See also: archived pre-prints


[81] Bálint M, Márton O, Schatz M, Düring R-A, Grossart H-P (in press)

Proper experimental design requires randomization/balancing of molecular ecology experiments

Ecology and Evolution 10.1002/ece3.3687


[80] 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 10.1093/gigascience/gix128

[79] Sosa-Hernández MA, Roy J, Hempel S, Kautz T, Köpke U, Uksa M, Schloter M, Caruso T, Rillig MC (2017).

Subsoil arbuscular mycorrhizal fungal communities in arable soil differ from those in topsoil

Soil Biology and Biochemistry 117:83-86

[78] Escalera-Zamudio M, Taboadada B, Rojas-Anaya E, Löber U, Loza-Rubio E, Arias CF, Greenwood AD (2017).

Viral communities among sympatric vampire bats and cattle

EcoHealth 10.1007/s10393-017-1297-y

[77] 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

[76] Rojas-Jimenez K, Wurzbacher C, Bourne EC, Chiuchiolo A, Priscu JC, Grossart HP (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

[75] Mestre M, Ferrera I, Borrull E, Ortega-Retuerta E, Mbedi S, Grossart HP, Sala MM (2017)

Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum

Molecular Ecology 26:6827-6840.

[74] 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

[73] 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

[72] Zanchi C, Johnston PR, Rolff J. 2017.

Evolution of defence cocktails: Antimicrobial peptide combinations reduce mortality and persistent infection

Molecular Ecology 26:5334–5343

[71] Gruenstaeudl M, Nauheimer L, Borsch T (in press).

Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships

Plant Systematics and Evolution 303:1251-1270

[70] 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. (in press).

Integrating chytrid fungal parasites into plankton ecology. Research gaps and needs

Environmental Microbiology 10.1111/1462-2920.13827

[69] 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

[68] 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

[67] 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

[66] 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

[65] 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

[64] 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

[63] Bonada N, SM Carlson, T Datry, D Finn, C Leigh, DA Lytle, Monaghan MT, PA Tedesco (in press).

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)

[62] 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

[61] 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

[60] 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



[59] Wurzbacher C, Grimmett IJ, Bärlocher F

Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada

F1000 Research 4:1378

[58] 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

[57] Duwe VK, Muller LAH, Borsch T, Ismail SA (2016).

Development of microsatellite markers for Crepis mollis (Asteraceae)

Applications in Plant Sciences 4:1600022

[56] 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

[55] 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

[54] 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

[53] 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

[52] 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.

[51] 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.

[50] 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.

[49] 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.

[48] 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.

[47] Obara I, Nielsen M, Jeschek M, Nijhof A, Mazzoni CJ, Svitek N, Steinaa L, Awino E, Olds C, Jabbar A, Clausen PH, 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.

[46] 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.

[45] 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.

[44] 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.

[43] 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.

[42] 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.

[41] 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

[40] 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

[39] 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.

[38] Gonzalez-Tortuero E, Rusek J, Turko P, Petrusek A, Pialek L, Tellenbach C, Giessler S, Spaak P, Wolinska J (online)

Daphnia parasite dynamics across multiple Caullerya epidemics indicate selection against common parasite genotypes.

Zoology 10.1016/j.zool.2016.04.003.

[37] 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 & Vectors 9:293.

[36] Berdan E, Blaneers T, Waurick I, Mazzoni CJ, Mayer F (online).

A genes eye view of ontogeny: De novo assembly and profiling of the Gryllus rubens transcriptome.

Molecular Ecology Resources 16:1478–1490.

[35] 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.

[34] 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.

[33] 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

[32] Alfano N et al. (2016).

Endogenous gibbon ape leukemia virus identified in a rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)

Journal of Virology 90:8169-8180

[31] 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

[30] 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.



[29] 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 Microbiologye 6:1297.

[28] 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.

[27] 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.

[26] 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.

[25] 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.

[24] 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.

[23] 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.

[22] 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.

[21] 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.

[20] 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.

[19] 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.

[18] 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.

[17] 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.

[16] 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.

[15] Korotkova N, Nauheimer L, Ter-Voskanyan H, Allgaier M, Borsch T. (2015).

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.


[14] Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B (2014).

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies.

Molecular Ecology Resources 15:526-542.

[13] 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.

[12] 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.

[11] 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.

[10] 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.

[9] 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 150:474-88.


[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.

(*contributed equally)

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