Ancient Genomics and Evolution


Group Interests

Burbano Lab has moved to UCL

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)


Natural selection on the Arabidopsis thaliana genome in present and future climates

Exposito-Alonso M., Genomes Field Experiment Team, Burbano H. A., Bossdorf O., Nielsen R. and Weigel D.
(2019), 573(7772) 126-129.

The origins and adaptation of European potatoes reconstructed from historical genomes

Gutaker R. M., Weiss C. L., Ellis D., Anglin N. L., Knapp S., Luis Fernandez-Alonso J., Prat S. and Burbano H. A.
Nat Ecol Evol
(2019), 3(7) 1093-1101.

Using herbaria to study global environmental change

Lang P. L. M., Willems F. M., Scheepens J. F., Burbano H. A. and Bossdorf O.
New Phytol
(2019), 221(1) 110-122.

Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

Bilinski P., Albert P. S., Berg J. J., Birchler J. A., Grote M. N., Lorant A., Quezada J., Swarts K., Yang J. and Ross-Ibarra J.
PLoS Genet
(2018), 14(5) e1007162.

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Weiss C. L., Pais M., Cano L. M., Kamoun S. and Burbano H. A.
BMC Bioinformatics
(2018), 19(1) 122.

The rate and potential relevance of new mutations in a colonizing plant lineage

Exposito-Alonso M., Becker C., Schuenemann V. J., Reiter E., Setzer C., Slovak R., Brachi B., Hagmann J., Grimm D. G., Chen J., Busch W., Bergelson J., Ness R. W., Krause J., Burbano H. A. and Weigel D.
PLoS Genet
(2018), 14(2) e1007155.

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

Exposito-Alonso M., Vasseur F., Ding W., Wang G., Burbano H. A. and Weigel D.
Nat Ecol Evol
(2018), 2(2) 352-358.

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

Swarts K., Gutaker R. M., Benz B., Blake M., Bukowski R., Holland J., Kruse-Peeples M., Lepak N., Prim L., Romay M. C., Ross-Ibarra J., Sanchez-Gonzalez J. J., Schmidt C., Schuenemann V. J., Krause J., Matson R. G., Weigel D., Buckler E. S. and Burbano H. A.
(2017), 357(6350) 512-515.

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.

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.
(2017), 356(6338) 605-608.

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), 18 321-356.

Extraction of ultrashort DNA molecules from herbarium specimens

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

Reinforcing plant evolutionary genomics using ancient DNA

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

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.

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.
(2015), 4.

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.

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.
(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)

Mining ancient microbiomes using selective enrichment of damaged DNA molecules

Weiß, C.L., Gansauge, M-T., Aximu-Petri, A., Meyer, M., Burbano, H.A.

bioarXiv preprint


A map of climate-change driven natural selection in Arabidopsis thaliana

Exposito-Alonso, M., Burbano, H.A., Bossdorf, O., Nielsen, R., Weigel, D.

bioRxiv preprint


A rainfall-manipulation experiment with 517 Arabidopsis accessions

Exposito-Alonso, M., [34 others], Burbano, H.A., Bossdorf, O., Weigel D.

bioRxiv preprint


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

Burbano, H.A.

Max Planck Society Yearbook 2014-2015.