Comparative Genomics

Our division “Comparative Genomics” revolves around a central question in genomics and evolutionary biology:

What is the genomic basis of phenotypic differences between species?

Our focus is explicitly on differences between species as opposed to differences within a species. We aim at discovering the genomic determinants of macroevolutionary trait differences, which is important to understand how nature’s spectacular phenotypic diversity has evolved. Our current focus is on studying the genomic basis of vertebrate traits that have potential applications in biomedicine or other fields.

To understand the molecular basis of biological diversity, we combine comparative genomics with genome sequencing and methods development. Our current research is interdisciplinary and includes 

  • sequencing reference-quality genomes and transcriptomes of selected species with interesting traits,
  • developing new computational approaches to align genes and genomes, to annotate genes and infer orthologs, to accurately detect relevant evolutionary changes in functional genomic regions, and to discover associations between genotype and phenotype,
  • running large-scale comparative genomic screens using existing and newly-sequenced genomes and our powerful methods toolbox to reveal the genomic basis of phenotypic adaptations and link phenotypic to genomic differences.
Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Grafik

News

2025

January

2024

October
September
  • Welcome to our new PhD student Alejandro Gonzales, who will work on gene annotation methods.
June
  • Welcome to our new postdoc Xueling Yi, who will work on dietary adaptations in bats.

2023

October
  • Michael has been awarded an ERC Synergy grant ‘BatProtect‘ to uncover the molecular mechanisms behind longevity and disease resistance in bats with three other PIs.
  • Leon was awarded a well-funded DFG grant to investigate genome evolution and population collapse in eels. Congrats !!
April
  • Huge congrats to Bogdan and the lab for the TOGA publication, now out in Science
February
  • Superathlete vs. couch potato: Scientific American featured our hummingbird story together with Nick Rohner’s cavefish work.
January

 

2022

October
  • Great to see 2 graduated PhD students moving on. Ekaterina does a postdoc at Harvard. Bogdan is a scientist at Quantgene (genomic medicine). All the best!!
August
July
  • Welcome to our new PhD student Yury Malovichko.
June
  • Attending EuroEvoDevo in Naples with 3 talks by lab members.
May
  • Huge congrats to Ekaterina Osipova, who did a great job defending her PhD.
April
  • We welcome Bernhard Bein as a new PhD student in the lab.
  • Welcome to our new Postdoc Shenglin Liu !!
March
February
  • Big congrats to Dimitris Kontopoulos for winning an EMBO Postdoc Fellowship.
January

2021

December
  • LOEWE-TBG successfully got funding for the next 3 years !!
November
  • Huge congrats to Bogdan Kirilenko, our TOGA master, for defending his PhD.
October
September
  • Ekaterina Osipova gave a great talk @EMBOEvolAnimalGenomes on gene losses in hummingbirds and metabolic adaptation
August
  • Welcome to our new Postdoc Leon Hilgers !!
May
  • Lab move to TBG and Senckenberg in Frankfurt

Selected Publications

Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium, Hiller M #. Integrating gene annotation with orthology inference at scale. Science, 380 (6643), eabn3107, 2023

Osipova E, Barsacchi R, Brown T, Sadanandan K, Gaede AH, Monte A, Jarrells J, Moebius C, Pippel M, Altshuler DL, Winkler S, Bickle M, Baldwin MW, Hiller M #. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science, 379(6628), 185-190, 2023 pdf of article

Blumer M, Brown T, Freitas MB, Destro AL, Oliveira JA, Morales A, Schell T, Greve C, Pippel M, Jebb D, Hecker N, Ahmed AW, Kirilenko BM, Foote M, Janke A, Lim BK, Hiller M #. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. Science Advances, 8 (12), eabm6494, 2022
press and blogs are listed at altmetric

Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, Winkler S, Jermiin LS, Skirmuntt EC, Katzourakis A, Burkitt-Gray L, Ray DA, Sullivan KAM, Roscito JG, Kirilenko BM, Dávalos LM, Corthals AP, Power ML, Jones G, Ransome RD, Dechmann D, Locatelli AG, Puechmaille SJ, Fedrigo O, Jarvis ED, Hiller M #, Vernes SC #, Myers EW #, Teeling EC #. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020
See also Nature Reviews Genetics highlight and Science feature. More press.

Huelsmann M, Hecker N, Springer MS, Gatesy J, Sharma V, Hiller M #. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Advances, 5(9), eaaw6671, 2019
some press: New York TimesScience NewsDiscover MagazineSmithsonianDaily HeraldGerman Radio
F1000 recommended

Hecker N, Sharma V, Hiller M #. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019

Roscito JG, Sameith K, Parra G, Langer BE, Petzold A, Moebius C, Bickle M, Rodrigues MT, Hiller M #. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolutionNature Communications, 9:4737, 2018

Lee JH, Lewis KM, Moural TW, Kirilenko B, Bogdanova B, Prange G, Koessl M, Huggenberger S, Kang C, and Hiller M #. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Advances, 4(9), eaat9660, 2018

Sharma V, Lehmann T, Stuckas H, Funke L, and Hiller M #. Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammalsPLoS Biology 16(6), e2005293, 2018
some Press: New York TimesSmithsonian MagazineInside ScienceScienmag

Sharma V, Hecker N, Roscito JG, Foerster L, Langer BE, and Hiller M #. A genomics approach reveals insights into the importance of gene losses for mammalian adaptationsNature Communications, 9(1), 1215, 2018

Nowoshilow S, Schloissnig S #, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M #, Tanaka EM #, Myers E. The axolotl genome and the evolution of key tissue formation regulatorsNature, 554(7690), 50-55, 2018.

Prudent X, Parra G, Schwede P, Roscito JG, Hiller M #. Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species’ phenotypic and genomic differences. Mol Biol Evol, 33(8), 2135-5, 2016.
See also MBE News.

Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, and Bejerano G. (2012): A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Reports, 2(4), 817-823. Read more on F1000

Contact

Thomas Hiller
Prof. Dr. Michael Hiller
Head of Comparative Genomics (SF)

Professor of Comparative Genomics
LOEWE Centre for Translational Biodiversity Genomics,
Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt &
Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany

SCIENTIFIC CAREER

since 09/2020
Professor of Comparative Genomics, LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Society for Nature Research & Goethe University, Frankfurt am Main, Germany

2018 – 2020
Senior Research Group Leader, jointly at the Max Planck Institute of Molecular Cell Biology and Genetics and the Max Planck Institute for the Physics of Complex Systems, Dresden

2011-2017
Research Group Leader, jointly at the Max Planck Institute of Molecular Cell Biology and Genetics and the Max Planck Institute for the Physics of Complex Systems, Dresden

2008-2011
Postdoctoral work at Stanford University, Department of Developmental Biology, USA

2007-2008
Postdoctoral work at University of Freiburg, Bioinformatics Group, Germany

2002-2006
PhD in Bioinformatics, University of Jena and University of Freiburg, Germany

AWARDS

2023
ERC Synergy Grant

2019
Young Investigator, Technical University Dresden

2013
German Life Science Award

2009-2011
Long-term Postdoc Fellowship from the Human Frontier Science Program (HFSP)

2008-2009
Postdoc fellowship from the German Research Foundation

Third party funding sources

Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Grafik
Comparative Genomics Research Projects