• Freund, F.. "Cannings models, populations size changes and multiple-merger coalescents" (2019) arXiv:1902.02155
  • Jacquemin, Julie, et al. "Levels and patterns of genetic diversity differ between two closely related endemic Arabidopsis species. (2016) bioRxiv: 048785. bioRxiv


  • Lampei, C. (2018), Multiple simultaneous treatments change plant response from adaptive parental effects to within‐generation plasticity, in Arabidopsis thaliana. Oikos. Accepted Author Manuscript. doi:10.1111/oik.05627

  • Eldon, B. and Freund, F. "Genealogical properties of subsamples in highly fecund populations" J Stat Phys, read-only version for non-subscribers available here


  • F. Freund and M. Möhle. On the size of the block of 1 for Ξ-coalescents with dust. Modern Stochastics: Theory and Applications 4(4), 407-425

  • Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colome-Tatche M, Durka W, Engelhardt J, Gaspar B, Gogol-Doring A, Grosse I, van Gurp TP, Heer K, Kronholm I, Lampei C, Latzel V, Mirouze M, Opgenoorth L, Paun O, Prohaska S, Rensing SA, Stadler P, Trucchi E, Ullrich K, Verhoeven KJF. 2017. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecology Letters, 20:1576–1590, OpenAccess, preprint

  • Thorwarth P, Ahlemeyer J, Bochard A-M, Krumnacker K, Blümel H, Laubach E, Knöchel N, Cselényi L, Ordon F, Schmid KJ (2017) Genomic prediction ability for yield-related traits in German winter barley elite material. Theoretical and Applied Genetics, in press.

  • Groot MP, Kubisch A, Ouborg NJ, Pagel J, Schmid KJ, Vergeer P, Lampei C (2017) Transgenerational effects of mild heat in Arabidopsis thaliana show strong genotype specificity that is explained by climate at origin. New Phytologist. doi:10.1111/nph.14642, PDF

  • M.G. Stetter and K.J.Schmid (2017) Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop. Molecular Phylogenetics and Evolution 109: 80-92. Publisher, bioRxiv

  • M.G. Stetter, T. Müller and K.J. Schmid (2017) Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus). Molecular Ecology doi:10.1111/mec.13974, Publisher, bioRxiv

  • Lampei C, Metz J and Tielbörger K (2017), Clinal population divergence in an adaptive parental environmental effect that adjusts seed banking. New Phytologist, 214:1230-1244. doi:10.1111/nph.14436, PDF


  • Bauer, E., Schmutzer, T., Barilar, I., Mascher, M., Gundlach, H., Martis, M. M., Twardziok, S. O., Hackauf, B., Gordillo, A., Wilde, P., Schmidt, M., Korzun, V., Mayer, K. F.X., Schmid, K., Schön, C.-C. and Scholz, U. (2016), Towards a whole-genome sequence for rye (Secale cereale L.). Plant J. Publisher

  • Novikova, P. Y., Hohmann, N., Nizhynska, V., Tsuchimatsu, T., Ali, J., Muir, G., Guggisberg, A., Paape, T., Schmid, K. and Fedorenko, O., Holm, S., Säll, T., Schlötterer, C., Marhold, K., Widmer, A., Sese, J., Shimizu K. K., Weigel, D., Krämer U., Koch Marcus A.,, Nordborg, M. (2016). Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics, 48, 1077–1082. Publisher

  • M. G. Stetter​, L. Zeitler, A. Steinhaus, K. Kroener, M. Biljecki and K. J. Schmid (2016) Crossing methods and cultivation conditions for rapid production of segregating populations in three grain amaranth species. Frontiers in Plant Science DOI:10.3389/flps.2016.00819, Publisher, preprint

  • T. Günther,C. Lampei, I. Barilar and K. J. Schmid (2016) Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps. Molecular Ecology DOI: 10.1111/mec.13705 Publisher, preprint

  • Toni I Gossmann, Dounia Saleh, Marc W Schmid, Michael A Spence, Karl J Schmid (2016) Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes. Mol. Biol. Evol. 33:1669–1678 Publisher (OpenAccess)

  • The Arabidopsis 1001 Genomes Consortium (2016) 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell doi:10.1016/j.cell.2016.05.063 Publisher (OpenAccess) 1001 Genomes Website

  • Russell, J., Mascher, M., Dawson, I.K., Kyriakidis, S., Calixto, C., Freund, F., Bayer, M., Milne, I., Marshall-Griffiths, T., Heinen, S., Hofstad, A., Sharma, R., Himmelbach, A., Knauft, M., van Zonneveld, M., Brown, J.W.S., Schmid, K., Kilian, B., Muehlbauer, G.J., Stein, N. and Waugh, R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nature Genetics 48,1024-1030


  • W. Gebrelassie, B. Lakew, B. I. G. Haussmann, K. J. Schmid (2015) Ethiopian barley landraces show higher yield stability and comparable yield to improved varieties in multi-environment field trials. J. Plant Breeding Crop Sci. 7:275-291 DOI: 10.5897/JPBCS2015.0524 Publisher, PDF

  • S. Hübner, A. B. Korol and K. J. Schmid (2015) RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum BMC Plant Biology 15:134 Publisher, data

  • M. G. Stetter, K. J. Schmid and U. Ludewig (2015) Uncovering genes and ploidy involved in the high diversity in root hair density, length and response to local scarce phosphate in Arabidopsis thaliana PLOS ONE Publisher

  • I. Gawenda, P. Thorwarth, T. Günther, F. Ordon and K. J. Schmid (2015) Genome-wide association studies in elite varieties of German winter barley using single-marker and haplotype-based methods. Plant Breeding 134,28–39 (2015) Plant Breeding

  • B. Eldon, M. Birkner, J. Blath, and F. Freund. Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents? Genetics 199(3), 841-856


  • T. Müller, F. Freund, H. Wildhagen and K. J. Schmid (2014) Targeted re-sequencing of five Douglas-fir provenances reveals population structure and putative target genes of positive selection. Tree Genetics & Genomes

  • G Bedada, A Westerbergh, T Müller, E Galkin, E Bdolach, M Moshelion, E Fridman and K J Schmid Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts. BMC Genomics.2014, 15:995 Biomedcentral

  • Eltohamy A. A. Yousef, Christian Lampei, Karl J. Schmid (2014) Evaluation of cauliflower genebank accessions under organic and conventional cultivation in Southern Germany. Euphytica Springer, data & R-script available here

  • K. J. Schmid and P. Thorwarth. Genomic Selection. In: Biotechnological Approaches to Barley Improvement. N. Stein and J. Kumlehn (Eds.). Springer

  • F. Freund and A. Siri-Jégousse. Minimal clade size in the Bolthausen-Sznitman coalescent. J. Appl. Probab. 51(3), 657-668

  • M Siqueira, ML Bonatelli, T Günther, I Gawenda, KJ Schmid, VA Pavinato, EA Veasey (2014) Water yam (//Dioscorea alata// L.) diversity pattern in Brazil: an analysis with SSR and morphological markers, Genetic Resources and Crop Evolution 61:611-624 Publisher

  • G Bedada, A Westerbergh, E Nevo, A Korol and K J Schmid (2014) DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel. Heredity 112, 646–655. PubMed

  • Gossmann TI, Schmid MW, Grossniklaus U, Schmid KJ (2014) Selection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana. Mol Biol Evol. 2014 31:574-83. PubMed


  • T. Günther, G. Coop (2013) Robust identification of local adaptation from allele frequencies. Genetics. 195:205-220 PubMed

  • J.S. Dhersin, F. Freund, A. Siri-Jégousse and L. Yuan (2013) On the length of an external branch in the Beta-coalescent. Stoch. Proc. Appl. 123, 1691–1715.

  • S Hübner, E Bdolach, S Ein-Gedi, K J Schmid, Abraham Korol, E Fridman (2013) Phenotypic Landscapes: Phenological Patterns in Wild and Cultivated Barley. J. Evol. Biol. 26: 163-74PubMed

  • T. Günther, C. Lampei and K. J. Schmid. (2013) Mutational bias and gene conversion affect the intraspecific nitrogen stoichiometry of the Arabidopsis thaliana transcriptome. Mol. Biol. Evol. 30:561-8 PubMed


  • T. Müller, I. Ensminger, K. J. Schmid. A Douglas-fir (Pseudotsuga menziesii) unigene catalogue based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings (2012) BMC Genomics 13:673 BioMedCentral

  • Hübner S, Günther T., Flavell A, Fridman E, Graner A., Korol A. and Schmid K. J. (2012) Islands and Streams: Clusters and gene flow in wild barley populations from the Levant. Molecular Ecology 21:1115-1129 PubMed

  • F. Freund. Almost sure asymptotics for the number of types for simple Ξ-coalescents. ECP 17, article 3


  • Gossmann T. I. and Schmid K. J. (2011) Selection-driven divergence after gene duplication in Arabidopsis thaliana. J. Mol. Evol. 73: 153-165 PubMed

  • Cao J., Schneeberger K., Ossowski S., Günther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Wang X., Ott F., Müller J., Alonso-Blanco C., Borgwardt K., Schmid K.J., and Weigel D. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics 43:956-963 PubMed

  • Günther T. and Schmid K.J. (2011) Improved haplotype-based detection of ongoing selective sweeps towards an application in Arabidopsis thaliana. BMC Research Notes 4:232 PubMed, PDF

  • Günther T., Gawenda I. and Schmid K.J. (2011) phenosim - A software to simulate phenotypes for testing in genome-wide association studies. BMC Bioinformatics 12:265 PubMed, PDF


  • O'Connell MJ, Loughran NB, Walsh TA, Donoghue MT, Schmid KJ, Spillane C (2010) A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals. Mamm. Genome DOI 10.1007/s00335-010-9283-5 PubMed

  • Günther T. and K. J. Schmid (2010) Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice. Theor. Appl. Genetics 121:157-168. PubMed

  • Childs L, H. Witucka-Wall H., T. Günther, R Sulpice , M v. Korff-Schmising, M Stitt, D Walther, K J Schmid, T Altmann (2010) Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11:188. PubMed, PDF


  • Hübner S., Höffken M., Oren E., Haseneyer G., Stein N., Graner A., Schmid K.J. and E. Fridman (2009) Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation. Molecular Ecology 18, 1523–1536.

  • Song B.-H., Windsor A. J., Schmid, K. J., Ramos-Onsins S., Schranz M. E., Heidel A. J., and T. Mitchell-Olds (2009) Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis. Genetics 181: 1021–1033


  • Oyama, R., Formanova N., Clauss, M. J., Kroymann, J., Schmid, K. J., Vogel H., Weniger K., Windsor A., and T. Mitchell-Olds (2008) The shrunken genome of Arabidopsis thaliana. Plant Systematics 273: 257-271

  • Schmid K. J. and Z. Yang (2008) The trouble with sliding windows and the selective pressure in BRCA1. PLoS ONE 3(11): e3746


  • Korves T.M., Schmid K. J., Caicedo, A. L., Mays, C., Stinchcombe, J. R., Purugganan, M. D., and J. Schmitt (2007) Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field. American Naturalist 169: E141-157

  • Spillane C., Schmid, K. J., Pien S., Laoueille-Duprat S., Page D. R., Baroux C., Escobar-Restrepo J.-M., Köhler C., Wolfe K., and U. Grossniklaus (2007) Positive darwinian selection at the imprinted MEDEA locus in plants. Nature 448: 349-352


  • Schmid, K. J., O. Törjek, R. Meyer, H. Schmuths, M. Hoffmann, T. Altmann (2006) Evidence for large scale population structure in Arabidopsis thaliana from genome-wide SNP markers. Theoret. Appl. Genetics, 112: 1104-1114.


  • Schmid, K. J., S. Ramos-Onsins, J. Ringys-Beckstein, B. Weisshaar, T. Mitchell-Olds (2005) A multilocus analysis of sequence variation in Arabidopsis thaliana reveals a genome-wide departure from the standard neutral model of sequence evolution. Genetics, 169: 1601-1615.


  • Schein M., Z. Yang, T. Mitchell-Olds and K. J. Schmid (2004) Rapid evolution of a pollen specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol. Biol. Evol., 21: 659-669.


  • Schmid K. J., T. Rosleff Sörensen, R. Stracke, O. Torjek T. Altmann, T. Mitchell-Olds and B. Weisshaar (2003) Large-scale identification and and analysis of genome-wide single nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Research, 13:1250- 1257.

  • Törjek, O, D. Berger, R. C. Meyer, C. Müssig, K. J. Schmid, T. Rosleff Sörensen, B. Weisshaar, T. Mitchell-Olds and T. Altmann (2003) Establishment of a high-efficiency SNP- based framework marker set. Plant J., 36:122-140.


  • Schmid K. J. and C.F. Aquadro (2001) The evolutionary analysis of “orphans” from the Drosophila genome identifies rapidly evolving and incorrectly annotated genes. Genetics, 159: 589-598

2000 and older

  • Wang. Z.G., K. J. Schmid and S. Ackerman (1999) The Drosophila gene 2A5 complements the defect in mitochondrial F1 -ATPase assembly in yeast lacking the molecular chaperone Atp11p. FEBS Lett. 452: 305-308

  • Schmid K. J. and D. Tautz (1999) Large differences in sequence length and trinucleotide repeat composition between homologous developmental genes from Drosophila melano-gaster and Tribolium castaneum. J. Mol. Evol., 49: 558-566

  • Schmid K. J., L. Nigro, C. F. Aquadro and D. Tautz (1999) High number of replacement polymorphisms at three fast evolving genes in populations of Drosophila melanogaster and D. simulans: Implications for genome-wide surveys. Genetics, 153: 1717-1729

  • Schmid K. J. and D. Tautz (1998) Sequence and expression of DmMKLP1, a homolog of the human MKLP1 kinesin-like protein from Drosophila melanogaster. Dev. Genes Evol., 208: 474-476.

  • Schmid K. J. and D. Tautz (1997) A screen for fast evolving genes from Drosophila. Proc. Natl. Acad. Sci. USA, 94: 9746-9750.

  • K. J. Schmid (1996) Untersuchungen zur evolutionären Konservierung von transkribierten Sequenzen aus Drosophila melanogaster, Ph. D. Thesis, LMU München.

  • Kilger C. and K. J. Schmid (1994) Rapid characterization of bacterial clones by microwave treatment and PCR, Trends Genet., 10: 149.