H. (2019) Using Norway spruce clones in Swedish forestry: Implications of clones for management.

2018

• Tan, B., Grattapaglia, D., Wu, H.X., Ingvarsson, P.K. (2018) Genomic prediction reveals significant non- additive effects for growth in hybrid Eucalyptus.
• Michelson, I., Ingvarsson, P.K., Robinson, K., Edlund, E., Eriksson, M., Nilsson, O., Jansson, S. (2018) Autumn senescence in aspen is not triggered by day length.
• Grimberg Å, Lager I, Street NR, Robinson KM, Marttila S, Mähler N, Ingvarsson PK, Bhalerao RP. (2018) Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen.
• Wang, J., Ding, J., Tan, B., Johansson, A., Nystedt, B., Robinson, K.M., Michelson, I., Scofield, D.G., Nilsson, O., Jansson, S., Street, N.R., Ingvarsson, P.K. (2018) A major locus controls local adaptation and adaptive life history variation in a perennial plant.
• Cole, C.T., Ingvarsson, P.K. (2018) Pathway position constrains the evolution of an ecologically important pathway in aspens (Populus tremula L.)
• Lin, Y-C., Wang, J., Delhomme, N., Shiffthaler, B., Sundström, G., Zuccolo, A., Nystedt, N., Hvidsten, T.R., de la Torre, A., Cossu, R.M., Hoppner, M.P., Lantz, H., Scofield, D.G., Zamani, N., Johansson, A., Mannapperuma, C., Robinson, K.M., Mähler, N., Leitch, I., Pellicer, J., Park, E-J., Van Montaguvan, M., Van de Peer, Y., Grabherr, M., Jansson, S., Ingvarsson, P.K., Street, N.R. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.

2017

• Ingvarsson, P.K. and Wang, J. (2017) Small and large-scale heterogeneity in genetic variation across the collard flycatcher genome: implications for estimating genetic diversity in non-model organisms.
• Li Z., La Torre De A. R., Sterck L., Canovas F. M., Avila C., Merino Sierra I., Antonio Cabezas J., Teresa Cervera M., Ingvarsson P. K., Van de Peer Y., 2017 Single-copy genes as molecular markers for phylogenomic studies in seed plants.
• Mähler, N., Wang, J., Terebieniec, B.K., Ingvarsson, P.K., Street, N.R., Hvidsten, T.R. (2017) Gene co-expression network connectivity is an important determinant of selective constraint.
• De La Torre, A., Li, Z., Van de Peer, Y., Ingvarsson, P.K. (2017) Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants.
•  Tan, B., Grattapaglia, D., Salgado Martins, G., Zamprogno Ferreira, K., Sundberg, B., Ingvarsson, P.K. (2017) Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F1 hybrids. 
• Schiffthaler, B., Bernhardsson, C., Ingvarsson, P.K., Street, N.R. A parallel implementation of the OneMap R package for fast computation of F₁ linkage maps in outcrossing species.

2016

• Ingvarsson, P.K., Hvidsten, T.R., and Street, N.R. (2016) Genome assembly, comparative genomics and populations genetics of forest trees. 
• Wang, J., Street, N.R., Scofield, D.G., Ingvarsson, P.K. Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens.
• Scott, A.D., Stenz, N., Ingvarsson, P.K., Baum, D.A. Whole-genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers. 
• Wang, J., Street, N.R., Scofield, D.G., Ingvarsson, P.K. (2016) Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species.

2015

• Porth, I., Klápště, J., McKown, A.D., La Mantia, J., Guy, R.D., Ingvarsson, P.K., Hamelin, R., Mansfield, S.D., Ehlting, J., Douglas, C.J., El-Kassaby, Y.A. (2015) Evolutionary Quantitative Genomics of Populus trichocarpa.
• Du, S., Wang, Z., Ingvarsson, P.K., Wang, D., Wang, J., Wu, Z., Tembrock, L.R., and Zhang, J. (2015) Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species.
• De La Torre, A.R., Lin, Y-C, Van de Peer, Y., Ingvarsson, P. K. (2015) Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families.
• De La Torre, A., Ingvarsson, P. K., Aitken, S.N. (2015) Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea.
• Du, Q., Tian, J., Yang, X., Pan, W., Xu, B., Li, B., Ingvarsson, P.K., and Zhang, D. (2015) Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa.
• Wang, J. Scofield, D. Street, N.R., Ingvarsson, P.K. (2015) Variant calling using NGS data in European aspen (Populus tremula). In: Advances in the Understanding of Biological Sciences using Next Generation Sequencing (NGS) Approaches. Sablok, G., Kumar, S., Ueno, S., Kuo, J., Varotto, C. (eds). Springer Verlag. ISBN 978-3-319-17157-9

2014

• Robinson, K.M., Delhomme, N., Mähler, N., Önskog, J., Albrectsen, B.R., Ingvarsson, P.K., Hvidsten, T.R., Jansson, S., Street, N.R. (2014) Populus tremula (European aspen) shows no evidence of sexual dimorphism in gene expression, phenotype, secondary defence or herbivory.
• Wang, J. Abbott, R.J., Ingvarsson, P.K., Liu, J. (2014) Increased genetic divergence between two closely related fir species in areas of range overlap.

2013

• Nystedt, B., Street, N.R., Wetterbom, A., Zuccolo, A., Lin, Y-C., Scofield, D.G., Vezzi, F., Delhomme, N., Alexeyenko, A., Giacomello, S., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Niittylä, T., Olson, Å., Rilakovic, N., Ritland, C., Rosselló, J.A., Sena, J., Svensson, T, Talavera-López, C., Theißen, G., Tuominen, H., Vanneste, K., Wu, Z-Q., Zhang, B., Zerbe, P., Arvestad, L., Bhalerao, R., Bohlmann, J., Bousquet, J., Garcia-Gil, R., Hvidsten, T.R., de Jong, P., MacKay, J., Morgante, M., Ritland, K., Sundberg, B., Thompson, S.L., Van de Peer, Y., Andersson, B., Nilsson, O., Ingvarsson, P.K., Lundeberg, J., Jansson, S. (2103) The 20 Gbp Norway spruce genome sheds light on conifer genome evolution.
• Bernhardsson, C., Robinson, K. M., Abreu, I. N., Jansson, S., Albrectsen, B.R., Ingvarsson, P.K. (2013) Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defense genes.
• Johansson, H., Stoks, R., Nilsson-Örtman, V., Ingvarsson, P.K., Johansson, F. (2013) Large-scale patterns in genetic variation, gene flow and differentiation in five species of European Coenagrionid damselfly provide mixed support for the central-marginal hypothesis. 

2012

• Klintenäs, M., Pin, P.A., Benlloch, R., Ingvarsson, P.K., Nilsson, O. (2012) Analysis of conifer FT/TFL1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage.
• Gao, J., Wang, B., Mao, J.F., Ingvarsson, P.K., Zeng, Q.Y., Wang, X.R. (2012) Historical demography of the homoploid hybrid pine Pinus densata on the Tibetan Plateau.
• Ismail, M., Soolanayakanahally, R.Y., Ingvarsson, P.K., Guy, R.D., Jansson, S., Silim, S.N. and El-Kassaby, Y.A. (2012) Comparative nucleotide diversity across North American and European Populus species.
• Johansson, F., Lind, M.I., Ingvarsson, P.K. and Bokma, F. (2012) Evolution of the G-matrix in life history traits in the common frog during a recent colonisation of an island system.
• Robinson, K.M., Ingvarsson, P.K., Jansson, S. and Albrectsen, B.R. (2012) Genetic variation in functional traits influences arthropod community composition in European aspen (Populus tremula L.).
• Bernhardsson, C. and Ingvarsson, P.K. (2012) Geographic structure and adaptive population differentiation in herbivore defense genes in European aspen (Populus tremula L., Salicaceae).
• Johansson, H., Ingvarsson, P.K., and Johansson, F. (2012) Cross-species amplification and development of microsatellites for six species of European Coenagrionid damselflies.

2011

• Bernhardsson, C. and Ingvarsson, P.K. (2011) Molecular population genetics of elicitor-induced resistance genes in European aspen (Populus tremula L., Salicaceae).
• Keller, S.R. Levsen, N., Ingvarsson, P.K., Olson, M.S. and Tiffin, P. (2011) Local selection across a latitudinal gradient shapes nucleotide diversity in Balsam poplar, Populus balsamifera L.
• Hall, D., Ma, X-F., and Ingvarsson, P.K. (2011) Adaptive evolution of the Populus tremula photoperiod pathway.
• Lind, M.I., Ingvarsson, P.K., Johansson, H., Hall, D., and Johansson, F. (2011) Gene flow and selection on phenotypic plasticity in an island system.

2010

• Ma, X-F., Hall. D., St. Onge, K.R., Jansson, S., and Ingvarsson, P.K. (2010) Genetic differentiation, clinal variation and phenotypic associations with growth cessation across the Populus tremula photoperiodic pathway.
• Berglund, Å.M.M., Ingvarsson, P.K., Danielsson, H., Nyholm, N.E.I. (2010) Lead exposure and biological effects in pied flycatchers (Ficedula hypoleuca) before and after the closure of a lead mine in northern Sweden.
• de Carvalho, D., Ingvarsson, P.K, Joseph, J., Suter, L., Sedivy, C., Macaya-Sanz, D., Cottrell, J., Heinze, B., Schanzer, I., Lexer, C. (2010) Admixture facilitates adaptation from standing variation in the European aspen (P. tremula L.), a widespread forest tree.
• Ingvarsson P.K. (2010) Natural selection on synonymous and non-synonymous mutations shape patterns of polymorphism in Populus tremula.
• Ingvarsson, P.K. (2010) Nucleotide polymorphism, linkage disequilibrium and complex trait dissection in Populus. In: Genetics and Genomics of Populus (Plant Genetics and Genomics: Crops and Models , Vol. 8). Jansson, S., Bhalerao, R.P. and Groover, A.T. (eds.), pp. 91-112, Springer Verlag. ISBN 978-1-4419-1541-2

List of older publications can be obtained from ORCID.