Genomic Evolution and Climate

Publications

Peer-reviewed Articles / ISI

2020

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

Merges DBalint MSchmitt IManning PNeuschulz 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.

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

Schmidt HWaldvogel 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.

2019

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.

2018

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.

2017

Bennett R, de Cock AWAM, Levesque CA, Thines M (2017) Calycofera gen. nov., an estuarine sister taxon to Phytopythium, Peronosporaceae. Mycological Progress, 16, 947-954.

Bennett RThines M (2017) Confirmation that Phytophthora insolita (Peronosporaceae) is present as a marine saprotroph on mangrove leaves and first report of the species for the Philippines. Nova Hedwigia, 105, 185-196.

Bennett RM, Dedeles GR, Thines M (2017) Phytophthora elongata (Peronosporaceae) is present as an estuarine species in Philippine mangrove. Mycosphere, 8, 959-967.

Blank-Landeshammer B, Kollipara L, Biss K, Pfenninger M, Malcow S, Shuvaev K, Zahedi RP, Sickmann A (2017) Combining de novo peptide sequencing algorithms, a synergistic approach to boost both identifications and confidence in bottom-up proteomics. Journal of Proteome Research, 16, 3209-3218.

Buaya A, Ploch S, Hanic L, Nam BNigrelli L, Kraberg A, Thines M (2017) Phylogeny of Miracula helgolandica gen. et sp. nov. and Olpidiopsis drebesii sp. nov., two basal oomycete parasitoids of marine diatoms, with notes on the taxonomy of Ectrogella-like species. Mycological Progress, 16, 1041-1050.

Choi YJThines M, Choi IY, Shin HD (2017) Perofascia is not monotypic: the description of the second taxon affecting the South American crop maca (Lepidium meyenii). Mycological Progress, 16, 857-864.

Choi YJ, Wong J, Runge F, Mishra B, Michelmore R, Thines M (2017) BrRxLR11 – a new phylogenetic marker with high resolution in the downy mildew genus Bremia and related genera. Mycological Progress, 16, 185-190.

Dal Grande FSharma RMeiser A, Rolshausen G, Büdel B, Mishra BThines MOtte JPfenninger MSchmitt I (2017) Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus. BMC Evolutionary Biology, 17, 93.

Dodt WGallus S, Phillips MJ, Nilsson MA (2017) Resolving kangaroo phylogeny and overcoming retrotransposon ascertainment bias. Scientific Reports, 7, 16811.

Dostál P, Fischer M, Chytrý M, Prati D (2017) No evidence for larger leaf trait plasticity in ecological generalists compared to specialists. Journal of Biogeography, 44, 511-521.

Feldmeyer B, Elsner D, Alleman A, Foitzik S (2017) Species-specific genes under selection characterize the coevolution of slavemaker and host lifestyles. BMC Evolutionary Biology, 17, 237.

Fellows Yates JA, Drucker DEG, Reiter E, Heumos S, Welker F, Münzel SC, Wojtal P, Lázničková-Galetová M, Conard NJ, Herbig A, Bocherens H, Krause J (2017) Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes. Scientific Reports, 7, 17714.

Fennessy J, Winter S, Reuss FKumar VNilsson MAVamberger MFritz UJanke A (2017) Response to “How many species of giraffe are there?”. Current Biology, 27, R137-R138.

Gent DH, Cohen Y, Runge F (2017) Homothallism in Pseudoperonospora humuli. Plant Pathology, 66, 1508-1516.

Glynou K, Tahir A, Kia SH, Thines M, Maciá-Vicente JG (2017) Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation. Molecular Ecology, 36, 4618-4630.

Gomez-Zeledon J, Grasse W, Runge F, Land A, Spring O (2017) TaqMan qPCR pushes boundaries for the analysis of millennial wood. Journal of Archaeological Science, 79, 53-61.

Görg M, Ploch SKruse J, Kummer V, Runge F, Choi YJThines M (2017) Revision of Plasmopara (Oomycota, Peronosporales) parasitic to Impatiens. Mycological Progress, 16, 791-799.

Herrmann MHenning-Lucass N, Cordellier M, Schwenk K (2017) A genotype-phenotype association approach to reveal thermal adaptation in Daphnia galeata. Journal of Experimental Zoology Part A – Ecological Genetics and Physiology, 327, 53-65.

Hof CFritz SA, Prinzinger R, Pfenninger MBöhning-Gaese KKhaliq I (2017) Phylogenetic signals in thermal traits remain stronger in the tropics if we can believe published physiological data. A reply to McKechnie et al., “Data quality problems undermine analyses of endotherm upper critical temperatures”. Journal of Biogeography, 44, 2427-2431.

Hof CKhaliq I, Prinzinger R, Böhning-Gaese KPfenninger M (2017) Global patterns of thermal tolerances and vulnerability of endotherms to climate change remain robust irrespective of varying data suitability criteria. Proceedings of the Royal Society B-Biological Sciences, 284, 20170232.

Iloh ACSchmidt MMuellner-Riehl AN, Ogundipe OT, Paule J (2017) Pleistocene refugia and genetic diversity patterns in West Africa: Insights from the liana Chasmanthera dependens (Menispermaceae). PLOS One, 12, e0170511.

Khaliq IBöhning-Gaese K, Prinzinger R, Pfenninger MHof C (2017) The influence of thermal tolerances on geographical ranges of endotherms. Global Ecology and Biogeography, 26, 650-668.

Kia SH, Glynou K, Nauss T, Thines M, Piepenbring M, Maciá-Vicente JG (2017) Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants. ISME Journal, 11, 777-790.

Kohlmeier P, Negroni MA, Kever M, Emmling S, Stypa H, Feldmeyer B, Foitzik S (2017) Intrinsic worker mortality depends on behavioral caste and the queens’ presence in a social insect. The Science of Nature – Naturwissenschaften, 104, 34.

Kokko H, Chaturvedi A, Croll D, Fischer MC, Guillaume F, Karrenberg S, Kerr B, Rolshausen G, Stapley J (2017) Can Evolution Supply What Ecology Demands? Trends in Ecology & Evolution, 32, 187-197.

Kreß AOppold AKuch UOehlmann JMüller R (2017) Cold tolerance of the Asian tiger mosquito Aedes albopictus and its response to epigenetic alterations. Journal of Insect Physiology, 99, 113-121.

Kruse JChoi YJThines M (2017) New smut-specific primers for the ITS barcoding of Ustilaginomycotina. Mycological Progress, 16, 213-221.

Kruse J, Doehlemann G, Kemen E, Thines M (2017) Asexual and sexual morphs of Moesziomyces revisited. IMA Fungus, 8, 117-129.

Kruse JMishra BChoi YJSharma RThines M (2017) New smut-specific primers for multilocus genotyping and phylogenetics of Ustilaginaceae. Mycological Progress, 16, 917-925.

Kumar VLammers FBidon TPfenninger M, Kolter L, Nilsson MAJanke A (2017) The evolutionary history of bears is characterized by gene low across species. Scientific Reports, 7, 46487.

Lagostina E, Dal Grande F, Ott S, Printzen C (2017) Fungus-specific SSR markers in the Antarctic lichens Usnea antarctica and U. aurantiacoatra (Parmeliaceae, Ascomycota). Applications in Plant Sciences, 5, 1-5.

Lammers FGallus SJanke ANilsson MA (2017) Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable ElementInsertions in Low Coverage Genomes. Genome Biology and Evolution, 9, 2862-2878.

Lammers FJanke ARuecklé C, Zizka V, Nilsson MA (2017) Screening for the ancient polar bear mitochondrial genome reveals low integration of mitochondrial pseudogenes (numts) in bears. Mitochondrial DNA Part B Resources, 2, 251-254.

Lange JA, Sharma R, Schmidt SI, Bahrdt S, Horn HG, Alguero-Muniz M, Nam B, Achterberg EP, Boersma M, Thines MSchwenk K (2017) Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak. PLOS One, 12, e0175808.

Lorberau KE, Botnen SS, Mundra S, Aas AB, Rozema J, Eidesen PB, Kauserud H (2017) Does warming by open-top chambers induce change in the root-associated fungal community of the arctic dwarf shrub Cassiope tetragona (Ericaceae)? Mycorrhiza, 27, 513-524.

Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu SF, et. al. EA, Bocherens H, et. al. EA, Gilbert MTP (2017) Comparative performance of the BGISEQ-500 versus Illumina HISeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience, 6, 1-13.

Meiser AOtte JSchmitt IDal Grande F (2017) Sequencing genomes from mixed DNA samples – evaluating the metagenome skimming approach in lichenized fungi. Scientific Reports, 7, 14881.

Moretti A, Pavanelli J, Nolasco P, Leisegang M, Tanaka L, Fernandes C, Wosniak JJ, Kajihara D, Dias M, Fernandes D, Jo H, Tran N, Ebersberger I, Brandes R, Bonatto D, Laurindo R (2017) Conserved gene microsynteny unveils functional interaction between protein disulfide isomerase and Rho Guanine-dissociation inhibitor families. Scientific Reports, 7, 17262.

Oppold ASchmidt HRose M, Hellmann L, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M (2017) Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Molecular Ecology, 2017, 3256-3275.

Paule J, Wagner ND, Weising K, Zizka G (2017) Ecological range shift in the polyploid members of the South American genus Fosterella (Bromeliaceae). Annals of Botany, 120, 233-243.

Petrželová I, Choi YJ, Jemelková M, Doležalová I, Kruse JThines M, Kitner M (2017) Confirmation of Peronospora agrimoniae as a distinct species. European Journal of Plant Pathology, 47, 887-896.

Reiners TE, Fuchs M, Hailer FJanke ANowak C (2017) Establishing species-specific sexing markers suitable for non- invasive samples of species lacking genomic resources: an example using the highly endangered common hamster Cricetus cricetus. Conservation Genetics Resources, 9, 253-255.

Rieder V, Blank-Landeshammer B, Stuhr M, Schell T, Biss K, Kollipara L, Meyer A, Pfenninger M, Westphal H, Sickmann A (2017) DISMS2: A flexible algorithm for direct proteome-wide distance calculation of LC-MS/MS runs. BMC Bioinformatics, 18, 148.

Rottstock T, Kummer V, Fischer M, Joshi J (2017) Rapid transgenerational effects in Knautia arvensis in response to plant-community diversity. Journal of Ecology, 105, 714-725.

Rulik BR, Eberle J, von der Mark L, Thormann J, Jung M, Köhler F, Apfel W, Weigel A, Kopetz A, Köhler J, Fritzlar F, Hartmann M, Hadulla K, Schmidt J, Hörren T, Krebs D, Theves F, Eulitz U, Skale A, Rohwedder D, Kleeberg A, Astrin JJ, Geiger MF, Wägele JW, Grobe P, Ahrens D, Yu D (2017) Using taxonomic consistency with semi-automated data pre-processing for high quality DNA barcodes. Methods in Ecology and Evolution, 8, 1878-1887.

Say EKP, Yabut TV, Cinco NET, Caguimbal NALE, Devanadera MKP, Bennett RM, Arafiles KHV, Aki T, Dedeles GR (2017) Growth and Fatty Acid Production of Halophytophthora S13005YL1-3.1 under Different Salinity and pH Levels. Philippine Agricultural Scientist, 100, S6-S11.

Schell TFeldmeyer BSchmidt HGreshake B, Tills O, Truebano M, Rundle SD, Paule JEbersberger IPfenninger M (2017) An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca). Genome Biology and Evolution, 9, 585-592.

Schmidt H, Malik A, Bicker A, Poetzsch G, Avivi A, Shams I, Hankeln T (2017) Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax – a liver transcriptomics approach. Scientific Reports, 7, 14348.

Segev U, Burkert L, Feldmeyer B, Foitzik S (2017) Pace-of-life in a social insect: behavioral syndromes in ants shift along a climatic gradient. Behavioral Ecology, 28, 1149-1159.

Singh GDal Grande F, Divakar PK, Otte J, Crespo A, Schmitt I (2017) Fungal–algal association patterns in lichen symbiosis linked to macroclimate. New Phytologist, 214, 317-329.

Stuckas H, Knöbel L, Schade H, Breusing C, Hinrichsen HH, Bartel M, Langguth C, Melzner F (2017) Combining hydrodynamic modelling with genetics: Can passive larval drift shape the genetic structure of Baltic Mytilus populations? Molecular Ecology, 26, 2765-2782.

Szivak I, Mikes T, Szalontai B, Kucinic M, Vučković I, Vadkerti E, Kisfali P, Pauls SUBalint M (2017) Ecological divergence of Chaetopteryx rugulosa species complex (Insecta, Trichoptera) linked to climatic niche diversification. Hydrobiologia, 794, 31-47.

Tahir AMuñoz-Fuentes VBuch AK, Celik A, Dutbayev A, Gabrielyan I, Glynou K, Khaliq I, Kitner M, Nigrelli LPloch S, Runge F, Schmuker A, Solovyeva IXia X, Vakhrusheva L, Maciá-Vicente JG, Nowak CThines M (2017) Genetic patterns reflecting Pleistocene range dynamics in the annual calcicole plant Microthlaspi erraticum across its Eurasian range. Flora, 236-237, 132-142.

Tobias N, Wolff H, Djahanschiri B, Grundmann F, Kronenwerth M, Shi Y, Simonyi S, Grün P, Shapiro-Ilan D, Pidot S, Stinear T, Ebersberger I, Bode HB (2017) Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus. Nature Microbiology, 2, 1676-1685.

Tucker CM, Cadotte MW, Carvalho S, Davies TJ, Ferrier S, Fritz SA, Grenyer R, Helmus MR, Jin LS, Mooers AO, Pavoine S, Purschke O, Redding D, Rosauer DF, Winter M, Mazel F (2017) A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biological Reviews, 92, 698-715.

Winter S, Friedman ALL, Astrin JJ, Gottsberger B, Letsch H (2017) Timing and host plant associations in the evolution of the weevil tribe Apionini (Apioninae, Brentidae, Curculionoidea, Coleoptera) indicate an ancient co-diversification pattern of beetles and flowering plants. Molecular Phylogenetics and Evolution, 107, 179-190.

Peer-reviewed Articles / Non-ISI

2020

Waldvogel AMFeldmeyer 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, 4, 4-18.

2019

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.

2018

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.

2017

Oppold APfenninger M (2017) Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in Chironomus riparius. Evolution Letters, 1, 86-92.

Sagor GHM, Kusano T, Berberich T (2017) Identification of the actual coding region for polyamine oxidase 6 from rice (OsPAO6) and its partial characterization. Plant Signaling & Behaviour, 12, e1359456.

Articles in other Journals

2020

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2019

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2018

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2017

Jage H, Klenke F, Kruse J, Kummer V, Scholler M, Thiel H, Thines M (2017) Neufunde und bemerkenswerte Bestätigungen phytoparasitischer Kleinpilze in Deutschland – Albuginales (Weißroste) und obligat biotrophe Peronosporales (Falsche Mehltaue). Schlechtendalia, 33, 1-134.

Books

2020

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2019

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

2018

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2017

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Book section

2020

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2019

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2018

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.

2017

Beakes GW, Thines M (2017) Hyphochytriomycota and Oomycota. Handbook of the Protists. Springer International Publishing, 435-505.

Bennett R, Honda D, Beakes GW, Thines M (2017) Labyrinthulomycota. Handbook of the Protists. Springer International Publishing, 507-542.

Berberich T, Sagor GHM, Kusano T (2017) Abiotic Stress Phenotyping of Polyamine Mutants. In: Alcazar R, Tiburcio A (Eds) Polyamines, Methods and Protocols. Springer/Humana Press, New York, NY, New York, 389-403.

Kusano T, Sagor GHM, Berberich T (2017) Molcules for sensing polyamines a transdurcing their action in plants. In: Alcazar R, Tiburcio A (Eds) Polyamines, Methods and Protocols. Springer/Humana Press, New York, NY, New York, 25-35.

Oppold AMüller R (2017) Epigenectics – A Hidden Target of Insecticides. Advances in Insect Physiology. Elsevier, 313-324.

Work and Discussion Paper

2020

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2019

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).

2018

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2017

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