Evolutionary Genetics


Group Interests

Phenotype-first approaches for the identification of natural variants with potential roles in adaptation continue to be an important part of our research. Arabidopsis thaliana can be found in very different habitats, and the species varies in many morphological, physiological and life history traits. Several are likely to be important for local adaptation, such as the onset of flowering. This is less obvious for others, but their investigation can nevertheless lead to interesting biology. For example, while studying a temperature-dependent growth defect, we discovered the first example of a naturally occurring genetic defect associated with a triplet repeat expansion outside humans. Similarly, from the study of leaf morphology differences we found examples of natural variation in the efficiency of miRNA processing.

An essential resource for theses studies is the genome information and germplasm made available through the 1001 Genomes Project. We are also systematically sampling local plant populations, both around Tübingen and in North America, where many individuals belong to a single lineage that has diversified for about 300 years. Phenotypic and molecular analyses addressing the spread of (epi)mutations in populations and ultimately the mechanisms of adaptation range from field experiments in different ecological settings and controlled growth studies using thousands of small raspberry-pi controlled cameras to large-scale expression and methylome profiling.

A new direction is the systematic analysis of gene x genotype interactions, where we investigate how the expression of mutant phenotypes is modulated by genetic background. The experimental strategy employs the CRISPR/Cas9 technology to knock out the same genes in different natural accessions. These efforts are an important step toward exploiting naturally occurring genetic variation for a systems understanding of biological processes.

  • Systematic analysis of gene-by-genotype (GxG) interactions
  • Naturally occurring segregation distortion
  • Evolution of herbicide resistance

Collaboration Partners



Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity

Wibowo A., Becker C., Marconi G., Durr J., Price J., Hagmann J., Papareddy R., Putra H., Kageyama J., Becker J., Weigel D. and Gutierrez-Marcos J.
(2016), 5.

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

Rigal M., Becker C., Pelissier T., Pogorelcnik R., Devos J., Ikeda Y., Weigel D. and Mathieu O.
Proc Natl Acad Sci U S A
(2016), 113(14) 2083-92.

Cooperation and Conflict in the Plant Immune System

Chae E., Tran D. T. and Weigel D.
PLoS Pathog
(2016), 12(3) e1005452.

Population Genomics for Understanding Adaptation in Wild Plant Species

Weigel D. and Nordborg M.
Annu Rev Genet
(2015), 49 315-38.

Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors

Venturelli S., Belz R. G., Kamper A., Berger A., von Horn K., Wegner A., Bocker A., Zabulon G., Langenecker T., Kohlbacher O., Barneche F., Weigel D., Lauer U. M., Bitzer M. and Becker C.
Plant Cell
(2015), 27(11) 3175-89.

KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1

Karlsson P., Christie M. D., Seymour D. K., Wang H., Wang X., Hagmann J., Kulcheski F. and Manavella P. A.
Proc Natl Acad Sci U S A
(2015), 112(45) 14096-101.

Adenylate cyclase 5 is required for melanophore and male pattern development in the guppy (Poecilia reticulata)

Kottler V. A., Kunstner A., Koch I., Flotenmeyer M., Langenecker T., Hoffmann M., Sharma E., Weigel D. and Dreyer C.
Pigment Cell Melanoma Res
(2015), 28(5) 545-558.

THO2, a core member of the THO/TREX complex, is required for microRNA production in Arabidopsis

Francisco-Mangilet A. G., Karlsson P., Kim M. H., Eo H. J., Oh S. A., Kim J. H., Kulcheski F. R., Park S. K. and Manavella P. A.
Plant J
(2015), 82(6) 1018-29.

Beyond the thale: comparative genomics and genetics of Arabidopsis relatives

Koenig D. and Weigel D.
Nat Rev Genet
(2015), 16(5) 285-98.

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

Hagmann J., Becker C., Muller J., Stegle O., Meyer R. C., Wang G., Schneeberger K., Fitz J., Altmann T., Bergelson J., Borgwardt K. and Weigel D.
PLoS Genet
(2015), 11(1) e1004920.

Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

Fraser B. A., Kunstner A., Reznick D. N., Dreyer C. and Weigel D.
Mol Ecol
(2015), 24(2) 389-408.

Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae

Smith L. M., Burbano H. A., Wang X., Fitz J., Wang G., Ural-Blimke Y. and Weigel D.
Plant J
(2015), 81(4) 597-610.

Plant Genetic Archaeology: Whole-Genome Sequencing Reveals the Pedigree of a Classical Trisomic Line

Salome P. A. and Weigel D.
G3 (Bethesda)
(2014), 5(2) 253-9.

Recent geographic convergence in diurnal and annual temperature cycling flattens global thermal profiles

Wang G. and Dillon M. E.
Nature Clim. Change
(2014), 4(11) 988-992.

Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization

Seymour D. K., Koenig D., Hagmann J., Becker C. and Weigel D.
PLoS Genet
(2014), 10(11) e1004785.

Multiple pigment cell types contribute to the black, blue, and orange ornaments of male guppies (Poecilia reticulata)

Kottler V. A., Koch I., Flotenmeyer M., Hashimoto H., Weigel D. and Dreyer C.
PLoS One
(2014), 9(1) e85647.

Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata

Sharma E., Kunstner A., Fraser B. A., Zipprich G., Kottler V. A., Henz S. R., Weigel D. and Dreyer C.
BMC Genomics
(2014), 15 400.

Pigment pattern formation in the guppy, Poecilia reticulata, involves the Kita and Csf1ra receptor tyrosine kinases

Kottler V. A., Fadeev A., Weigel D. and Dreyer C.
(2013), 194(3) 631-46.

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Slotte T., Hazzouri K. M., Agren J. A., Koenig D., Maumus F., Guo Y. L., Steige K., Platts A. E., Escobar J. S., Newman L. K., Wang W., Mandáková T., Vello E., Smith L. M., Henz S. R., Steffen J., Takuno S., Brandvain Y., Coop G., Andolfatto P., Hu T. T., Blanchette M., Clark R. M., Quesneville H., Nordborg M., Gaut B. S., Lysak M. A., Jenkins J., Grimwood J., Chapman J., Prochnik S., Shu S., Rokhsar D., Schmutz J., Weigel D. and Wright S. I.
Nat Genet
(2013), 45(7) 831-5.

Transposon variants and their effects on gene expression in Arabidopsis

Wang X., Weigel D. and Smith L. M.
PLoS Genet
(2013), 9(2) e1003255.

Estimates of genetic differentiation measured by F(ST) do not necessarily require large sample sizes when using many SNP markers

Willing E. M., Dreyer C. and van Oosterhout C.
PLoS One
(2012), 7(8) e42649.

Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella

Guo Y. L., Todesco M., Hagmann J., Das S. and Weigel D.
(2012), 192(2) 729-39.

Natural variation in Arabidopsis: from molecular genetics to ecological genomics

Weigel D.
Plant Physiol
(2012), 158(1) 2-22.

Natural variation in biogenesis efficiency of individual Arabidopsis thaliana microRNAs

Todesco M., Balasubramanian S., Cao J., Ott F., Sureshkumar S., Schneeberger K., Meyer R. C., Altmann T. and Weigel D.
Curr Biol
(2012), 22(2) 166-70.

On epigenetics and epistasis: hybrids and their non-additive interactions

Smith L. M. and Weigel D.
(2012), 31(2) 249-50.

The recombination landscape in Arabidopsis thaliana F2 populations

Salome P. A., Bomblies K., Fitz J., Laitinen R. A., Warthmann N., Yant L. and Weigel D.
Heredity (Edinb)
(2012), 108(4) 447-55.

Developmental genetics and new sequencing technologies: the rise of nonmodel organisms

Rowan B. A., Weigel D. and Koenig D.
Dev Cell
(2011), 21(1) 65-76.

Evolution of the S-locus region in Arabidopsis relatives

Guo Y. L., Zhao X., Lanz C. and Weigel D.
Plant Physiol
(2011), 157(2) 937-46.

Genetic architecture of flowering-time variation in Arabidopsis thaliana

Salome P. A., Bomblies K., Laitinen R. A., Yant L., Mott R. and Weigel D.
(2011), 188(2) 421-33.

Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis

Guo Y. L., Fitz J., Schneeberger K., Ossowski S., Cao J. and Weigel D.
Plant Physiol
(2011), 157(2) 757-69.

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Becker C., Hagmann J., Muller J., Koenig D., Stegle O., Borgwardt K. and Weigel D.
(2011), 480(7376) 245-9.

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Hu T. T., Pattyn P., Bakker E. G., Cao J., Cheng J. F., Clark R. M., Fahlgren N., Fawcett J. A., Grimwood J., Gundlach H., Haberer G., Hollister J. D., Ossowski S., Ottilar R. P., Salamov A. A., Schneeberger K., Spannagl M., Wang X., Yang L., Nasrallah M. E., Bergelson J., Carrington J. C., Gaut B. S., Schmutz J., Mayer K. F., Van de Peer Y., Grigoriev I. V., Nordborg M., Weigel D. and Guo Y. L.
Nat Genet
(2011), 43(5) 476-81.

Whole-genome sequencing of multiple Arabidopsis thaliana populations

Cao J., Schneeberger K., Ossowski S., Gunther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Lippert C., Wang X., Ott F., Muller J., Alonso-Blanco C., Borgwardt K., Schmid K. J. and Weigel D.
Nat Genet
(2011), 43(10) 956-63.

Arabidopsis and relatives as models for the study of genetic and genomic incompatibilities

Bomblies K. and Weigel D.
Philos Trans R Soc Lond B Biol Sci
(2010), 365(1547) 1815-23.

Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing

Laitinen R. A., Schneeberger K., Jelly N. S., Ossowski S. and Weigel D.
Plant Physiol
(2010), 153(2) 652-4.

Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana

Bomblies K., Yant L., Laitinen R. A., Kim S. T., Hollister J. D., Warthmann N., Fitz J. and Weigel D.
PLoS Genet
(2010), 6(3) e1000890.

The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana

Ossowski S., Schneeberger K., Lucas-Lledo J. I., Warthmann N., Clark R. M., Shaw R. G., Weigel D. and Lynch M.
(2010), 327(5961) 92-4.

A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana

Sureshkumar S., Todesco M., Schneeberger K., Harilal R., Balasubramanian S. and Weigel D.
(2009), 323(5917) 1060-3.

Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation

Tripathi N., Hoffmann M., Willing E. M., Lanz C., Weigel D. and Dreyer C.
Proc Biol Sci
(2009), 276(1665) 2195-208.

Linkage analysis reveals the independent origin of Poeciliid sex chromosomes and a case of atypical sex inheritance in the guppy (Poecilia reticulata)

Tripathi N., Hoffmann M., Weigel D. and Dreyer C.
(2009), 182(1) 365-74.

QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines

Balasubramanian S., Schwartz C., Singh A., Warthmann N., Kim M. C., Maloof J. N., Loudet O., Trainer G. T., Dabi T., Borevitz J. O., Chory J. and Weigel D.
PLoS One
(2009), 4(2) e4318.

Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck

Guo Y. L., Bechsgaard J. S., Slotte T., Neuffer B., Lascoux M., Weigel D. and Schierup M. H.
Proc Natl Acad Sci U S A
(2009), 106(13) 5246-51.

Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae

Warthmann N., Das S., Lanz C. and Weigel D.
Mol Biol Evol
(2008), 25(5) 892-902.

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

Clark R. M., Schweikert G., Toomajian C., Ossowski S., Zeller G., Shinn P., Warthmann N., Hu T. T., Fu G., Hinds D. A., Chen H., Frazer K. A., Huson D. H., Scholkopf B., Nordborg M., Ratsch G., Ecker J. R. and Weigel D.
(2007), 317(5836) 338-42.