Publications

[210] Thomé PC, I Irisarri, J Wolinska, MT Monaghan, JFH Strassert (2023)
Single-cell genomics reveals new rozellid lineages and supports their sister relationship to Microsporidia
Biology Letters 10.1098/rsbl.2023.0398

[209] Manthey C, PR Johnston, S Nakagawa, J Rolff (2023)
Complete metamorphosis and microbiota turnover in insects
Molecular Ecology 10.1111/mec.16673

[208] Sire​ L, P Schmidt Yáñez, A Bézier, B Courtia, S Mbedi, S Sparmann, L Larrieu, R Rougerie, C Bouget, MT Monaghan, EA Herniou, C Lopez-Vaamonde (2023)
Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps
PeerJ 10.7717/peerj.16022

[207] Bernardes SC , T von Rintelen, S Alexander, F Lorenz, K von Rintelen (2023)
Assessing ‘non-destructive’ DNA extraction method in small crustaceans kept in wet collections
Research Ideas and Outcomes 10.3897/rio.9.e113299

[206] Baird CN, M Ernst, I Waurick, MPK Blom, F Bibi (2023)
Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, tragelaphus scriptus (mammalia: bovidae)
Zoological Journal of the Linnean Society 10.1093/zoolinnean/zlad096

[205] Schimani K, N Abarca, O Skibbe, H Mohamad, R Jahn, WH Kusber, GL Campana, J Zimmermann (2023)
Exploring benthic diatom diversity in the west antarctic peninsula: insights from a morphological and molecular approach
Metabarcoding and Metagenomics 10.3897/mbmg.7.110194

[204] Ferreira SCM, VH Jarquín-Díaz, E Heitlinger (2023)
Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent coccidia (eimeria)
SpringerLink 10.1186/s13071-023-05800-6

[203] Tsangaras K, J Mayer, O Mirza, A Dayaram, DP Higgins, B Bryant, M Campbell-Ward, C Sangster, A Casteriano, D Höper, M Beer, AD Greenwood (2023)
Evolutionarily young african rhinoceros gammaretroviruses
Journal of Virology 10.1128/jvi.01932-22

[202] Arantes LS , JA Caccavo, JK Sullivan, S Sparmann, S Mbedi, OP Höner, CJ Mazzoni (2023)
Scaling-up RADseq methods for large datasets of non-invasive samples: lessons for library construction and data preprocessing
Molecular Ecology Resources 10.1111/1755-0998.13859

[201] Danabalan R, K Merkel, I Bærholm Schnell, M Arandjelovic, C Boesch, G Brazzola, P Dieguez, J Dupain, M Kambale-Vyalengerera, H S Kühl, C Hoffmann, J Lapuente, VN Thinh, F Zimmermann, FH Leendertz, MTP Gilbert, C Roos, C Mazzoni, JF Gogarten, S Calvignac-Spencer (2023)
Mammal mitogenomics from invertebrate-derived DNA
Environmental DNA 10.1002/edn3.436

[200] Danabalan R , A Planillo, S Butschkau, S Deeg, G Pierre, C Thion, S Calvignac-Spencer, S Kramer-Schadt, C Mazzoni (2023)
Comparison of mosquito and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany
Environmental DNA 10.1002/edn3.398

[199] Bentley BP, T Carrasco-Valenzuela, EKS Ramos, H Pawar, L Souza Arantes, A Alexander, SM Banerjee, P Masterson, M Kuhlwilm, M Pippel, J Mountcastle, B Haase, M Uliano-Silva, G Formenti, K Howe, W Chow, A Tracey, Y Sims, S Pelan, J Wood, K Yetsko, JR Perrault, KeKlly Stewart, SR Benson, Y Levy, EV Todd, HB Shaffer, P Scott, BT Henen, RW Murphy, D W Mohr, A F Scott, DJ Duffy, NJ Gemmell, A Suh, S Winkler, F Thibaud-Nissen, MF Nery, T Marques-Bonet, A Antunes, Y Tikochinski, PH Dutton, O Fedrigo, EW Myers, ED Jarvis, CJ Mazzoni, LM Komoroske
Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.
PNAS 10.1073/pnas.2201076120.

[198] Theissinger K et al.
How genomics can help biodiversity conservation.
Trends in Genetics 10.1016/j.tig.2023.01.005.

[197] Meyer BS, M Moiron, C Caswara, W Chow, O Fedrigo, G Formenti, B Haase, K Howe, J Mountcastle, M Uliano-Silva, J Wood, ED Jarvis, M Liedvogel, S Bouwhuis
Sex-specific changes in autosomal methylation rate in ageing common terns.
Frontiers in Ecology and Evolution 10.3389/fevo.2023.982443.

[196] Vilaça, ST, F Maroso, P Lara, B de Thoisy, D Chevallier, LS Arantes, FR Santos, G Bertorelle, CJ Mazzoni
Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids.
Molecular Ecology 10.1111/mec.16773.



[195] Midha A, VH Jarquín-Díaz, F Ebner, U Löber, R Hayani, A Kundik, A Cardilli, E Heitlinger, SK Forslund, S Hartmann (2022)
Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host.
Microbiome 10:229.

[194] Whitehead J, J Roy, S Hempel, MC Rillig (2022)
Soil microbial communities shift along an urban gradient in Berlin, Germany.
Frontiers in Microbiology 10.3389/fmicb.2022.972052.

[193] Damas J, M Corbo, J Kim, J Turner-Maier, M Farré, DM Larkin, OA Ryder, C Steiner, ML Houck, S Hall, L Shiue, S Thomas, T Swale, M Daly, J Korlach, M Uliano-Silva, CJ Mazzoni, BW Birren, DP Genereux, J Johnson, K Lindblad-Toh, EK Karlsson, MT Nweeia, RN Johnson, Zoonomia Consortium, HA Lewin (2022)
Evolution of the ancestral mammalian karyotype and syntenic regions.
Proceedings of the National Academy of Sciences USA 119:e22091391.

[192] Christin Manthey, Paul R. Johnston, Shinichi Nakagawa, Jens Rolff
Complete metamorphosis and microbiota turnover in insects
https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16673

[191] Premke K, C Wurzbacher, K Felsmann, J Fabian, R Taube, P Bodmer, K Attermeyer, KN Nitzsche, S Schroer, M Koschorreck, E Hübner, TH Mahmoudinejad, CCM Kyba, MT Monaghan, F Hölker (2022)
Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes.
Environmental Pollution 308:119627.

[190] Scholz C, CC Voigt (2022)
Diet analysis of bats killed at wind turbines suggests large‐scale losses of trophic interactions.
Conservation Science and Practice 10.1111/csp2.12744.

[189] Roy J, R Reichel, N Brüggemann, MC Rillig (2022)
Functional, not taxonomic, composition of soil fungi reestablishes to pre-mining initial state after 52 years of recultivation.
Microbial Ecology 10.1007/s00248-022-02058-w.

[188] Urbański A, PR Johnston, E Bittermann, M Keshavarz, V Paris, K Walkowiak-Nowicka, N Konopińska, P Marciniak, J Rolff (2022)
Tachykinin-related peptides modulate immune-gene expression in the mealworm beetle Tenebrio molitor L.
Scientific Reports 12:17277.

[187] Hilgers L, S Hartmann, J Pfaender, N Lentge-Maaß, RM Marwoto, T von Rintelen, M Hofreiter (2022)
Evolutionary divergence and radula diversification in two ecomorphs from an adaptive radiation of freshwater snails.
Genes 13:1029.

[186] NMF Sousa, J Roy, S Hempel, MC Rillig, LC Maia (2022)
Precipitation and temperature shape the biogeography of arbuscular mycorrhizal fungi across the Brazilian Caatinga.
Journal of Biogeography 49:1137–1150.

[185] Weyrich A, TP Guerrero-Altamirano, S Yasar, GÁ Czirják, B Wachter, J Fickel (2022)
First steps towards the development of epigenetic biomarkers in female cheetahs (Acinonyx jubatus).
Life 6:920.

[184] Hatami E, KE Jones, N Kilian (2022)
New insights into the relationships within subtribe Scorzonerinae (Cichorieae, Asteraceae) using hybrid capture phylogenomics (Hyb-Seq).
Frontiers in Plant Science 13:851716.

[183] De Panis D, SA Lambertucci, G Wiemeyer, H Dopazo, FC Almeida, CJ Mazzoni, M Gut, I Gut, J Padró (2022)
Mitogenomic analysis of extant condor species provides insight into the molecular evolution of vultures.
Scientific Reports 11:17109.

[182] Giorgashvili E, Reichel K, Caswara C, Kerimov V, Borsch T, Gruenstaeudl M (2022)
Software choice and sequencing coverage can impact plastid genome assembly: a case study in the narrow endemic Calligonum bakuense.
Frontiers in Plant Science 10.3389/fpls.2022.779830.

[181] Strassert JFH, MT Monaghan (2022)
Phylogenomic insights into the early diversification of fungi.
Current Biology 32:3628-3635.e3.

[180] Sieksmeyer T, S He, MA Esparza-Mora, S Jiang, V Petrašiūnaitė, B Kuropka, R Banasiak, MJ Julseth, C Weise, PR Johnston, A Rodríguez-Rojas, DP McMahon (2022)
Eating in a losing cause: limited benefit of modified macronutrient consumption following infection in the oriental cockroach Blatta orientalis.
BMC Ecology and Evolution 22:67.

[179] Abdallah K, Stock SC, Heeger F, Koester M, Nájera F, Matus F, Merino C, Spielvogel S, Gorbushina AA, Kuzyakov Y, Dippold AM (2022)
Nitrogen gain and loss along an ecosystem sequence: from semi-desert to rainforest.
Frontiers in Soil Science 10.3389/fsoil.2022.817641

[178] G Formenti, K Theissinger, C Fernandes, I Bista, A Bombarely, C Bleidorn, F Čiampor, C Ciofi, A Crottini, JA Godoy, J Hoglund, J Malukiewicz, A Mouton, Rebekah A Oomen, S Paez, PJ Palsbøll, C Pampoulie, MJ Ruiz-López, H Svardal, C Theofanopoulou, J de Vries, A-M Waldvogel, G Zhang, CJ Mazzoni, E Jarvis, M Bálint, SA Aghayan, TS Alioto, I Almudi, N Alvarez, PC Alves, IR Amorim, A Antunes, P Arribas, P Baldrian, PR Berg, G Bertorelle, A Böhne, A Bonisoli-Alquati, LL Boštjančić, B Boussau, CM Breton, E Buzan, PF Campos, C Carreras, LF Castro, LJ Chueca, E Conti, R Cook-Deegan, D Croll, MV Cunha, F Delsuc, AB Dennis, D Dimitrov, R Faria, A Favre, OD Fedrigo, R Fernández, GF Ficetola, J-F Flot, T Gabaldón, DR Galea Agius, GR Gallo, AM Giani, MTP Gilbert, T Grebenc, K Guschanski, R Guyot, B Hausdorf, O Hawlitschek, PD Heintzman, B Heinze, M Hiller, M Husemann, A Iannucci, I Irisarri, KS Jakobsen, S Jentoft, P Klinga, A Kloch, CF Kratochwil, H Kusche, KKS Layton, JA Leonard, E Lerat, G Liti, T Manousaki, T Marques-Bonet, P Matos- Maraví, M Matschiner, F Maumus, AM McCartney, S Meiri, J Melo-Ferreira, X Mengual, MT Monaghan, M Montagna, RW Mysłajek, MT Neiber, V Nicolas, M Novo, P Ozretić, F Palero, L Pârvulescu, M Pascual, OS Paulo, M Pavlek, C Pegueroles, L Pellissier, G Pesole, CR Primmer, A Riesgo, L Rüber, D Rubolini, D Salvi, O Seehausen, M Seidel, S Secomandi, B Studer, S Theodoridis, M Thines, L Urban, A Vasemägi, A Vella, N Vella, SC Vernes, C Vernesi, DR Vieites, RM Waterhouse, CW Wheat, G Wörheide, Y Wurm, G Zammit (2022)
The era of reference genomes in conservation genomics.
Trends in Ecology and Evolution 37:197-202.

[177] Lewin et al. (2022)
The Earth BioGenome Project 2020: starting the clock.
Proceedings of the National Academy of Sciences USA 119:e2115635118.

[176] Sire L, P Schmidt Yáñez, C Wang, A Bézier, B Courtial, J Cours, D Fontaneto, L Larrieu, C Bouget, S Thorn, J Müller, DW Yu, MT Monaghan, EA Herniou, C Lopez-Vaamonde (2022)
Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species.
Communications Biology 5:57.

[175] Maasri A, SC Jähnig, MC Adamescu, R Adrian, C Baigun, DJ Baird, A Batista-Morales, N Bonada, LE Brown, Q Cai, JV Campos-Silva, V Clausnitzer, Topiltzin Contreras-MacBeath, Steven J. Cooke, T Datry, G Delacámara, Luc D Meester, KDB Dijkstra, Van T Do, S Domisch, D Dudgeon, T Erös, H Freitag, J Freyhof, J Friedrich, M Friedrichs-Manthey, J Geist, MO Gessner, P Goethals, M Gollock, C Gordon, HP Grossart, G Gulemvuga, PE Gutiérrez-Fonseca, P Haase, D Hering, HJ Hahn, CP Hawkins, F He, J Heino, V Hermoso, Z Hogan, F Hölker, JM Jeschke, M Jiang, RK Johnson, G Kalinkat, BK Karimov, A Kasangaki, IA Kimirei, B Kohlmann, M Kuemmerlen, JJ Kuiper, B Kupilas, SD Langhans, R Lansdown, F Leese, FS Magbanua, SS Matsuzaki, MT Monaghan, L Mumladze, J Muzon, PAM Ndongo, JC Nejstgaard, O Nikitina, C Ochs, ON Odume, JJ Opperman, H Patricio, SU Pauls, R Raghavan, A Ramírez, B Rashni, V Ross-Gillespie, MJ Samways, RB Schäfer, A Schmidt-Kloiber, O Seehausen, DN Shah, S Sharma, J Soininen, N Sommerwerk, JD Stockwell, F Suhling, RDT Shah, RE Tharme, JH Thorp, D Tickner, K Tockner, JD Tonkin, M Valle, J Vitule, M Volk, D Wang, C Wolter, S Worischka (2022)
A global agenda for advancing freshwater biodiversity research.
Ecology Letters 25: 255-263.

[174] Escobari B, T Borsch, TS Quedensley, M Gruenstaeudl (2022)
Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances.
American Journal of Botany 108: 2235-2256.

[173] Kehoe S, K Jewgenow, PR Johnston, BC Braun (2022)
Early preantral follicles of the domestic cat express gonadotropin and sex steroid signalling potential.
Biology of Reproduction 106:95-107.



[172] Grünfeld L, M Mola, M Wulf, S Hempel, SD Veresoglou
Disentangling the relative importance of spatio-temporal parameters and host specificity in shaping arbuscular mycorrhizal fungus communities in a temperate forest
https://link.springer.com/article/10.1007/s00572-021-01041-6

[171] Lozano YM, Aguilar-Trigueros CA, Roy J, Rillig MC (2021)
Drought induces shifts in soil fungal communities that can be linked to root traits across 24 plant species.
New Phytologist 232:1917-1929.

[170] Caccavo JA, H Christiansen, AJ Constable, L Ghigliotti, R Trebilco, CM Brooks, C Cotté, T Desvignes, T Dornan, CD Jones, P Koubbi, RA Saunders, A Strobel, M Vacchi, AP Van De Putte, A Walters, CM Waluda, BL Woods, JC Xavier (2021)
Productivity and change in fish and squid in the Southern Ocean.
Frontiers in Ecology and Evolution 10.3389/fevo.2021.624918.

[169] Paniagua Voirol LR, G Valsamakis, M Yu, PR Johnston, M Hilker (2021)
How the ‘kitome’ influences the characterization of bacterial communities in lepidopteran samples with low bacterial biomass.
Journal of Applied Microbiology 130:1780-1793.

[168] Heeger F, EC Bourne, C Wurzbacher, E Funke, A Lipzen, G He, V Ng, IV Grigoriev, D Schlosser, MT Monaghan (2021)
Evidence for lignocellulose-decomposing enzymes in the genome and transcriptome of the aquatic hyphomycete Clavariopsis aquatica.
Journal of Fungi 7:854.

[167] Caccavo JA, T Raclot, T Poupart, Y Ropert-Coudert, F Angelier (2021)
Anthropogenic activities are associated with shorter telomeres in chicks of Adélie penguin (Pygoscelis adeliae).
Polar Biology 44:1391-1399.

[166] Beng KC, J Wolinska, E Funke, S van den Wyngaert, AS Gsell, MT Monaghan (2021)
Temporal dynamics of freshwater planktonic parasites inferred using a DNA metabarcoding time-series.
Parasitology 148:1602-1611.

[165] Veresoglou SD, L Grünfeld, M Mola (2021)
Micro-landscape dependent changes in arbuscular mycorrhizal fungal community structure .
Applied Sciences 11:5297.

[164] Rutschmann S, P Chen, C Zhou, MT Monaghan (2021)
Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae).
Mitochondrial DNA Part B: Resources 6:2969-2971.

[163] Hoffmann M, MT Monaghan, K Reinert (2021)
PriSeT: Efficient de novo primer discovery.
Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics Article No.:2, pp. 1-12.

[162] Kehoe S, K Jewgenow, PR Johnston, S Mbedi, BC Braun (2021)
Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat.
Scientific Reports 11:2683

[161] Muller LAH, M-B Ballhausen, DR Andrade-Linares, L Pinek, P Golubeva, MC Rillig (2021)
Fungus–bacterium associations are widespread in fungal cultures isolated from a semi-arid natural grassland in Germany.
FEMS Microbiology Ecology 97:fiab059.

[160] Rodríguez-Rojas A, DY Baeder, PR Johnston, RR Regoes, J Rolff (2021)
Bacteria primed by antimicrobial peptides develop tolerance and persist.
PLoS Pathogens 17:e1009443.

[159] Olarte‐Castillo XA, JF Dos Remédios, F Heeger, H Hofer, S Karl, AD Greenwood, ML East (2021)
The virus–host interface: molecular interactions of Alphacoronavirus‐1 variants from wild and domestic hosts with mammalian aminopeptidase N.
Molecular Ecology 30:2607-2625.

[158] Roy J, R van Duijnen, EF Leifheit, S Mbedi, VM Temperton, MC Rillig (2021)
Legacy effects of pre-crop plant functional group on fungal root symbionts of barley.
Ecological Applications 31:e2378

[157] Rhie et al. (2021)
Towards complete and error-free genome assemblies of all vertebrate species.
Nature 592:737–746

[156] Rodriguez-Ezpeleta N, O Morissette, C Bean, S Manu, P Banerjee, A Lacoursiere, K Beng, E Alter, Fabian Roger, Luke Holman, Kathryn Stewart, MT Monaghan, Q Mauvisseau, L Mirimin, OS Wangensteen, C Antognazza, S Helyar, H de Boer, M-E Monchamp, R Nijland, C Abbott, H Doi, M Barnes, M Leray, P Hablützel, K Deiner (2021)
Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA.
Molecular Ecology 30:4601-4605.

[155] He S, T Sieksmeyer, Y Che, MA Esparza Mora, P Stiblik, R Banasiak, MC Harrison, J Šobotník, Z Wang, PR Johnston, DP McMahon (2021)
Evidence for reduced immune gene diversity and activity during the evolution of termites.
Proceedings of the Royal Society B 288:10.1098/rspb.2020.3168



[154] Alquezar‐Planas DE, U Löber, P Cui, C Quedenau, W Chen, AD Greenwood (2020)
DNA sonication inverse PCR for genome-scale analysis of uncharacterized flanking sequences.
Methods in Ecology and Evolution 12:182-195.

[153] Pöppe J, K Bote, A Ramesh, J Murugaiyan, B Kuropka, M Kühl, PR Johnston, U Roesler, O Makarova (2020)
Selection for resistance to a glyphosate-containing herbicide in Salmonella enterica does not result in a sustained activation of the tolerance response or increased cross-tolerance and cross-resistance to clinically important antibiotics.
Applied and Environmental Microbiology 10.1128/AEM.01204-2

[152] Stelbrink B, R Richter, F Köhler, F Riedel, EE Strong, B Van Bocxlaer, C Albrecht, T Hauffe, TJ Page, DC Aldridge, AE Bogan, L-N Du, MR Manuel-Santos, RM Marwoto, AA Shirokaya, T von Rintelen (2020)
Global diversification dynamics since the Jurassic: low dispersal and habitat-dependent evolution explain hotspots of diversity and shell disparity in river snails (Viviparidae).
Systematic Biology 69:944-961.

[151] Bracamonte SE, K Knopf, MT Monaghan (2020)
Encapsulation of Anguillicola crassus reduces the abundance of adult parasite stages in the European eel (Anguilla anguilla).
Journal of Fish Diseases 10.1111/jfd.13301.

[150] Brasier J, McCormack S, Bax N, Caccavo JA, Cavan E, Ericson JA, Figuerola B, Hancock A, Halfter S, Hellessey N, Höfer J, Puskic PS, de Oliveira CS, Subramaniam RC, Wallis J, Weldrick CK (2020)
Overcoming the obstacles faced by early career researchers in marine science: lessons from the Marine Ecosystem Assessment for the Southern Ocean.
Frontiers in Marine Science 7:692.

[149] Wurzbacher C, A-K Kreiling, S Svantesson, S Van den Wyngaert, E Larsson, F Heeger, HR Nilsson, S Pálsson (2020)
Fungal communities in groundwater springs along the volcanic zone of Iceland.
Inland Waters 10:418-427.

[148] Paniagua Voirol LR, A Weinhold, PR Johnston, NE Fatouros, M Hilker (2020)
Legacy of a butterfly’s parental microbiome in offspring performance.
Applied and Environmental Microbiology 10.1128/AEM.00596-20

[147] Brito C, S Torres Vilaça, A Luzia Lacerda, R Maggioni, MÂ Marcovaldi, G Vélez-Rubio, M Carneiro Proietti (2020)
Combined use of mitochondrial and nuclear genetic markers further reveal immature marine turtle hybrids along the South Western Atlantic.
Genetics and Molecular Biology 10.1590/1678-4685-gmb-2019-0098

[146] Arantes LS, LCL Ferreira, M Driller, FPMR Filho, CJ Mazzoni, FR Santos (2020)
Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output.
Scientific Reports 10:12847.

[145] Arantes LS, ST Vilaça, CJ Mazzoni, FR Santos (2020)
New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil.
Journal of Heredity 111:444–456.

[144] Dueñas JF, T Camenzind, J Roy, S Hempel, J Homeier, JP Suárez, MC Rillig (2020)
Moderate phosphorus additions consistently affect community composition of arbuscular mycorrhizal fungi in tropical montane forests in southern Ecuador.
New Phytologist 227:1505.

[143] Ballhausen M, R Hewitt, MC Rillig (2020)
Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase.
Scientific Reports 10:8533.

[142] Paniagua Voirol LR, G Valsamakis, V Lortzing, A Weinhold, PR Johnston, NE Fatouros, R Kunze, M Hilker (2020)
Plant responses to insect eggs are not induced by egg‐associated microbes, but by a secretion attached to the eggs.
Plant, Cell, and Environment 43:1815-1826.

[141] Tikochinski Y, C Carreras, G Tikochinski, ST Vilaça (2020)
Population-specific signatures of intra-individual mitochondrial DNA heteroplasmy and their potential evolutionary advantages.
Scientific Reports 10:211.

[140] Bourne EC, PR Johnston, E Funke, MT Monaghan (2020)
Gene expression analysis of litter-associated fungi using RNA-seq.
Methods to Study Litter Decomposition (eds. F Bärlocher, M Gessner, M Graça), Springer, pp. 355-367.

[139] Lu Y, E Ocaña-Pallarès, D López-Escardó, SR Dennis, MT Monaghan, I Ruiz-Trillo, P Spaak, J Wolinska (2020)
Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes.
Molecular Phylogenetics and Evolution 151:106891.

[138] Rodríguez-Rojas A, JJ Kim, PR Johnston, O Makarova, M Eravci, C Weise, R Hengge, J Rolff (2020)
Non-lethal exposure to H₂O₂ boosts bacterial survival and evolvability against oxidative stress.
PLoS Genetics 16:e1008649.

[137] Bellinvia S, PR Johnston, S Mbedi, O Otti (2020)
Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations.
Proc Roy Soc B 287 10.1098/rspb.2020.0302

[136] El Shazely B, G Yu, PR Johnston, J Rolff (2020)
Resistance evolution against antimicrobial peptides in Staphylococcus aureus alters pharmacodynamics beyond the MIC.
Frontiers in Microbiology 10.3389/fmicb.2020.00103

[135] He S, PR Johnston, DP McMahon (2020)
Analyzing immunity in non-model insects using de novo transcriptomics.
Immunity in Insects (eds. F Sandrelli, G Tettamanti), Springer, pp. 35-51.

[134] Bellinvia S, PR Johnston, K Reinhardt, O Otti (2020)
Bacterial communities of the reproductive organs of virgin and mated common bedbugs, Cimex lectularius.
Ecological Entomology 45:142-154.

[133] Jarquín‐Díaz VH, A Balard, A Mácová, J Jost, TR von Szepesbéla, K Berktold, S Tank, J Kvičerová, E Heitlinger (2020)
Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers.
Ecology and Evolution 10:1378-1389.


[132] Bracamonte SE, PR Johnston, MT Monaghan, K Knopf (2019)
Gene expression response to a nematode parasite in novel and native eel hosts.
Ecology and Evolution 9:13069-13084.

[131] Caccavo JA, JR Ashford, S Ryan, C Papetti, M Schröder, L Zane (2019)
Spatial structuring and life history connectivity of Antarctic silverfish along the southern continental shelf of the Weddell Sea.
Marine Ecology Progress Series 624:195-212.

[130] Johnston PR, V Paris, J Rolff (2019)
Immune gene regulation in the gut during metamorphosis in a holo- versus a hemimetabolous insect.
Philosophical Transactions of the Royal Society B 374: 10.1098/rstb.2019.0073.

[129] Rolff J, PR Johnston, S Reynolds (2019)
Complete metamorphosis of insects.
Philosophical Transactions of the Royal Society B 374: 10.1098/rstb.2019.0063.

[128] Heeger F, C Wurzbacher, EC Bourne, CJ Mazzoni, MT Monaghan (2019)
Combining the 5.8S and ITS2 to improve classification of fungi.
Methods in Ecology and Evolution 10:1702-1711.

[127] Jones KE, T Fér, RE Schmickl, RB Dikow, VA Funk, S Herrando‐Moraira, PR Johnston, N Kilian, CM Siniscalchi, A Susanna, M Slovák, R Thapa, LE Watson, JR Mandel (2019)
An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.
Applications in Plant Sciences 7:e11295.

[126] Elabed H, E González-Tortuero, C Ibacache-Quiroga, A Bakhrouf, PR Johnston, K Gaddour, J Blázquez, A Rodríguez-Rojas (2019)
Seawater salt-trapped Pseudomonas aeruginosa survives for years and gets primed for salinity tolerance.
BMC Microbiology 19:142.

[125] El Shazely B, A Urbański, PR Johnston, J Rolff (2019)
In vivo exposure of insect AMP resistant Staphylococcus aureus to an insect immune system.
Insect Biochemistry and Molecular Biology 110:60-68.

[124] Degrune F, K Dumack, AM Fiore-Donno, M Bonkowski, MA Sosa-Hernández, M Schloter, T Kautz, D Fischer, MC Rillig (2019)
Distinct communities of Cercozoa at different soil depths in a temperate agricultural field.
FEMS Microbiology Ecology 95:fiz041.

[123] Stöck M, F Fakharzadeh, H Kuhl, B Rozenblut-Kościsty, S Leinweber, R Patel, M Ebrahimi, S Voitel, JF Schmidtler, HG Kami, M Ogielska, DW Förster (2019)
Shedding light on a secretive Tertiary Urodelean relict: hynobiid salamanders (Paradactylodon persicus s.l.) from Iran, illuminated by phylogeographic, developmental, and transcriptomic data.
Genes 10:306.

[122] Seeber PA, GK McEwen, U Löber, DW Förster, ML East, J Melzheimer, AD Greenwood (2019)
Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes.
Molecular Ecology Resources 19:1486-1496.

[121] Mora D, N Abarca, S Proft, JH Grau, N Enke, J Carmona, O Skibbe, R Jahn, J Zimmermann (2019)
Morphology and metabarcoding: a test with stream diatoms from Mexico highlights the complementarity of identification methods.
Freshwater Science 38:448-464.

[120] Vilaça ST, CS Lima, CJ Mazzoni, FR Santos, B de Thoisy (2019)
Manatee genomics supports a special conservation area along the Guianas coastline under the influence of the Amazon River plume.
Estuarine, Coastal and Shelf Science 226:106286.

[119] Bracamonte SE, PR Johnston, K Knopf, MT Monaghan (2019)
Experimental infection with Anguillicola crassus alters immune gene expression in both spleen and head kidney of the European eel (Anguilla anguilla).
Marine Genomics 45:28-37.


[118] Darwall W, V Bremerich, A De Wever, AI Dell, J Freyhof, MO Gessner, H‐P Grossart, I Harrison, K Irvine, SC Jähnig, JM Jeschke, JJ Lee, C Lu, AM Lewandowska, MT Monaghan, JC Nejstgaard, H Patricio, A Schmidt‐Kloiber, SN Stuart, M Thieme, K Tockner, E Turak, O Weyl (2018)
The Alliance for Freshwater Life: A global call to unite efforts for freshwater biodiversity science and conservation.
Aquatic Conservation: Marine and Freshwater Ecosystems 28:1015-1022.

[117] Lu Y, PR Johnston, SR Dennis, MT Monaghan, U John, P Spaak, J Wolinska (2018)
Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism.
BMC Genomics 19:932.

[116] Gattolliat J-L, S Rutschmann, MT Monaghan, M Sartori (2018)
From molecular hypotheses to valid species: description of three endemic species of Baetis (Ephemeroptera: Baetidae) from the Canary Islands.
Arthropod Systematics and Phylogeny 76:509-528.

[115] Makarova O, PR Johnston, A Rodriguez-Rojas, B El Shazely, J Moreno Morales, J Rolff (2018)
Genomics of experimental adaptation of Staphylococcus aureus to a natural combination of insect antimicrobial peptides.
Scientific Reports 8:15359.

[114] Altmann S, JM Muino, V Lortzing, R Brandt, A Himmelbach, L Altschmied, M Hilker (2018)
Transcriptomic basis for reinforcement of elm anti‐herbivore defense mediated by insect egg deposition.
Molecular Ecology 27:4901-4915

[113] González-Tortuero E, J Rodríguez-Beltrán, R Radek, J Blázquez, A Rodríguez-Rojas (2018)
Clay-induced DNA breaks as a path for genetic diversity, antibiotic resistance, and asbestos carcinogenesis.
Scientific Reports 8:8504.

[112] Pecoraro C, M Babbucci, R Franch, C Rico, C Papetti, E Chassot, N Bodin, A Cariani, L Bargelloni, F Tinti (2018)
The population genomics of yellowfin tuna (Thunnus albacares) at global geographic scale challenges current stock delineation.
Scientific Reports 8:13890.

[111] Löber U, M Hobbs, A Dayaram, K Tsangaras, K Jones, DE Alquezar-Planas, Y Ishida, J Meers, J Mayer, C Quedenau, W Chen, RN Johnson, P Timms, PR Young, AL Roca, AD Greenwood (2018)
Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion.
Proceedings of the National Academy of Sciences USA 115:8609-8614.

[110] Heeger F, EC Bourne, C Baschien, A Yurkov, B Bunk, C Spröer, J Overmann, CJ Mazzoni, MT Monaghan (2018)
Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments.
Molecular Ecology Resources 18:1500-1514.

[109] Sosa-Hernández MA, J Roy, S Hempel, MC Rillig (2018)
Evidence for subsoil specialization in arbuscular mycorrhizal fungi.
Frontiers in Ecology and Evolution 10.3389/fevo.2018.00067.

[108] Weyrich A, M Jeschek, KT Schrapers, D Lenz, TH Chung, K Rübensam, S Yasar, M Schneemann, S Ortmann, K Jewgenow, J Fickel (2018)
Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs.
Environmental Epigenetics 4:dvy011.

[107] Dayaram A, K Tsangaras, S Pavulraj, W Azab, N Groenke, G Wibbelt, F Sicks, N Osterrieder, AD Greenwood (2018)
Novel divergent polar bear-associated mastadenovirus recovered from a deceased juvenile polar bear.
mSphere 3:e00171-18.

[106] Gruenstaeudl M, N Gerschler, T Borsch (2018)
Bioinformatic workflows for generating complete plastid genome sequences — an example from Cabomba (Cabombaceae) in the context of the phylogenomic analysis of the water-lily clade.
Life 8:25.

[105] Sosa-Hernandez MA, J Roy, S Hempel, T Kautz, U Koepke, M Uksa, M Schloter, T Caruso, MC Rillig (2018)
Subsoil arbuscular mycorrhizal fungal communities in arable soil differ from those in topsoil.
Soil Biology and Biochemistry 117:83-86.

[104] Camenzind T, Hammer EC, Lehmann J, Solomon D, Horn S, Rillig MC, S Hempel (2018)
Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths.
FEMS Microbiology Ecology 94:fiy033.

[103] He S, Johnston PR, Kuropka B, Lokatis S. Weise C, Plarre R, Kunte H-J, McMahon DP (2018)
Termite soldiers contribute to social immunity by synthesizing potent oral secretions.
Insect Molecular Biology 27:564-576.

[102] Fuselli S, Baptista RP, Panziera A, Magi A, Guglielmi S, Tonin R, Benazzo A, Bauzer LG, Mazzoni CJ, Bertorelle G (2018)
A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).
Heredity 10.1038/s41437-018-0070-5.

[101] Blankers T, Vilaça ST, Waurick I, Gray DA, Hennig RM, Mazzoni CJ, Mayer F, Berdan EL (2018)
Demography and selection shape transcriptomic divergence in field crickets.
Evolution 72:553-567.

[100] Hilgers L, Hartmann S, Hofreiter M, von Rintelen T (2018)
Novel genes, ancient genes, and gene co-option contributed to the genetic basis of the radula, a molluscan innovation.
Molecular Biology and Evolution 35:1638–1652.

[99] Cuadrat RRC, Ionescu D, Dávila AMR, Grossart H-P (2018)
Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics.
Frontiers in Microbiology 9:251.

[98] Bálint M, Márton O, Schatz M, Düring R-A, Grossart H-P (2018)
Proper experimental design requires randomization/balancing of molecular ecology experiments
Ecology and Evolution 8:1786-1793.

[97] Escalera-Zamudio M, Taboadada B, Rojas-Anaya E, Löber U, Loza-Rubio E, Arias CF, Greenwood AD (2018)
Viral communities among sympatric vampire bats and cattle.
EcoHealth 15:132-142.


[96] Menke S, M Meier, S Sommer (2017)
Shifts in the gut microbiome observed in wildlife faecal samples exposed to natural weather conditions: lessons from time‐series analyses using next‐generation sequencing for application in field studies.
Methods in Ecology and Evoluion 2:1080-1087.

[95] Wasimuddin, Menke S, Melzheimer J, Thalwitzer S, Heinrich S, Wachter B, Sommer S (2017)
Gut microbiomes of free-ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens.
Molecular Ecology 26:5515-5527.

[94] Lesniak I, Franz M, Heckmann I, Greenwood AD, Hofer H, Krone O (2017)
Surrogate hosts: Hunting dogs and recolonizing grey wolves share their endoparasites.
International Journal for Parasitology: Parasites and Wildlife 6:278-286.

[93] Uliano-Silva M, Dondero F, Otto TD, Costa I, Lima NCB, Americo JA, Mazzoni CJ, Prosdocimi F, de Freitas Rebelo M. (2017)
A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei.
GigaScience 7:gix128.

[92] TA Maia, ST Vilaça, LR Silva, FR Santos, GPM Dantas (2018)
DNA sampling from eggshells and microsatellite genotyping in rare tropical birds: Case study on Brazilian Merganser.
Genetics and Molecular Biology 40:808-812.

[91] Roy J, Reichel R, Brüggemann N, Hempel S, Rillig MC (2017)
Succession of arbuscular mycorrhizal fungi along a 52-year agricultural recultivation chronosequence.
FEMS Microbial Ecology 93:fix102.

[90] Rojas-Jimenez K, Wurzbacher C, Bourne EC, Chiuchiolo A, Priscu JC, Grossart H-P (2017)
Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica.
Scientific Reports 7:15348.

[89] Heitlinger E, S Ferreira, D Thierer, H Hofer, ML East (2017)
The intestinal eukaryotic and bacterial biome of spotted hyenas: the impact of social status and age on diversity and composition
Frontiers in Cellular and Infection Microbiology 7:262.

[88] Mestre M, Ferrera I, Borrull E, Ortega-Retuerta E, Mbedi S, Grossart H-P, Sala MM (2017)
Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum.
Molecular Ecology 26:6827-6840.

[87] Schwensow NI, Detering H, Pederson S, Mazzoni CJ, Sinclair R, Peacock D, Kovaliski J, Cooke B, Fickel J, Sommer S (2017)
Resistance to RHD virus in wild Australian rabbits: comparison of susceptible and resistant individuals using a genome‐wide approach.
Molecular Ecology 26:4551–4561.

[86] Watanabe K, Monaghan MT (2017)
Comparative tests of the species-genetic diversity correlation at neutral and non-neutral loci in four species of stream insect.
Evolution 71:1755-1764.

[85] Zanchi C, Johnston PR, Rolff J. 2017.
Evolution of defence cocktails: Antimicrobial peptide combinations reduce mortality and persistent infection.
Molecular Ecology 26:5334–5343.

[84] Gruenstaeudl M, Nauheimer L, Borsch T (2017)
Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships
Plant Systematics and Evolution 303:1251-1270.

[83] Frenken T, Alacid E, Berger SA, Bourne EC, Gerphagnon M. Grossart H-P, Gsell AS, Ibelings BW, Kagami M, Küpper FC, Letcher PM, Loyau A, Miki T, Nejstgaard JC, Rasconi S, Reñé A, Rohrlack T, Rojas-Jimenez K, Schmeller DS, Scholz B, Seto K, Sime-Ngando T, Sukenik A, Van de Waal DB, Van den Wyngaert S, Van Donk E, Wolinska J, Wurzbacher C, Agha R (2017)
Integrating chytrid fungal parasites into plankton ecology. Research gaps and needs.
Environmental Microbiology 19:3802-3822.

[82] Honnen A-C, Monaghan MT (2017)
City-dwellers and country folks: Lack of population differentiation along an urban-rural gradient in the mosquito Culex pipiens (Diptera: Culicidae).
Journal of Insect Science 17:107.

[81] Wurzbacher C, Attermeyer K, MT Kettner, C Flintrop, N Warthmann, Hilt S, Grossart H-P, Monaghan MT (2017)
DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom.
Environmental Microbiology Reports 9:383–388.

[80] Berdan EL, Finck J, Johnston PR, Waurick I, Mazzoni CJ, Mayer F (2017)
Transcriptome profiling of ontogeny in the acridid grasshopper Chorthippus biguttulus.
PLoS One 12:e0177367.

[79] Makarova O, Johnston PR, Walther B, Rolff J, Roesler U (2017)
Complete genome sequence of the disinfectant susceptibility testing reference strain Staphylococcus aureus subsp. aureus ATCC 6538.
Genome Announcements 5:e00293-17.

[78] Makarova O, Johnston PR, Walther B, Rolff J, Roesler U (2017)
Complete genome sequence of the livestock-associated Methicillin-resistant strain Staphylococcus aureus subsp. aureus 08S00974 (Sequence Type 398).
Genome Announcements 5:e00294-17.

[77] Wurzbacher C, Fuchs A, Attermeyer K, Frindte K, Grossart H-P, Hupfer M, Casper P, Monaghan MT (2017)
Shifts among Eukarya, Bacteria, and Archaea define the vertical organization of a lake sediment.
Microbiome 5:41.

[76] Bonada N, SM Carlson, T Datry, D Finn, C Leigh, DA Lytle, Monaghan MT, PA Tedesco (2017)
Genetic, evolutionary and biogeographical processes in intermittent rivers and ephemeral streams.
in Intermittent Rivers and Ephemeral Streams: Ecology and Management (eds. T Datry, N Bonada, A Boulton) Academic Press (ISBN: 9780128038352)

[75] Rousset F, A Gouy, C Martinez‐Almoyna, A Courtiol (2017)
The summary‐likelihood method and its implementation in the Infusion package.
in Molecular Ecology Resources 17:110-119.

[74] Gillingham MAF, Béchet A, Courtiol A, Rendón-Martos M, Amat JA, Samraoui B, Onmuş O, Sommer S, Cézilly F (2017)
Very high MHC Class IIB diversity without spatial differentiation in the mediterranean population of greater Flamingos.
BMC Evolutionary Biology 17:56.

[73] Soares LS, Bolten AB, Wayne ML, Vilaça ST, Santos FR, dei Marcovaldi MAG, Bjorndal KA (2017)
Comparison of reproductive output of hybrid sea turtles and parental species.
Marine Biology 164:9.

[72] Rutschmann S, Detering H, Simon S, Funk DH, Gattolliat J-L, Hughes SJ, Raposeiro PM, DeSalle R, Sartori M, Monaghan MT (2017)
Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome.
Molecular Phylogenetics and Evolution 107:27-38.

[71] Nikolin VM, Olarte-Castillo XA, Osterrieder N, Hofer H, Dubovi E, Mazzoni CJ, Brunner E, Goller KV, Fyumagwa RD, Moehlman PD, Thierer D, East ML (2017)
Canine distemper virus in the Serengeti ecosystem: molecular adaptation to different carnivore species.
Molecular Ecology 26:2111–2130.

[70] Rutschmann S, Detering H, Simon S, Fredslund J, Monaghan MT (2017)
DiscoMark: Nuclear marker discovery from orthologous sequences using draft genome data.
Molecular Ecology Resources 17:257–266.

[69] Schwensow NI, Mazzoni CJ, Marmesat E, Fickel J, Peacock D, Kovaliski J, Sinclair R, Cassey P, Cooke B, Sommer S (2017)
High adaptive variability and virus-driven selection on Major Histocompatibility Complex (MHC) genes in invasive wild rabbits in Australia
Biological Invasions 19:1255–1271.


[68] Wurzbacher C, Grimmett IJ, Bärlocher (2016)
Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada
F1000 Research 4:1378.

[67] Slater GJ, P Cui, AM Forasiepi, D Lenz, K Tsangaras, B Voirin, N de Moraes-Barros, RDE MacPhee, AD Greenwood (2016)
Evolutionary relationships among extinct and extant sloths: the evidence of mitogenomes and retroviruses
Genome Biology and Evolution 8:607-621.

[66] Rosenblad MA, Martín MP, Tedersoo L, Ryberg MK, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016)
Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota).
MycoKeys 13:21-33.

[65] Schroer S, Felsmann K, Hölker F, Mummert S, Monaghan MT, Wurzbacher C, Premke K (2016)
The impact of outdoor lighting on ecosystem function ? gaining information with a Citizen Science approach using a questionnaire.
Frontiers in Environmental Science 10.3389/conf.FENVS.2016.01.00008.

[64] Duwe VK, Muller LAH, Borsch T, Ismail SA (2016)
Development of microsatellite markers for Crepis mollis (Asteraceae)
Applications in Plant Sciences 4:1600022.

[63] Hilgers L, Grau JH, Pfaender J, von Rintelen T (2016)
The complete mitochondrial genome of the viviparous freshwater snail Tylomelania sarasinorum (Caenogastropoda: Cerithioidea)
Mitochondrial DNA Part B: Resources 1:330-331.

[62] Fróes AM, da Mota FF, Cuadrat RRC, Dávila AMR (2016)
Distribution and classification of serine β-lactamases in Brazilian hospital sewage and other environmental metagenomes deposited in public databases
Frontiers in Microbiology 10.3389/fmicb.2016.01790.

[61] Wurzbacher C, Warthmann N, Bourne E, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016)
High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany).
MycoKeys 16:17-44.

[60] Canu A, Vilaça ST, Iacolina L, Apollonio M, Bertorelle G, Scandura M (2016)
Lack of polymorphism at the MC1R wild-type allele and evidence of domestic allele introgression across European wild boar populations
Mammalian Biology – Zeitschrift für Säugetierkunde 81:477-479.

[59] Vuataz L, Rutschmann S, Monaghan MT, Sartori M (2016)
Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae).
BMC Evolutionary Biology 16:194.

[58] Uliano-Silva M, Americo JA, Costa I, Schomaker-Bastos A, Rebelo MD, Prosdocimi F (2016)
The complete mitochondrial genome of the golden mussel Limnoperna fortunei and comparative mitogenomics of Mytilidae.
Gene 577:202-208.

[57] Weyrich A, Benz S, Karl, Jeschek M, Jewgenow K, Fickel J (2016)
Paternal heat exposure causes DNA methylation and gene expression changes of Stat3 in Wild guinea pig sons.
Ecology and Evolution 6:2657-2666.

[56] Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjoling A, Nilsson RH (2016)
Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2.
Ecological Informatics 33:45-50.

[55] Makarova O, Rodriguez-Rojas A, Eravci M, Weise C, Dobson A, Johnston PR, Rolff J (2016)
Antimicrobial defence and persistent infection in insects revisited.
Philosophical Transactions of the Royal Society B 371:20150296.

[54] Schuster AC, Herde A, Mazzoni CJ, Eccard JA, Sommer S (2016)
Evidence for selection maintaining MHC diversity in a rodent species despite strong density fluctuations.
Immunogenetics 68:429-437.

[53] Marmesat E, Soriano L, Mazzoni CJ, Sommer S, Godoy JA (2016)
PCR strategies for complete allele calling in multigene families using high-throughput sequencing approaches.
PLoS One 11:e0157402.

[52] Johnston PR, Dobson AJ, Rolff J (2016)
Genomic signatures of experimental adaptation to antimicrobial peptides in Staphylococcus aureus.
G3-Genes Genomes Genetics 6:1535-1539.

[51] Frindte K, Allgaier M, Grossart H-P, Eckert W (2016).
Redox stability regulates community structure of active microbes at the sediment-water interface.
Environmental Microbiology Reports 8:798-804.

[50] Cui P, Löber U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL, Hartmann S, Greenwood AD (2016)
Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.
Peer J 4:e1847.

[49] Gonzalez-Tortuero E, Rusek J, Turko P, Petrusek A, Pialek L, Tellenbach C, Giessler S, Spaak P, Wolinska J (2016)
Daphnia parasite dynamics across multiple Caullerya epidemics indicate selection against common parasite genotypes.
Zoology 10.1016/j.zool.2016.04.003.

[48] Gonzalez-Tortuero E, Rusek J, Maayan I, Petrusek A, Pialek L, Laurent S, Wolinska J (2016)
Genetic diversity of two Daphnia-infecting microsporidian parasites, based on sequence variation in the internal transcribed spacer region.
Parasites and Vectors 9:293.

[47] Berdan E, Blaneers T, Waurick I, Mazzoni CJ, Mayer F (2016)
A genes eye view of ontogeny: De novo assembly and profiling of the Gryllus rubens transcriptome.
Molecular Ecology Resources 16:1478–1490.

[46] Obara, I, Nielsen M, Jeschek M, Nijhof A, Mazzoni CJ, Svitek N, Steinaa L, Awino E, Olds C, Jabbar A, Clausen P-H, Bishop, RP (2016)
Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters.
Immunogenetics 68:339-352.

[45] Weyrich A, Lenz D, Jeschek M, Chung TH, Rübensam K, Göritz F, Jewgenow K, Fickel J (2016)
Paternal intergenerational epigenetic response to heat exposure in male Wild guinea pigs.
Molecular Ecology 25:1729–1740.

[44] Cuadrat RRC, Ferrera I, Grossart HP, Davila AMR (2016)
Picoplankton bloom in Global South? A high fraction of aerobic anoxygenic phototrophic bacteria in metagenomes from a Coastal Bay (Arraial do Cabo-Brazil).
OMICS: A Journal of Integrative Biology 20:76-87.

[43] Alfano N, J Michaux, S Morand, K Aplin, K Tsangaras, U Löber, P-H Fabre, Y Fitriana, G Semiadi, Y Ishida, KM Helgen, AL Roca, MV Eiden, AD Greenwood (2016)
Endogenous gibbon ape leukemia virus identified in a rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)
Journal of Virology 90:8169-8180.

[42] Escalera-Zamudio M, Rojas-Anaya E, Kolokotronis S-O, Taboadad B, Loza-Rubio E, Méndez-Ojeda ML, Arias CF, Osterrieder N, Greenwood AD (2016)
Bats, primates, and the evolutionary origins and diversification of mammalian gammaherpesviruses
mBio 7:e01425-16.

[41] Honnen A-C, Johnston PR,Monaghan MT (2016)
Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night.
BMC Genomics 17:22.

[40] Santos PSC, A Courtiol, AJ Heidel, OP Höner, I Heckmann, M Nagy, F Mayer, M Platzer, CC Voigt, S Sommer (2016)
MHC-dependent mate choice is linked to a trace-amine-associated receptor gene in a mammal.
Scientific Reports 6:38490.

[39] Benazzo A, Alex Panziera, Giorgio Bertorelle (2015)
4P: fast computing of population genetics statistics from large DNA polymorphism panels.
Ecology and Evolution 5:172-175.

[38] Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B (2015)
Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies.
Molecular Ecology Resources 15:526-542.

[37]Bentzon-Tilia M, SJ Traving, M Mantikci, H Knudsen-Leerbeck, JLS Hansen, S Markager, L Riemann (2015)
Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries.
The ISME Journal 9:273-285.

[36] Severin I, M Bentzon-Tilia, PH Moisander, L Riemann (2015)
Nitrogenase expression in estuarine bacterioplankton influenced by organic carbon and availability of oxygen.
FEMS Microbiology Letters 362:fnv105.

[35] Rieck A, Herlemann DPR, Jürgens K, Grossart HP (2015)
Particle-associated differ from free-living bacteria in surface waters of the Baltic Sea.
Frontiers in Microbiology 6:1297.

[34] Muller LAH, HH Hilger (2015)
Insights into the effects of serpentine soil conditions on the community composition of fungal symbionts in the roots of Onosma echioides.
Soil Biology and Biochemistry 81:1-8.

[33] Frindte K, Allgaier M, Grossart HP, Eckert W (2015)
Microbial Response to experimentally controlled redox transitions at the sediment water interface.
PLoS One 10:e0143428.

[32] Clozato CL, Mazzoni CJ, Moraes-Barros N, Morgante JS, Sommer S (2015)
Spatial pattern of adaptive and neutral genetic diversity across different biomes in the lesser anteater (Tamandua tetradactyla).
Ecology and Evolution 21:4932–4948.

[31] Hartmann S, Hasenkamp N, Mayer J, Michaux J, Morand S, Mazzoni CJ, Roca AL, Greenwood AD (2015)
Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse.
BMC Genomics 16:613.

[30] Berdan E, Mazzoni CJ, Waurick I, Roehr J, Mayer F (2015)
A population genomic scan in Chorthippus grasshoppers unveils previously unknown phenotypic divergence.
Molecular Ecology 24:3918-3930.

[29] Escalera-Zamudio M, Zepeda Mendoza L, Heeger F, Loza-Rubio E, Rojas-Anaya E, Méndez-Ojeda ML, Taboada B, Mazzoni CJ, Arias CF, Greenwood AD (2015)
A novel endogenous betaretrovirus in the commmon vampire bat (Desmondus rotundus) suggests multiple independent infection and cross-species transmission events.
Journal of Virology 89:5180-5184.

[28] Schaer J, Reeder DAM, Vodzak ME, Olival KJ, Weber N, Mayer F, Matuschewski K, Perkins SL (2015)
Nycteria parasites of Afritropical insectivorus bats.
International Journal for Parasitology 45:375–384.

[27] González-Tortuero E, Rusek J, Petrusek A, Gießler S, Lyras D, Grath S, Castro-Monzón F, Wolinska J (2015)
The quantification of representative sequences pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia.
Molecular Ecology Resources 15:1385-1395.

[26] Hölker F,Wurzbacher C, Weißenborn C, Holzhauer S, Monaghan MT, Premke K (2015).
Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night.
Philosophical Transactions of the Royal Society B 370:20140130.

[25] Olarte-Castillo XA, Heeger F, Mazzoni CJ, Greenwood AD, Fyumagwa RD, Moehlmann PD, Hofer H, East ML (2015)
Molecular characterization of canine kobuvirus in wild carnivores and the domestic dog in Africa.
Virology 477:89–97.

[24] Ismail SA, Duwe VK, Fleischer-Notter H, Borsch T (2015).
Development of ten polymorphic microsatellite markers for Scabiosa canescens Waldst. & Kit. (Dipsacaceae).
Conservation Genetics Resources 7:725-728.

[23] Attermeyer K, Tittel J, Allgaier M, Frindte K, Wurzbacher C, Hilt, S, Kamjunke N, Grossart H-P (2015)
Effects of light and autochthonous carbon additions on microbial turnover of allochthonous organic carbon and community composition.
Microbial Ecology 69:361-371.

[22] Duwe VK, Ismail SA, Buser A, Sossai E, Borsch T, Muller, LAH (2015)
Fourteen polymorphic microsatellite markers for the threatened Arnica montana L. (Asteraceae).
Applications in Plant Sciences 3:10.3732/apps.1400091.

[21] Cuadrat RRC, Cury JC, Davila AMR (2015)
Metagenomic analysis of upwelling-affected Brazilian coastal seawater reveals sequence domains of type I PKS and modular NRPS.
International Journal of Molecular Sciences 16:28285-28295.

[20] Geiger et al. (2014)
Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes.
Molecular Ecology Resources 14:1210-1221.

[19] Pauls SU, M Alp, M Bálint, P Bernabò, F Čiampor, Z Čiamporová‐Zaťovičová, DS Finn, J Kohout, F Leese, V Lencioni, I Paz‐Vinas, MT Monaghan (2014)
Integrating molecular tools into freshwater ecology: developments and opportunities.
Freshwater Biology 59:1559-1576.

[18] Tsangaras K, N Wales, T Sicheritz-Pontén, S Rasmussen, J Michaux, Y Ishida, S Morand, M-L Kampmann, MTP Gilbert, AD Greenwood (2014)
Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank).
PLoS ONE 9:e109101.

[17] Salka I, Srivastava A, Allgaier M, Grossart HP (2014)
The draft genome sequence of Sphingomonas sp. strain FuKuSWIS1, obtained from acidic lake Grosse Fuchskuhle, indicates photoheterotrophy and a potential for humic matter degradation.
Genome Announcements 6:e01183-14.

[16] Menke S, Wasimuddin, M Meier, J Melzheimer, JKE Mfune, S Heinrich, S Thalwitzer, B Wachter, S Sommer (2014)
Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.
Frontiers in Microbiology 5:526.

[15] Weyrich A, Schüllermann T, Heeger F, Jeschek M, Mazzoni CJ, Chen W, Schumann K, Fickel J (2014)
Whole genome sequencing and methylome analysis of the wild guinea pig.
BMC Genomics 15:1036.

[14] Majarooamova EH, Muller L, Korotkova N, Borsch T (2014)
Development of nuclear microsatellites for the Arcto-Tertiary tree Zelkova carpinifolia (Ulmaceae) using 454 pyrosequencing.
Applications in Plant Sciences 2:1300072.

[13] Korotkova N, Nauheimer L, Ter-Voskanyan H, Allgaier M, Borsch T (2014)
Variability among the most rapidly evolving plastid genomic regions is lineage-specific: implications of pairwise genome comparisons in Pyrus (Rosaceae) and other angiosperms for marker choice.
PloS One 9:e112998.

[12] Perez et al. (2014)
Genetic variation and population structure in the endangered Hermann’s tortoise: the roles of geography and human-mediated processes.
Journal of Heredity 105:70-81.

[11] Szentiks CA, Tsangaras K, Abendroth B, Scheuch M, Stenglein MD, Wohlsein P, Heeger F, Höveler R, Chen W, Sun W, Damiani A, Nikolin V, Gruber AD, Grobbel M, Kalthoff D, Höper D, Czirják GÁ, DeRisi J, Mazzoni CJ, Schüle A, Aue A, East ML, Hofer H, Beer M, Osterrieder N, Greenwood AD (2014)
Polar bear encephalitis: establishment of a comprehensive next-generation pathogen analysis pipeline for captive and free-living wildlife.
Journal of Comparative Pathology 150:474-488.

[10] Watanabe K, So Kazama, Tatsuo Omura, Michael T Monaghan (2014)
Adaptive genetic divergence along narrow environmental gradients in four stream insects.
PloS One 9:e93055.

[9] Gómez MJ, Héctor Díaz-Maldonado, Enrique González-Tortuero, Francisco J López de Saro (2014)
Chromosomal replication dynamics and interaction with the β sliding clamp determine orientation of bacterial transposable elements.
Genome Biology and Evolution 6:727-740.


[8] Sommer S, Courtiol A, Mazzoni CJ (2013)
MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout.
BMC Genomics 14:542.

[7] Dadheech PK, Glöckner G, Casper P, Kotut K, Mazzoni CJ, Mbedi S, Krienitz L (2013)
Cyanobacterial diversity in the hot spring, pelagic and benthic habitats of a tropical soda lake.
FEMS Microbial Ecology 85:389-401.

[6] Mayer J, Tsanarars K, Heeger F, Ávila-Arcos M, Stenglein MD, Chen W, Mazzoni CJ, Osterrieder N, Greenwood AD (2013)
A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca).
Virology 443:1-10.

[5] Araki AS, Ferreira GEM, Mazzoni CJ, Souza NA, Machado RC, Bruno RV, Peixoto AA (2013)
Multilocus analysis of divergence and introgression in sympatric and allopatric sibling species of the Lutzomyia longipalpis complex in Brazil.
Plos Neglected Tropical Diseases 7:e2495.

[4] He SM, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn RH, Kyrpides NC, Warnecke F, Tringe SG, Hugenholtz P (2013)
Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites.
Plos One 8:e61126.

[3] Dziales C, Allgaier M, Monaghan MT, Grossart HP (2012)
Act together — implications of symbioses in aquatic ciliates.
Frontiers in Microbiology 3:288.

[2] Azevedo RVDM, Dias DBS, Bretãs JAC, Mazzoni CJ, Souza NA, Albano RM, Wagner G, Davila AMR, Peixoto AA (2012)
The transcriptome of Lutzomyia longipalpis (Diptera: Psychodidae) male reproductive organs.
Plos One 7:e34495.

[1] Mayer J, Mazzoni CJ, Greenwood AD (2012)
Comparing PreXMRV-2 gag sequence diversity in laboratory and wild mice using deep sequencing.
Virus Research 169:30-37.