Genomic Evolution and Climate


Peer-reviewed Articles / ISI


Bräuer A, Zhou Q, Grammbitter GLC, Schmalhofer M, Rühl M, Kaila VRI, Bode HB, Groll M (2020) Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis. Nature Chemistry12, 755–763.

Feurdean A, Vannière B, Finsinger W, Warren DL, Connor SC, Forrest M, Liakka J, Panait A, Andrič M, Bobek P, Carter VA, Davis BAS, Diaconu AC, Dietze E, Feeser I, Florescu G, Gałka M, Giesecke T, Jahns S, Jamrichová E, Kajukało K, Kaplan JO, Karpińska-Kołaczek M, Kołaczek P, Kuneš P, Kupriyanov D, Lamentowicz M, Lemmen C, Magyari EK, Marcisz K, Marinova E, Niamir A, Novenko E, Obremska M, Pędziszewska A, Pfeiffer M, Poska A, Rösch M, Słowiński M, Stancikaite M, Szal M, Święta-Musznicka J, Tanţău I, Theuerkauf M, Tonkov S, Valkó O, Vassiljev J, Veski S, Vincze I, Wacnik A, Wiethold J, Hickler T(2020) Fire hazard modulation by long-term dynamics in land cover and dominant forest type in eastern and central Europe. Biogeosciences 17, 1213–1230.

Greshake Tzovaras B, Segers FHID, Bicker A, Dal Grande F, Otte J, Anvar SY, Hankeln T, Schmitt I, Ebersberger I (2020) What is in Umbilicaria pustulata? A metagenomic approach to reconstruct the holo-genome of a lichen. Genome Biology and Evolution, 12, 309-324.

Gstöttl C, Stoldt M, Jongepier E, Bornberg‐Bauer E, Feldmeyer B, Heinze JR, Foitzik S (2020) Comparative analyses of caste, sex, and developmental stage‐specific transcriptomes in two Temnothorax ants. Ecology and Evolution, 10, 4193-4203.

Hoffmeister M, Gabriel D, Thines M, Maier W (2020) Epidemiology of sage downy mildew, Peronospora salviae-officinalis. European Journal of Plant Pathology, 156, 1147-1162.

Janke A, Lammers F, Schell T, Gupta DK, Petersen M, Nilsson MA, Wolf M, Coimbra RTF, De Raad J, Winter S, Prost S (2020) Education in the genomics era: Generating high-quality genome assemblies in university courses. GigaScience, 9.

Jiang Z, Carlantoni C, Allanki S, Ebersberger I, Stainier DYR (2020) Tek/Tie2 is not required for cardiovascular development in zebrafish. Development, dev.193029.

Kegler C, Bode HB (2020) Artificial Splitting of a Non‐Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angewandte Chemie, 3, 13463-13467.

Kennedy SR, Prost S, Overcast I, Rominger AJ, Gillespie RG, Krehenwinkel H (2020) High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities. Development Genes and Evolution, 230, 185-201.

Knöbel L, Breusing C, Bayer T, Sharma V, Hiller M, Melzner F, Stuckas H (2020) Comparative de novo assembly and annotation of mantle transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus). Marine Genomics, 51, 100700.

Körner M, Vogelweith F, Libbrecht R, Foitzik S, Feldmeyer B, Meunier JL (2020) Offspring reverse transcriptome responses to maternal deprivation when reared with pathogens in an insect with facultative family life. Proceedings of the Royal Society B: Biological Sciences, 287, 20200440.

Krajcarz M, Krajcarz MT, Baca M, Baumann C, Van Neer W, Popović D, Sudoł-Procyk M, Wach B, Wilczyński J, Wojenka M, Bocherens H (2020) Ancestors of domestic cats in Neolithic Central Europe – isotopic evidence of a synanthropic diet. PNAS, 117, 1771-1779.

Le NH, Peters K, Espaillat A, Sheldon JR, Gray J, Di Venanzio G, Lopez J, Djahanschiri B, Mueller EA, Hennon SW, Levin PA, Ebersberger I, Skaar EP, Cava F, Vollmer W, Feldman MF (2020) Peptidoglycan editing provides immunity to Acinetobacter baumannii during bacterial warfare. Science Advances, 6, eabb5614.

Lipson M, Ribot I, Mallick S, Rohland N, Olalde I, Adamski N, Broomandkhoshbacht N, Lawson AM, Lopez S, Oppenheimer J, Stewardson K, Asombang R, Bocherens H, Bradman N, Cornelissen E, Crevecoeur I, Lavachery P, de Maret P, Mindzie CM, et al. EA, Reich D (2020) Ancient West African foragers in the context of deep human genetic history. Nature, 577, 665-670.

Loog L, Thalmann O, Sinding MHS, Schuenemann VJ, Perri A, Germonpre M, Bocherens H, et al. EA, Manica A (2020) Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia. Molecular Ecology, 162, 2015.

Machado RAR, Thönen L, Arce CCM, Theepan V, Prada F, Wüthrich D, Robert CAM, Vogiatzaki E, Shi YM, Schaeren OP, Notter M, Bruggmann RM, Hapfelmeier S, Bode HB, Erb M (2020) Engineering bacterial symbionts of nematodes improves their biocontrol potential to counter the western corn rootworm. Nature Biotechnology, 38, 600-608.

Merges D, Balint M, Schmitt I, Manning P, Neuschulz EL (2020) High throughput sequencing combined with null model tests reveals specific plant‐fungi associations linked to seedling establishment and survival. Journal of Ecology, 108, 574-585.

Mikaeeli S, Susan‐Resiga D, Girard E, Ben Djoudi Ouadda A, Day R, Prost S, Seidah NG (2020) Functional analysis of natural PCSK 9 mutants in modern and archaic humans. The FEBS Journal, 287, 515-528.

Mishra B, Ploch S, Runge F, Schmuker A, Xia X, Gupta DK, Sharma R, Thines M (2020) The Genome of Microthlaspi erraticum (Brassicaceae) Provides Insights into the Adaptation to Highly Calcareous Soils. Frontiers in Plant Science, 11.

Moodley Y, Westbury MV, Russo IRM, Gopalakrishnan S, Rakotoarivelo A, Olsen RA, Prost S, Tunstall T, Ryder OA, Dalén L, Bruford MW, Harris K (2020) Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros. Molecular Biology and Evolution 37, 3105–3117.

Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de los Rios MA, Estrada-de los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Hedlund BP, Reysenbach AL (2020) Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5, 987-994.

Naito YI, Meleg IN, Robu M, Drucker DG, Wißing C, Hofreiter M, Barlow A, Bocherens H (2020) Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis. Scientific Reports, 10.

Paule J, Heller S, Maciel JR, Monteiro RF, Leme EMC, Zizka G (2020) Early diverging and core Bromelioideae (Bromeliaceae) reveal contrasting patterns of genome size evolution and polyploidy. Frontiers in Plant Science, 11, 1295.

Pfenninger M, Foucault Q (2020) Genomic processes underlying rapid adaptation of a natural Chironomus riparius population to unintendedly applied experimental selection pressures. Molecular Ecology, 29, 536-548.

Pizarro D, Divakar PK, Grewe F, Crespo A, Dal Grande F, Lumbsch HT, Stajich J (2020) Genome-wide analysis of biosynthetic gene cluster reveals correlated gene loss with absence of usnic acid in lichen forming fungi. Genome Biology and Evolution, 12, 1858–1868.

Prost S, Petersen M, Grethlein M, Hahn SJ, Kuschik-Maczollek N, Olesiuk ME, Reschke JO, Schmey TE, Zimmer C, Gupta DK, Schell T, Coimbra R, De Raad J, Lammers F, Winter S, Janke A (2020) Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master’s Course. Genes|Genomes|Genetics, 10, 2179-2183.

Riaz M, Kuemmerlen M, Wittwer C, Cocchiararo B, Khaliq I, Pfenninger M, Nowak C (2020) Combining environmental DNA and species distribution modeling to evaluate reintroduction success of a freshwater fish. Ecological Applications, 30, e02034.

Rolshausen G, Hallmann U, Dal Grande F, Otte J, Knudsen K, Schmitt I (2020) Expanding the mutualistic niche: parallel symbiont turnover along climatic gradients. The Royal Society, 287, 1924.

Roodgar M, Babveyh A, Huong L, Zhou W, Sinha R, Lee H, Hanks JB, Avula M, Jiang L, Lee H, Song G, Chaib H, Weissman IL, Batzoglou S, Holmes S, Smith DG, Mankowski JL, Prost S, Snyder MP (2020) Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. GigaScience, 9, giaa069.

Schiessl SV, Quezada-Martinez D, Orantes-Bonilla M, Snowdon RJ (2020) Transcriptomics reveal high regulatory diversity of drought tolerance strategies in a biennial oil crop. Plant Science, 297, 1-12.

Schmidt H, Waldvogel AM, Hellmann SRL, Feldmeyer B, Hankeln T, Pfenninger M (2020) A high-quality genome assembly from short and long reads for the non-biting midge Chironomus riparius (Diptera). Genes, Genomes, Genetics, 10, 1151-1157.

Seah A, Lim MCW, McAloose D, Prost S, Seimon TA (2020) MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples. Genes, 11, 445.

Sheffer MM, Uhl G, Prost S, Lueders T, Urich T, Bentsson MM (2020) Tissue- and Population-Level Microbiome Analysis of the Wasp Spider Argiope bruennichi Identified a Novel Dominant Bacterial Symbiont. Miccroorganisms, 19, E8.

Smith HB, Dal Grande F, Muggia L, Keuler R, Divakar PK, Grewe F, Schmitt I, Lumbsch HT, Leavitt SD (2020) Metagenomic data reveal diverse fungal and algal communities associated with the lichen symbiosis. Symbiosis, 82, 133-147.

Thines M, Buaya A, Ploch S, Naim YB, Cohen Y (2020) Downy mildew of lavender caused by Peronospora belbahrii in Israel. Mycological Progress, 19, 1537-1543.

von Reumont BRM, Lüddecke T, Timm T, Lochnit GN, Vilcinskas A, von Döhren JR, Nilsson MA (2020) Proteo-Transcriptomic Analysis Identifies Potential Novel Toxins Secreted by the Predatory, Prey-Piercing Ribbon Worm Amphiporus lactifloreus. Marine Drugs, 18, 407.

Waldvogel AM, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M (2020) Evolutionary genomics can improve prediction of species’ responses to climate change. Evolution Letters.

Waldvogel AM, Schreiber D, Pfenninger M, Feldmeyer B (2020) Climate Change Genomics Calls for Standardized Data Reporting. Frontiers in Ecology and Evolution, 8.

Watsa M, Erkenswick GA, Pomerantz A, Prost S (2020) Portable sequencing as a teaching tool in conservation and biodiversity research. PLOS Biology, 18, e3000667.

Watsa M, Prost S (2020) Rigorous wildlife disease surveillance. Science, 369, 145-147.

Watzel J, Hacker C, Duchardt-Ferner E, Bode HB, Wöhnert J (2020) A New Docking Domain Type in the Peptide-Antimicrobial-Xenorhabdus Peptide Producing Nonribosomal Peptide Synthetase from Xenorhabdus bovienii. ACS Chemical Biology, 15, 982-989.

Xie ZJ, Yao, HF, Potapov M, Dong J, Wu DH, Scheu S, Sun X (2020) The complete mitochondrial genome of an enigmatic predaceous springtail Metisotoma macnamarai from northeast China. Mitochondrial DNA Part B Resources.

Zając KS, Hatteland BRA, Feldmeyer B, Pfenninger M, Filipiak A, Noble LR, Lachowska-Cierlik D (2020) A comprehensive phylogeographic study of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Pulmonata: Arionidae) in Europe. Organisms Diversity & Evolution, 20, 37-50.


Alleman A, Stoldt M, Feldmeyer B, Foitzik S (2019) Tandem‐running and scouting behaviour are characterized by up‐regulation of learning and memory formation genes within the ant brain. Molecular Ecology, 28, 2342-2359.

Armaleo D, Müller O, Lutzoni FO, Andrésson LS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi PT, Talbot NJ, Veneault-Fourrey C, Xavier BB (2019) The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics, 20.

Bandini D, Oertel B, Ploch SAli T, Vauras J, Schneider A, Scholler M, Eberhardt U, Thines M (2019) Revision of some central European species of Inocybe (Fr.: Fr.) Fr. subgenus Inocybe, with the description of five new species. Mycological Progress, 8, 247-294.

Bode E, Heinrich AK, Hirschmann M, Abebew D, Shi YN, Vo TD, Wesche F, Shi YM, Grün PSimonyi S, Keller N, Engel Y, Wenski S, Bennet R, Beyer S, Bischoff I, Buaya A, Brandt S, Cakmak I, Çimen H, Eckstein S, Frank D, Fürst R, Gand M, Geisslinger G, Hazir S, Henke M, Heermann R, Lecaudey V, Schäfer W, Schiffmann S, Schüffler A, Schwenk R, Skaljac M, Thines E, Thines M, Ulshöfer T, Vilcinskas A, Wichelhaus TA, Bode HB (2019) Promoter Activation in Δhfq Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing. Angewandte Chemie International Edition, 58, 18957-18963.

Buaya A, Kraberg A, Thines M (2019) Dual culture of the oomycete Lagenisma coscinodisci Drebes and Coscinodiscus diatoms as a model for plankton/parasite interactions. Helgoland Marine Research, 73.

Cornetti L, Fields PD, Van Damme K, Ebert D (2019) A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae. Molecular Phylogenetics and Evolution, 137, 250-262.

Dapporto L, Cini A, Vodă R, Dincă V, Wiemers M, Menchetti M, Magini G, Talavera G, Shreeve T, Bonelli S, Casacci LP, Balletto E, Scalercio S, Vila R (2019) Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies. Molecular Ecology Resources, 19, 1623-1636.

Foucault QWieser AWaldvogel AMPfenninger M (2019) Establishing laboratory cultures and performing ecological and evolutionary experiments with the emerging model species Chironomus riparius. Journal of Applied Entomology, 143, 584-592.

Frank AC, Ebersberger S, Fink AF, Lampe S, Weigert A, Schmid T, Ebersberger I, Syed SN, Brüne B (2019) Apoptotic tumor cell-derived microRNA-375 uses CD36 to alter the tumor-associated macrophage phenotype. Nature Communications, 10.

Franke K, Karl I, Centeno TP, Feldmeyer B, Lassek C, Oostra V, Riedel K, Stanke M, Wheat CW, Fischer K (2019) Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation. BMC Evolutionary Biology, 19.

Goodman KR, Prost S, Bi K, Brewer MS, Gillespie RG (2019) Host and geography together drive early adaptive radiation of Hawaiian planthoppers. Molecular Ecology, 28, 4513-4528.

Gretzinger J, Molak M, Reiter E, Pfrengle S, et al. EA, Conard NJ, et al. EA, Drucker DG, et al. EA, Bocherens H, Schuenemann VJ (2019) Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear. Scientific Reports, 9, 10700.

Hagh Doust N, Safaie N, Schmitt I, Otte J, Bálint MS, Santini A (2019) Culture‐based methods using low‐temperature incubation revealed cold‐adapted fungal endophytes from semiarid forests. Forest Pathology, e12515.

Hartke JSchell T, Jongepier E, Schmidt H, Sprenger PP, Paule J, Bornberg-Bauer E, Schmitt T, Menzel F, Pfenninger MFeldmeyer B, Katz LA (2019) Hybrid Genome Assembly of a Neotropical Mutualistic Ant. Genome Biology and Evolution, 11, 2306-2311.

Hartke J, Sprenger PP, Sahm J, Winterberg H, Orivel JRM, Baur H, Beuerle T, Schmitt TFeldmeyer B, Menzel F (2019) Cuticular hydrocarbons as potential mediators of cryptic species divergence in a mutualistic ant association. Ecology and Evolution, 9, 9160-9176.

Hassett BT, Thines MBuaya APloch S, Gradinger R (2019) A glimpse into the biogeography, seasonality, and ecological functions of arctic marine Oomycota. IMA Fungus, 1.

Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P (2019) The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biology, 20.

Jain A, von Haeseler A, Ebersberger I (2019) The evolutionary traceability of proteins. Genome Biology and Evolution, 11, 531-545.

Kaur R, Stoldt M, Jongepier E, Feldmeyer B, Menzel F, Bornberg-Bauer E, Foitzik S (2019) Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite. Philosophical Transactions of the Royal Society B: Biological Sciences, 374, 20180192.

Kohlmeier P, Alleman AR, Libbrecht R, Foitzik S, Feldmeyer B (2019) Gene expression is more strongly associated with behavioural specialization than with age or fertility in ant workers. Molecular Ecology, 28, 658-670.

Kotrade P, Sehr EM, Wischnitzki E, Brüggemann W (2019) Comparative transcriptomics-based selection of suitable reference genes for normalization of RT-qPCR experiments in drought-stressed leaves of three European Quercus species. Tree Genetics & Genomes, 15, UNSP 38.

Krehenwinkel H, Pomerantz A, Henderson JB, Kennedy SR, Lim JY, Swamy V, Shoobridge JD, Graham N, Patel NH, Gillespie RG, Prost S (2019) Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale. GigaScience, 8.

Mangaravite R, Silveira TC, Huamán‐Mera A, Oliveira LO, Muellner‐Riehl AN, Schnitzler J (2019) Genetic diversity of Cedrela fissilis (Meliaceae) in the Brazilian Atlantic Forest reveals a complex phylogeographic history driven by Quaternary climatic fluctuations. Journal of Systematics and Evolution, 57, 655-669.

Meyer C, Lopes BA, Caye-Eude AL, Cavé HLN, Arfeuille C, Cuccuini W, Sutton R, Venn NC, Oh SH, Tsaur G, Escherich G, Feuchtinger T, Kosasih HJ, Khaw SL, Ekert PG, Pombo-de-Oliveira MS, Bidet A, Djahanschiri B, Ebersberger I, Zaliova M, Zuna J, Zermanova Z, Juvonen V, Grümayer RP, Fazio G, Cazzaniga G, Larghero P, Emerenciano M, Marschalek R (2019) Human MLL/KMT2A gene exhibits a second breakpoint cluster region for recurrent MLL–USP2 fusions. Leukemia, 33, 2306-2340.

Müller R, Shinn CN, Waldvogel AM, Oehlmann JR, Ribeiro R, Moreira-Santos M (2019) Long-term effects of the fungicide pyrimethanil on aquatic primary producers in macrophyte-dominated outdoor mesocosms in two European ecoregions. Science of The Total Environment, 665, 982-994.

Negroni MA, Foitzik S, Feldmeyer B (2019) Long-lived Temnothorax ant queens switch from investment in immunity to antioxidant production with age. Scientific Reports, 9.

Pizarro D, Dal Grande F, Leavitt SD, Dyer PS, Schmitt I, Crespo A, Thorsten Lumbsch H, Divakar PK, Barluenga M (2019) Whole-Genome Sequence Data Uncover Widespread Heterothallism in the Largest Group of Lichen-Forming Fungi. Genome Biology and Evolution, 11, 721-730.

Radchuk V, Reed T, Teplitsky CL, van de Pol M, Charmantier A, Hassall C, Adamík P, Adriaensen F, Ahola MP, Arcese P, Miguel Avilés JS, Balbontin J, Berg KS, Borras A, Burthe S, Clobert J, Dehnhard N, de Lope F, Dhondt AA, Dingemanse NJ, Doi H, Eeva T, Fickel J, Filella I, Fossøy F, Goodenough AE, Hall SJG, Hansson B, Harris M, Hasselquist D, Hickler T, Joshi J, Kharouba H, Martínez JG, Mihoub JB, Mills JA, Molina-Morales M, Moksnes A, Ozgul A, Parejo D, Pilard P, Poisbleau M, Rousset F, Rödel MO, Scott D, Senar JC, Stefanescu C, Stokke BRG, Kusano T, Tarka M, Tarwater CE, Thonicke K, Thorley J, Wilting A, Tryjanowski P, Merilä J, Sheldon BC, Pape Møller A, Matthysen E, Janzen F, Dobson FS, Visser ME, Beissinger SR, Courtiol A, Kramer-Schadt S (2019) Adaptive responses of animals to climate change are most likely insufficient. Nature Communications, 10.

Rey-Iglesia A, García-Vázquez A, Treadaway EC, van der Plicht J, Baryshnikov GF, Szpak P, Bocherens H, Boeskorov GG, Lorenzen ED (2019) Evolutionary history and palaeoecology of Brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains. Scientific Reports, 9.

Sharma R, Ökmen B, Doehlemann G, Thines M (2019) Saprotrophic yeasts formerly classified as Pseudozyma have retained a large effector arsenal, including functional Pep1 orthologs. Mycological Progress, 18, 763-768.

Singh G, Kukwa M, Dal Grande F, Łubek A, Otte JR, Schmitt I (2019) A Glimpse into Genetic Diversity and Symbiont Interaction Patterns in Lichen Communities from Areas with Different Disturbance Histories in Białowieża Forest, Poland. Microorganisms, 7, 335.

Smith AB, Godsoe W, Rodríguez-Sánchez F, Wang HH, Warren D (2019) Niche Estimation Above and Below the Species Level. Trends in Ecology & Evolution, 34, 260-273.

Smith O, Dunshea GJ, Sinding MHS, Fedorov S, Germonpre M, Bocherens H, Gilbert MTP (2019) Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. PLOS Biology, 17, e3000166.

Sprenger PP, Hartke JFeldmeyer B, Orivel JRM, Schmitt T, Menzel F (2019) Influence of Mutualistic Lifestyle, Mutualistic Partner, and Climate on Cuticular Hydrocarbon Profiles in Parabiotic Ants. Journal of Chemical Ecology, 45, 741-754.

Tanaka S, Schweizer G, Rössel N, Fukada F, Thines M, Kahmann R (2019) Neofunctionalization of the secreted Tin2 effector in the fungal pathogen Ustilago maydis. Nature Microbiology, 4, 251-257.

Thines M (2019) An evolutionary framework for host shifts – jumping ships for survival. New Phytologist, 224, 605-617.

Tietgen M, Kramer JS, Brunst S, Djahanschiri B, Wohra S, Higgins PG, Weidensdorfer M, Riedel-Christ S, Pos KM, Gonzaga A, Steglich M, Nübel U, Ebersberger I, Proschak E, Göttig S (2019) Identification of the novel class D β-lactamase OXA-679 involved in carbapenem resistance in Acinetobacter calcoaceticus. Journal of Antimicrobial Chemotherapy, 74, 1494-1502.

Vallet M, Baumeister TUH, Kaftan F, Grabe V, Buaya A, Thines M, Svatoš A, Pohnert G (2019) The oomycete Lagenisma coscinodisci hijacks host alkaloid synthesis during infection of a marine diatom. Nature Communications, 10.

Wieser AReuss FNiamir A, Müller R, O’Hara RBPfenninger M (2019) Modelling seasonal dynamics, population stability, and pest control in Aedes japonicus japonicus (Diptera: Culicidae). Parasites & Vectors, 12, 142.

Winter SCoimbra RTF, Bronec A, Hay C, Salb AL, Fennessy J, Janke A (2019) Species assignment and conservation genetics of giraffe in the Republic of Malawi. Conservation Genetics, 20, 665-670.


Aime MC, Castlebury LA, Abbasi M, Begerow D, Berndt R, Kirschner R, Marvanová L, Ono Y, Padamsee M, Scholler M, Thines M, Rossman AY (2018) Competing sexual and asexual generic names in Pucciniomycotina and Ustilaginomycotina (Basidiomycota) and recommendations for use. IMA Fungus, 9, 75-89.

Alleman A, Feldmeyer B, Foitzik S (2018) Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes. Scientific Reports, 8, 1951.

Arnason U, Lammers FKumar VNilsson MAJanke A (2018) Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Science Advances, 4, eaap9873.

Ashoub A, Müller N, Jiménez-Gómez JM, Brüggemann W (2018) Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions. Physiologia Plantarum, 163, 18-29.

Bálint MSPfenninger M, Grossart HP, Taberlet P, Vellend M, Leibold MA, Englund GR, Bowler D (2018) Environmental DNA Time Series in Ecology. Trends in Ecology & Evolution, 33, 945-957.

Barth MBBuchwalder K, Kawahara AY, Zhou X, Liu S, Krezdorn N, Rotter B, Horres R, Hundsdoerfer AK (2018) Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes. Frontiers in Zoology, 15, 20.

Bennett RM, Devanadera MK, Dedeles GRThines M (2018) A revision of Salispina, its placement in a new family, Salispinaceae (Rhipidiales), and description of a fourth species, S. hoi sp. nov. IMA Fungus, 9, 259-269.

Blaschke U, Suwono B, Zafari S, Ebersberger I, Skiebe E, Jeffries CM, Svergun DI, Wilharm G (2018) Recombinant production of A1S_0222 from Acinetobacter baumannii ATCC 17978 and confirmation of its DNA-(adenine N6)-methyltransferase activity. Protein Expression and Purification, 151, 78-85.

Brandrud TE, Schmidt-Stohn G, Liimatainen K, Niskanen T, Frøslev TG, Soop K, Bojantchev D, Kytövuori I, Jeppesen TS, Bellù F, Saar GN, Oertel B, Ali TThines M, Dima BL (2018) Cortinarius sect. Riederi: taxonomy and phylogeny of the new section with European and North American distribution. Mycological Progress, 17, 1323-1354.

Choi YJ, Kruse JThines M (2018) Hyaloperonospora erucae sp. nov. (Peronosporaceae; Oomycota), the downy mildew pathogen of arugula (Eruca sativa). European Journal of Plant Pathology, 151, 549-555.

Chueca L, Gomez-Moliner B, Madeira M, Pfenninger M (2018) Molecular phylogeny of Candidula (Geomitridae) land snails inferred from mitochondrial and nuclear markers reveals the polyphyly of the genus. Molecular Phylogenetics and Evolution, 118, 257-268.

Dal Grande FMeiser A, Greshake Tzovaras B, Otte JREbersberger ISchmitt I (2018) The draft genome of the lichen-forming fungus Lasallia hispanica (Frey) Sancho & A. Crespo. Lichenologist, 50, 329-340.

Dal Grande FRolshausen G, Divakar PK, Crespo A, Otte JSchleuning MSchmitt I (2018) Environment and host identity structure communities of green algal symbionts in lichens. New Phytologist, 217, 277-289.

Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricop M, Vandepoele K, Ebersberger I, Blake J, Breis JTF, Boeckmann B, Gabaldon T, Sonnhammer E, Dessimoz C, Lewis S (2018) Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics, 34, 323-329.

Foucault QWieser AWaldvogel AMFeldmeyer BPfenninger M (2018) Rapid adaptation to high temperatures in Chironomus riparius. Ecology and Evolution, 8, 12780-12789.

Glynou K, Nam BThines M, Maciá-Vicente JG (2018) Facultative root‐colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species. New Phytologist, 217, 1190-1202.

Gupta DK, Rühl M, Mishra B, Kleofas V, Hofrichter M, Herzog R, Pecyna MJ, Sharma R, Kellner H, Hennicke FThines M (2018) The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes. BMC Genomics, 19, 48.

Gupta S, Jain A, Syed SN, Snodgrass RG, Pflüger-Müller B, Leisegang MS, Weigert A, Brandes RP, Ebersberger I, Brüne B, Namgaladze D (2018) IL-6 augments IL-4-induced polarization of primary human macrophages through synergy of STAT3, STAT6 and BATF transcription factors. OncoImmunology, 7, e1494110.

Kelleher ES, Azevedo RBR, Zheng Y (2018) The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element. Genome Biology and Evolution, 3038-3057.

Kersken D, Kocot K, Janussen DSchell TPfenninger MMartinez Arbizu P (2018) First insights into the phylogeny of deep-sea glass sponges (Hexactinellida) from polymetallic nodule fields in the Clarion-Clipperton Fracture Zone (CCFZ), northeastern Pacific. Hydrobiologia, 811, 283-293.

Kohlmeier P, Feldmeyer B, Foitzik S (2018) Vitellogenin-like A–associated shifts in social cue responsiveness regulate behavioral task specialization in an ant. PLOS Biology, 16, e2005747.

Kruse J, Dietrich W, Zimmermann H, Klenke F, Richter U, Richter H, Thines M (2018) Ustilago species causing leaf-stripe smut revisited. IMA Fungus, 9, 49-73.

Kukwa M, Schmitt I, Ertz D (2018) Ochrolechia incarnata comb. nov. (Lecanoromycetes, Ascomycota), a distinct species of the O. parella group from Europe and Macaronesia. Phytotaxa, 371, 119.

Lendvay B, Bálint MS, Pál I, Vincze I, Orbán I, Magyari EK (2018) Plant macrofossils from lake sediment as the material to assess ancient genetic diversity: Did deforestation influence Norway spruce (Picea abies) in the South Carpathians? Quaternary International, 477, 106-116.

Mathieson I, Alpaslan Roodenberg S, Szécsényi-Nagy A, Rohland N, Mallick S, Broomandkhoshbacht N, Cheronet O, Fernandes D, Ferry M, Gamarra B, Haak W, Harney E, Michel M, Nägele K, Novak M, Olade I, Oppenheimer J, Patterson N, Posth C, Sirak K, Stewardson K, Vai S, Alexandrov S, Alt KW, Andreescu R, Ash A, Atanassova N, Bacvarov K, Bocherens HBolus M, Boroneant A, Boyadzhiev Y, Budnik A, Burmaz J, Chohadzhiev S, Conard NJ, Cottiaux R, Cupillard C, Drucker DG, Elenski N, Francken M, Galabova B, Ganetovski G, Gely B, Hajdu T, Harvati K, et. al. EA, Krause J, Pinhasi R, Reich D (2018) The Genomic History of Southeastern Europe. Nature, 555, 197-210.

Menzel F, Zumbusch M, Feldmeyer B (2018) How ants acclimate: Impact of climatic conditions on the cuticular hydrocarbon profile. Functional Ecology, 32, 657-666.

Merges DBalint MSchmitt IBöhning-Gaese KNeuschulz EL (2018) Spatial patterns of pathogenic and mutualistic fungi across the elevational range of a host plant. Journal of Ecology, 106, 1545-1557.

Milián-García Y, Russello MA, Castellanos-Labarcena J, Cichon MKumar V, Espinosa G, Rossi N, Mazzotti F, Hekkala E, Amato G, Janke A (2018) Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles. PeerJ, 6, e5836.

Mirzaee MR, Ploch SNigrelli L, Sajedi S, Thines M (2018) First confirmed report of white blister rust disease caused by Albugo candida on Isatis emarginata. Journal of Plant Pathology, 100, 587-587.

Mishra BChoi YJThines M (2018) Phylogenomics of Bartheletia paradoxa reveals its basal position in Agaricomycotina and that the early evolutionary history of basidiomycetes was rapid and probably not strictly bifurcating. Mycological Progress, 17, 333-341.

Mishra BGupta DKPfenninger MHickler T, Langer E, Nam B, Paule J, Sharma R, Ulaszewski B, Warmbier J, Burczyk J, Thines M (2018) A reference genome of the European beech (Fagus sylvatica L.). GigaScience, 7, giy063.

Moros-Nicolás C, Chevret P, José Izquierdo-Rico M, Holt W, Esteban-Díaz D, López-Béjar M, Martínez-Nevado E, Nilsson MA, Ballesta J, Avilés M (2018) Composition of marsupial zona pellucida: a molecular and phylogenetic approach. Reproduction, Fertility and Development, 30, 721-733.

Müller R, Knautz T, Vollroth S, Berger RKreß AReuss F, Groneberg DA, Kuch U (2018) Larval superiority of Culex pipiens to Aedes albopictus in a replacement series experiment: prospects for coexistence in Germany. Parasites & Vectors, 11, 80.

Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A (2018) Speciation generates mosaic genomes in kangaroos. Genome Biology and Evolution, 10, 33-44.

Park JH, Thines M, Lee HB, Shin HD, Choi YJ (2018) Bremia polycephala and Bremia sawadae spp. nov. (Peronosporaceae; Oomycota), parasitic to Northeast Asian Asteraceae. Nova Hedwigia, 107, 303-314.

Paul FOtte JRSchmitt IDal Grande F (2018) Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens. Scientific Reports, 8, 8624.

Paul F, Otte JRSchmitt IGrande FD (2018) Author Correction: Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens. Scientific Reports, 8, 17229.

Ploch SChoi YJThines M (2018) The only known white blister rust on a basal angiosperm is a member of the genus Albugo. Organisms Diversity & Evolution, 18, 63-69.

Reuss FWieser ANiamir ABálint MSKuch UPfenninger MMüller R (2018) Thermal experiments with the Asian bush mosquito (Aedes japonicus japonicus) (Diptera: Culicidae) and implications for its distribution in Germany. Parasites & Vectors, 11, 81.

Rolshausen GDal Grande FSadowska-Des ADOtte JSchmitt I (2018) Quantifying the climatic niche of symbiont partners in a lichen symbiosis indicates mutualist-mediated niche expansions. Ecography, 41, 1380-1392.

Santonja M, Foucault Q, Rancon AS, Gauquelin T, Fernandez C, Baldy V, Mirleau P (2018) Contrasting responses of bacterial and fungal communities to plant litter diversity in a Mediterranean oak forest. Soil Biology & Biochemistry, 125, 27-36.

Sapp M, Ploch S, Fiore-Donne AM, Bonkowski M, Rose LE (2018) Protists are an integral part of the Arabidopsis thaliana microbiome. Environmental microbiology, 20, 30-43.

Scharf KD, Berberich T, Ebersberger I, Nover L (2018) Corrigendum to “The plant heat stress transcription factor (Hsf) family: Structure, function and evolution” [BBAGRM 1819 (2) 104–119]. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms, 1861, 60.

Singh G, Dal Grande F, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys, 36, 1-19.

Thines M (2018) Oomycetes. Current Biology, 28, R812-R813.

Thines M, Crous PW, Aime MC, Aoki T, Cai L, Hyde KD, Miller AN, Zhang N, Stadler M (2018) Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus, 9, 177-183.

Tills O, Truebano M, Feldmeyer BPfenninger M, Morgenroth H, Schell T, Rundle SD (2018) Transcriptomic responses to predator kairomones in embryos of the aquatic snail Radix balthica. Ecology and Evolution, 8, 11071-11082.

Tran NV, Greshake Tzovaras B, Ebersberger I, Schwartz R (2018) PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles. Bioinformatics, 34, 3041-3043.

Waldvogel AWieser ASchell TPatel SSchmidt H, Hankeln T, Feldmeyer BPfenninger M (2018) The genomic footprint of climate adaptation in Chironomus riparius. Molecular Ecology, 27, 1439-1456.

Winter S, Fennessy J, Janke A (2018) Limited introgression supports division of giraffe into four species. Ecology and Evolution, 8, 10156-10165.

Zheng Y, Janke A (2018) Gene flow analysis method, the D-statistic, is robust in a wide parameter space. BMC Bioinformatics, 19, 10.

Peer-reviewed Articles / Non-ISI



Kotrade P, Werner A, Ebersberger I, Brüggemann W (2020) Comparative transcriptomics reveal insights into the drought response of the three Panicum species P. bisulcatum, P. laetum and P. turgidum. Plant Gene, 23, 100232.


Berz J, Simm S, Schuster S, Scharf KD, Schleiff E, Ebersberger I (2019) HEATSTER: A Database and Web Server for Identification and Classification of Heat Stress Transcription Factors in Plants. Bioinformatics and Biology Insights, 13, 117793221882136.

Erzinger F, Rotter B, Kretzdorn N, Pauls SU (2019) Gene expression profiling in the aquatic caddisfly larvae Micropterna lateralis (Insecta: Trichoptera) in relation to stream drying. Zoosymposia, 54-58.


Winter S, Fennessy J, Fennessy S, Janke A (2018) Matrilineal population structure and distribution of the Angolan giraffe in the Namib desert and beyond. Ecological Genetics and Genomics, 7-8, 1-5.

Articles in other Journals













Prinz R, Thines M (2019) 3rd Wild Plant Pathosystems Conference, Primedia E-launch LLC, Germany, 96pp.



Book section







Jain A, Roustan V, Weckwerth W, Ebersberger I (2018) Studying AMPK in an Evolutionary Context. In: Neumann D, Benoit V (Eds) AMPK Methods and Protocols. Springer, 111-142.

Lenz OKWilde VRiegel W (2018) Paläoklima – aus der Vergangenheit für die Zukunft lernen. In: Schaal SFKSmith KTHabersetzer JR (Eds) Messel – Ein fossiles Tropenökosystem. E. Schweizerbart‘sche Verlagsbuchhandlung, 17-24.

Lenz OKWilde VRiegel W (2018) Paleoclimate – Learning from the Past for the Future. In: Smith KTSchaal SFKHabersetzer JR (Eds) Messel – An ancient Greenhouse Ecosystem. E. Schweizerbart‘sche Verlagsbuchhandlung, 17-24.

Müller RReuss F, Kendrovski V, Montag D (2018) Vector-borne diseases. In: Marselle MR, Stadler J, Korn K, Irvine KN, Bonn A (Eds) Biodiversity and Health in the face of Climate Change. Springer, 67-90.

Work and Discussion Paper





van Dijk J, Carss D, Keune H, Vikström S, Flandroy L, Rook G, Haahtela T, Mehring M, Birzle-Harder B, Reuss F, Müller R, Luque S, Garcia Rodrigues JO (2019) Invited background document on biodiversity and health for the Global Sustainable Development Report 2019 drafted by the Independent Group of Scientists. Norwegian Institute for Nature Research (nina).