Ancient Genomics and Evolution

Paul
Paul
Hernán
Hernán
Katrin
Katrin
Rafal
Rafal
Sergio
Sergio
Kelly
Kelly
Clemens
Clemens

Group Interests

Evolutionary geneticists have traditionally applied a comparative approach, where the relationships between closely related species (or between individuals of the same species) are determined by contrasting their DNA sequences. DNA retrieved from museum specimens, fossil remains and archeological findings -collectively known as ancient DNA (aDNA) – have added an exciting new dimension to evolutionary studies; instead of indirectly inferring the likely state of DNA sequences from former generations of extant organism or from extinct species, aDNA allows the direct inspection and timing of the changes that have happened in a given species or evolutionary lineage throughout time. The aDNA field has recently blossomed thanks to the advent of high-throughput sequencing (HTS), which has radically increased the amount of data that can be produced from ancient samples. Although herbaria are present almost ubiquitously in natural history museums, their collections have not been extensively used for aDNA studies, and especially not for whole-genome analysis. We are using this largely untapped source to address a broad range of evolutionary questions in three main research avenues.

  • The dynamics of past plant-pathogen epidemics
  • Identification and timing of key events in crop domestication
  • Colonization of new ecological niches by invasive or introduced species


Collaboration Partners

References (peer-reviewed)

9.

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Durvasula A., Fulgione A., Gutaker R. M., Alacakaptan S. I., Flood P. J., Neto C., Tsuchimatsu T., Burbano H. A., Pico F. X., Alonso-Blanco C. and Hancock A. M.
Proc Natl Acad Sci U S A
(2017), 114(20) 5213-5218.
8.

Neandertal and Denisovan DNA from Pleistocene sediments

Slon V., Hopfe C., Weiss C. L., Mafessoni F., de la Rasilla M., Lalueza-Fox C., Rosas A., Soressi M., Knul M. V., Miller R., Stewart J. R., Derevianko A. P., Jacobs Z., Li B., Roberts R. G., Shunkov M. V., de Lumley H., Perrenoud C., Gusic I., Kucan Z., Rudan P., Aximu-Petri A., Essel E., Nagel S., Nickel B., Schmidt A., Prufer K., Kelso J., Burbano H. A., Paabo S. and Meyer M.
Science
(2017), 356(6338) 605-608.
7.

A Robust Framework for Microbial Archaeology

Warinner C., Herbig A., Mann A., Fellows Yates J. A., Weiss C. L., Burbano H. A., Orlando L. and Krause J.
Annu Rev Genomics Hum Genet
(2017), .
6.

Extraction of ultrashort DNA molecules from herbarium specimens

Gutaker R. M., Reiter E., Furtwangler A., Schuenemann V. J. and Burbano H. A.
Biotechniques
(2017), 62(2) 76-79.
5.

Reinforcing plant evolutionary genomics using ancient DNA

Gutaker R. M. and Burbano H. A.
Curr Opin Plant Biol
(2017), 36 38-45.
4.

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

Weiss C. L., Schuenemann V. J., Devos J., Shirsekar G., Reiter E., Gould B. A., Stinchcombe J. R., Krause J. and Burbano H. A.
R Soc Open Sci
(2016), 3(6) 160239.
3.

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data

Weiß C. L., Dannemann M., Prüfer K. and Burbano H. A.
eLife
(2015), 4.
2.

Mining herbaria for plant pathogen genomes: back to the future

Yoshida K., Burbano H. A., Krause J., Thines M., Weigel D. and Kamoun S.
PLoS Pathog
(2014), 10(4) e1004028.
1.

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Yoshida K., Schuenemann V. J., Cano L. M., Pais M., Mishra B., Sharma R., Lanz C., Martin F. N., Kamoun S., Krause J., Thines M., Weigel D. and Burbano H. A.
Elife
(2013), 2 e00731.

The complete list of publications of Hernán A. Burbano can be found in his google citations profile:

Hernán A. Burbano's Google Citation profile

References (non peer-reviewed)

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

Exposito-Alonso M., Vasseur F., Ding W., Wang G., Burbano H.A., Weigel, D.

bioRxiv preprint


The rate and effect of de novo mutations in Natural populations of Arabidopsis thaliana

Exposito-Alonso M., Becker C., Schuenemann V.J., Reiter E., Setzer C., Slovak R., Brachi B., Hagmann J., Grimm D.G., Jiahui C., Busch W., Bergelson J., Ness R.W., Krause J., Burbano H.A., Weigel D.

bioRxiv preprint doi:http://dx.doi.org/10.1101/050203

 

Herbarium genomics: investigating plant and microbial evolution using historic and modern samples.

Burbano, H.A.

Max Planck Society Yearbook 2014-2015.