Publications and some useful R code:

    2017
  • Zan, Y., Sheng, Z., Lillie, M., Rönnegård, L., Honaker, C.F., Siegel, P.B., & Carlborg, O. (2017) Artificial selection response due to polygenic adaptation from a multi-locus, multi-allelic genetic architecture. Molecular Biology and Evolution (accepted).

  • Lee, Y., Rönnegård, L. & Noh, M. (2017) Data Analysis Using Hierarchical Generalized Linear Models with R. Chapman and Hall/CRC. ISBN 9781138627826.
  • (R code used in the book is available here and can also be downloaded as a txt file at http://users.du.se/~lrn/DUweb/R_code_in_LRN2017.txt)

  • Silva, C., McFarlane, S.E., Hagen, I., Rönnegård, L., Billing, A., Kvalnes, T., Kemppainen, P., Rønning, B., Ringsby, T., Sæther, B.-E., Qvarnström, A., Ellegren, H., Jensen, H. & Husby, A. (2017) Insights into the genetic architecture of morphological traits in two passerine bird species. Heredity 119:197-205


  • Nelson, R.M., Temnykh, S.V., Johnson, J.L., Kharlamova, A.V., Vladimirova, A.V., Gulevich, R.G., Shepeleva, D.V., Oskina, I.N., Acland, G.M., Rönnegård, L., Trut, L.N., Carlborg, O, & Kukekova, A.V. (2017) Genetics of interactive behavior in silver foxes (Vulpes vulpes). Behavior Genetics 47: 88-101. doi:10.1007/s10519-016-9815-1.


  • 2016
  • Sivertsen, T.R, Ahman, B., Steyaert, S.M.J.G., Rönnegård, L., Frank, J., Segerstrom, P., Stoen, O.G., & Skarin, A. (2016) Reindeer habitat selection under the risk of brown bear predation during calving season. Ecosphere 7(11):e01583.

  • Lee, Y., Alam, M., Noh, M., Rönnegård, L., & Skarin, A. (2016) Spatial modelling of data with excessive zeros applied to reindeer pellet-group counts. Ecology and Evolution 6:7047-7056.

  • Svenson, K., Li, Y., Macuchova, Z., & Rönnegård, L. (2016) Evaluation needs of road maintenance in Sweden with the mixed proportional hazards model. Transportation Research Record: Journal of the Transportation Research Board 2589:51-58.

  • Rönnegård, L., McFarlane, S.E., Husby, A., Kawakami, T., Ellegren, H., & Qvarnstrom, A. (2016) Increasing the power of genome wide association studies in natural populations using repeated measures: evaluation and implementation. Methods in Ecology and Evolution 7:792-799.

  • (The paper above evaluates the method implemented in the R package RepeatABEL , which is part of the GenABEL suite of packages.)

  • Han, M., Håkansson, J. & Rönnegård, L. (2016) To what extent do neighbouring populations affect local population change over time? Population, Space & Place 22:68-83 .


  • 2015
  • Alam, M., Rönnegård, L. & Shen, X. (2015) Fitting Conditional and Simultaneous Autoregressive Spatial Models in hglm. The R Journal 7(2): 5-18.

  • Casals, M., Langohr, K., Carrasco, J.L. & Rönnegård, L. (2015) Parameter Estimation of Poisson Generalized Linear Mixed Models Based on Three Different Statistical Principles: a Simulation Study. Statistics and Operations Research Transactions 39(2):281-308.

  • Skarin, A., Nelleman, C., Rönnegård, L., Sandstrom, P. & Lundqvist, H. (2015) Wind farm construction impacts reindeer migration and movement corridors. Landscape Ecology, 30(8): 1527-1540.

  • Husby, A., Kawakami, T., Rönnegård, L., Smeds, L., Ellegren, H. & Qvarnstrom, A. (2015) Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life history trait. Proceedings of the Royal Society B: Biological Sciences, 282(1806), 20150156.

  • 2014
  • Åhman, B., Svensson, K. & Rönnegård, L. (2014) High female mortality resulting in herd collapse in free-ranging domesticated reindeer (Rangifer tarandus tarandus) in Sweden. PLoS One 9(10):e111509.

  • Shen, X., Li, Y., Rönnegård, L., Uden, P. & Carlborg, O. (2014) Application of a genomic model for high-dimensional chemometric analysis. Journal of Chemometrics 28(7):548-557

  • Shen, X., Alam, M. & Rönnegård, L. (2014) Mixed Models Through the Lens of hglm: Applications and Grand Challenges. In JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association. 1254-1263.

  • 2013
  • Rönnegård, L. & Lee, Y. (2013) Editorial: Exploring the potential of hierarchical generalized linear models in animal breeding and genetics. Journal of Animal Breeding and Genetics 130:415-416

  • Nelson, R.M., Nettelblad, C.,Pettersson, M.E., Shen, X., Crooks, L., Besnier, F., Alvarez-Castro, J., Rönnegård, L., Ek, W., Sheng, Z., Kierczak, M., Holmgren, S. & Carlborg O. (2013) MAPfastR: QTL Mapping in Outbred Line Crosses. G3 3(12): 2147-2149

  • Shen, X. & Rönnegård, L. (2013) Issues with data transformation in genome-wide association studies for phenotypic variability [v1; ref status: approved 1, http://f1000r.es/1xl] F1000Research 2013, 2:200 ( doi: 10.12688/f1000research.2-200.v1)

  • Sonesson, A.K., Ødegård, J. & Rönnegård, L. 2013. Genetic heterogeneity of within-family variance of body weight in Atlantic salmon (Salmo salar). Genetics Selection Evolution 45:41

  • Strandberg, E., Felleki, M., Fikse, W.F., Franzen, J., Mulder, H.A., Rönnegård, L., Urioste, J.I. & Windig, J.J. 2013. Statistical tools to select for robustness and milk quality. Advances in Animal Biosciences 4(3):606-611

  • Mulder, H.A., Rönnegård, L., Fikse, W.F., Veerkamp, R.F. & Strandberg, E. 2013. Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models. Genetics Selection Evolution 45(1):23

  • Shen, X., Alam, M., Fikse, W.F. & Rönnegård, L. 2013. A novel generalized ridge regression method for quantitative genetics. Genetics 193(4):1255-1268

  • Rönnegård, L., Felleki, M., Fikse, W.F., Mulder H.A. & Strandberg, E. 2013. Variance component and breeding value estimation for genetic heterogeneity of residual variance in Swedish Holstein dairy cattle. Journal of Dairy Science 96:2627-2636


  • 2012
  • Felleki, M., Lee, D., Lee, Y., Gilmour, A. & Rönnegård, L. 2012. Estimation of breeding values for mean and dispersion, their variance and correlation using double hierarchical generalized linear models. Genetics Research 94:307-317.

  • (Here you find example files for doing the DHGLM estimation in ASReml. The file IRWLSofDHGLM.as includes the ASReml code and IRWLSofDHGLMdata.dat is the input data file. The output produced by ASReml is shown in IRWLSofDHGLM.asr, and the R code for generating the simulated data in the input file is found in IRWLSofDHGLM_simulation_of_data.r)

  • Shen, X., Pettersson, M., Rönnegård, L. & Carlborg O. 2012. Inheritance beyond plian heritability: variance-controlling genes in Arabidopsis thaliana. PLoS Genetics 8(8): e1002839.

  • Rönnegård, L. & Valdar W. 2012. Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability. BMC Genetics 13:63.

  • Alvarez-Castro, J.M., Carlborg, O. & Rönnegård, L. 2012. Estimation and interpretation of genetic effects with epistasis using the NOIA model. Methods in Molecular Biology 871:191-204.


  • 2011
  • Shen, X., Rönnegård, L. & Carlborg O. 2011. How to deal with genotype uncertainty in variance component quantitative trait loci analyses. Genetics Research 93:333-342.

  • Rönnegård, L. & Valdar W. 2011. Detecting major genetic loci controlling phenotypic variability in experimental crosses. Genetics 188:435-447.

  • Shen, X., Rönnegård, L. & Carlborg O. 2011. Hierarchical likelihood opens a new way of estimating genetic values using genome-wide dense marker maps. BMC Proceedings 5(Suppl 3):S14.

  • Al-Sarraj, R, Qie, W & Rönnegård, L. 2011. Evaluation of variance component estimators based on Henderson's Method. Centre of Biostochastics Research Report 2011:1

  • Besnier, F, Wahlberg, P, Rönnegård, L, Ek, W, Andersson, L, Siegel, P & Carlborg, O. 2011. Fine mapping and replication of QTL in outbred chicken advanced intercross lines. Genetics Selection Evolution 43:3.


  • 2010
  • Rönnegård, L & Lee, Y. 2010. Hierarchical generalized linear models have a great potential in genetics and animal breeding. In proceedings: World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. (Download pdf)

  • Rönnegård, L, Shen, X & Alam, M. 2010. hglm: A package for fitting hierarchical generalized linear models. The R Journal 2:20-28.

  • Rönnegård, L, Felleki, M, Fikse, F, Mulder, HA & Strandberg, E. 2010. Genetic heterogeneity of residual variance - estimation of variance components using double hierarchical generalized linear models. Genetics Selection Evolution 42:8.

  • (Here you find code for doing the DHGLM estimation in ASReml using the R interface, together with some WinBUGS code for comparison.)

  • Mishchenko, K, Rönnegård, L, Holmgren, S & Mishchenko, V. 2010. Assessing a multiple QTL search using the variance component model. Computational Biology and Chemistry 34:34-41.


  • 2009
  • Rönnegård, L, Besnier, F & Carlborg, O. 2009. Modelling dominance in a flexible intercross analysis. BMC Genetics 10:30.

  • Rönnegård, L, Al-Sarraj, R. & von Rosen, D. 2009. Non-iterative variance component estimation in QTL analysis. Journal of Animal Breeding and Genetics 126:110-116.

  • (Here you find an R-function to calculate the non-iterative VC estimates)

    2008
  • Rönnegård, L, Besnier, F & Carlborg, O. 2008. An improved method for QTL detection and identification of within-line segregation in F2 intercross designs. Genetics 178:2315-2326.
    ( Here you find an unpublished R package for IBD matrix estimation used in FIA).

  • Mishchenko, K, Holmgren S. & Rönnegård, L. 2008. Newton-type methods for REML estimation in genetic analysis of quantitative traits. Journal of Computational Methods in Sciences and Engineering 8:53-67.

  • Rönnegård, L, Pong-Wong, R & Carlborg, O. 2008. Defining the assumptions underlying modelling of epistatic QTL using variance component methods. Journal of Heredity 99:421-425.

  • Rönnegård, L, Sand, H., Andren, H., Månsson, J. & Pehrson, A. 2008. Evaluation of four methods used to estimate population density of moose (Alces alces). Wildlife Biology 14(3):358-371.


  • 2007
  • Mishchenko, K., Holmgren, S. & Rönnegård, L. 2007. Efficient implementation of the AI-REML iteration variance component QTL analysis. Research Report No. 2007-4, ISSN 1404-4978. Mälardalen University, Sweden.

  • (Here you find some R-code for constructing a reduced IBD matrix as shown in the paper.)
  • Rönnegård, L., Mischenko, K., Holmgren, S. & Carlborg, O. 2007. Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices. Genetics 176:1935-1938

  • Rönnegård, L. & Carlborg, O. 2007. Separation of base allele and sampling term effects gives new insights in variance component QTL analysis. BMC Genetics 8:1

  • (Here you find the AI-REML R-function given in the paper)

    2006 and earlier
  • Rönnegård, L. & Carlborg, O. A new efficient method for QTL mapping in divergent intercrosses incorporating within line variation. 8th World Conference on Genetics Applied to Livestock Production, Belo Horizonte, Brazil, 2006.

  • Mattson-Petersen C., Berg P.E.O. and Rönnegård L. 2005. Quality control of waste to incineration - waste composition analysis in Lidköping, Sweden. Waste Management and Research 23:527-533.

  • Carling, K., Rönnegård, L. and Roszbach, K. 2004. An analysis of portfolio credit risk when counterparties are interdependent within industries. Working paper 2004. No. 168, Sveriges Riksbank, Stockholm.

  • Rönnegård, L., Woolliams, J.A. & Danell, O. 2003. Breeding schemes in reindeer husbandry. Rangifer 23(2):45-55.

  • Rönnegård, L. & Woolliams, J.A. 2003. Predicted rates of inbreeding with additive maternal effects. Genetical Research 82: 67-77.

  • Rönnegård, L. & Danell, O. 2003. Genetic response to selection on reindeer calf weights. Rangifer 23(1): 13-20.

  • Rönnegård, L. 2003. Selection, Maternal Effects and Inbreeding in Reindeer Husbandry. Doctoral Thesis, Swedish University of Agricultural Sciences, Dpt. Animal Breeding and Genetics, Uppsala, Sweden. Download here

  • Rönnegård, L. Forslund, P. & Danell, O. 2002. Lifetime patterns in adult female mass, reproduction and offspring mass in semidomesticated reindeer (Rangifer tarandus tarandus). Canadian Journal of Zoology 80:2047-2055.

  • Rönnegård, L. & Danell, O. 2001. Gene flow and potential selection response in age-structured subpopulations having a common male pool. Animal Science 72: 427-440.