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Preprints are available here

Maasri et al. in press.
A Global agenda for advancing freshwater biodiversity research.
Ecology Letters 10.1111/ele.13931

Welti et al. in press.
Temperature drives variation in flying insect biomass across a German malaise trap network.
Insect Conservation and Diversity 10.1111/icad.12555

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

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

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

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.

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.

Regilme MAF, M Sato,T Tamura, R Arai, MO Sato, S Ikeda, M Gamboa, MT Monaghan, K Watanabe. 2021.
Comparative population genetic structure of two ixodid tick species (Acari:Ixodidae) (Ixodes ovatus and Haemaphysalis flava) in Niigata prefecture, Japan.
Infection, Genetics and Evolution 94:104999.

Bracamonte SE, K Knopf, MT Monaghan. 2021.
Encapsulation of Anguillicola crassus reduces the abundance of adult parasite stages in the European eel (Anguilla anguilla).
Journal of Fish Diseases 44:771-782.

van Rees CB, KA Waylen, A Schmidt‐Kloiber, SJ Thackeray, G Kalinkat, K Martens, S Domisch, AI Lillebø, V Hermoso, H‐P Grossart, R Schinegger, K Decleer, T Adriaens, L Denys, I Jarić, JH Janse, MT Monaghan, A De Wever, I Geijzendorffer, MC Adamescu, SC Jähnig. 2021.
Safeguarding freshwater life beyond 2020: recommendations for the new Global Biodiversity Framework from the European experience.
Conservation Letters 14:e12771.

Jähnig SC, V Baranov, F Altermatt, P Cranston, M Friedrichs-Manthey, J Geist, F He, J Heino, D Hering, F Hölker, J Jourdan, G Kalinkat, J Kiesel, F Leese, A Maasri, MT Monaghan, RB Schäfer, K Tockner, JD Tonkin, S Domisch. 2021.
Revisiting global trends in freshwater insect biodiversity.
WIREs Water 8:e1506.

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.

Serlet AJ, GA López Moreira M, G Zolezzi, G Wharton, F Hölker, AM Gurnell, K Tockner, W Bertoldi, MC Bruno, S Jähnig, J Lewandowski, MT Monaghan, MC Rillig, M Rogato, M Toffolon, SD Veresoglou, C Zarfl. 2020.
SMART Research: Towards interdisciplinary river science in Europe.
Frontiers in Environmental Science 8:63.

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

Honnen A-C, JL Kypke, F Hölker, MT Monaghan. 2019
Artificial light at night influences clock-gene expression, activity, and fecundity in the mosquito Culex pipiens f. molestus.
Sustainability 11:6220.

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.

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.

Jähnig SC, MT Monaghan, D Hering. 2019.
In-depth approach to river management. (corresp.)
Nature 572:32.

Wegner B, AL Kronsbein, M Gillefalk, K Van de Weyer, J Köhler, E Funke, MT Monaghan, S Hilt. 2019. Mutual facilitation among invading Nuttall’s waterweed and quagga mussels.
Frontiers in Plant Science 10:789.

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.

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.

Gattoliatt 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.

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.

Manfrin A, S Larsen, M Scalici, S Würtz, MT Monaghan. 2018.
Stress response of Chironomus riparius to changes in water temperature and oxygen concentration in a lowland stream.
Ecological Indicators 95:720-725.

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 Research 28:1015-1022.

Grubisic M, RHA van Grunsven, A Manfrin, MT Monaghan, F Hölker. 2018.
A transition to white LED increases ecological impacts of nocturnal illumination on aquatic primary producers in a lowland agricultural drainage ditch.
Environmental Pollution 240:630-638.

Manfrin A, D Lehmann, RHA van Grunsven, S Larsen, J Syväranta, G Wharton, CC Voigt, MT Monaghan*, F Hölker*. 2018.
Dietary changes in predators and scavengers in a nocturnally illuminated riparian ecosystem.
Oikos 127:960-969.

Grubisic M, G Singer, MC Bruno, RHA van Grunsven, A Manfrin, MT Monaghan, F Hölker. 2018.
A pigment composition analysis reveals community changes in pre-established stream periphyton under low-level artificial light at night.
Limnologica 69:55-58.

Honnen A-C, MT Monaghan. 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.

Grubisic M, G Singer, MC Bruno, RHA van Grunsven, A Manfrin, MT Monaghan, F Hölker. 2017.
Artificial light at night decreases biomass and alters community composition of benthic primary producers in a sub-alpine stream.
Limnology and Oceanography 62:2799-2810.

Manfrin A, G Singer, S Larsen, N Weiß, RHA van Grunsven, N-S Weiß, S Wohlfahrt, MT Monaghan*, F Hölker*. 2017.
Artificial light at night affects organism flux across ecosystem boundaries and drives community structure in the recipient ecosystem.
Frontiers in Environmental Science 5:61.

Watanabe K, MT Monaghan. 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.

Wurzbacher C, K Attermeyer, MT Kettner, C Flintrop, N Warthmann, S Hilt, H-P Grossart, MT Monaghan. 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.

Frenken T, E Alacid, SA Berger, EC Bourne, M Gerphagnon, H-P Grossart, AS Gsell, BW Ibelings, M Kagami, FC Küpper, PM Letcher, A Loyau, T Miki, JC Nejstgaard, S Rasconi, A Reñé, T Rohrlack, K Rojas-Jimenez, DS Schmeller, B Scholz, K Seto, T Sime-Ngando, A Sukenik, DB Van de Waal, S Van den Wyngaert, E Van Donk, J Wolinska, C Wurzbacher, R Agha. 2017.
Integrating chytrid fungal parasites into plankton ecology: Research gaps and needs.
Environmental Microbiology 19:3802-38222.

Bonada N, SM Carlson, T Datry, D Finn, C Leigh, DA Lytle, MT Monaghan, PA Tedesco. 2017.
Genetic, evolutionary and biogeographical processes in intermittent rivers and ephemeral streams.
pp. 405-431 in Intermittent Rivers and Ephemeral Streams: Ecology and Management (eds. T Datry, N Bonada, A Boulton) Academic Press (eBook ISBN 9780128039045; Paperback ISBN 9780128038352)

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

Rutschmann S*, H Detering*, S Simon, J Fredslund, MT Monaghan. 2017.
DiscoMark: Nuclear marker discovery from orthologous sequences using draft genome data.
Molecular Ecology Resources 17:257-266.

Rutschmann S, H Detering, S Simon, DH Funk, J-L Gattolliat, SJ Hughes, PM Raposeiro, R DeSalle, M Sartori, MT Monaghan. 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.

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

Schroer S, K Felsmann, F Hölker, S Mummert, MT Monaghan, C Wurzbacher, K Premke. 2016.
The impact of outdoor lighting on ecosystem function – gaining information with a Citizen Science approach using a questionnaire.
Frontiers in Environmental Science – Conference Abstract: Austrian Citizen Science Conference 2016. 10.3389/conf.FENVS.2016.01.00008

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

Wurzbacher, C, N Warthmann, EC Bourne, K Attermeyer, M Allgaier, JR Powell, H Detering, S Mbedi, H-P Grossart, MT Monaghan. 2016.
High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin.
MycoKeys 16:17-44.

Hjalmarsson A, J Bergsten, MT Monaghan. 2015.
Dispersal is linked to habitat use in 59 species of water beetles (Coleoptera: Adephaga) on Madagascar.
Ecography 38:732-739.

Holzhauer SIJ, S Franke, CCM Kyba, A Manfrin, R Klenke, CC Voigt, D Lewanzik, M Oehlert, MT Monaghan, S Schneider, S Heller, H Kuechly, A Brüning, A-C Honnen, F Hölker. 2015.
Out of the dark: establishing a large-scale field experiment to assess the effects of artificial light at night on species and food webs.
Sustainability 7:15593-15616.

Hölker F, C Wurzbacher, C Weißenborn, MT Monaghan, SIJ Holzhauer, K Premke. 2015.
Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night.
Philisophical Transactions of the Royal Society B

Rutschmann S, J-L Gattolliat, SJ Hughes, M Báez, M Sartori*, MT Monaghan*. 2014.
Evolution and island-endemism of morphologically cryptic Baetis and Cloeon species (Ephemeroptera, Baetidae) on the Canary Islands and Madeira.
Freshwater Biology 59:2516-2527.

Toussaint EFA, R Hall, MT Monaghan, K Sagata, S Ibalim, HV Shaverdo, AP Vogler, J Pons, M Balke. 2014.
The towering orogeny of New Guinea as a trigger of arthropod megadiversity.
Nature Communications 5:4001.

Dijkstra, K-D B, MT Monaghan, SU Pauls. 2014.
Freshwater biodiversity and aquatic insect diversification.
Annual Review of Entomology 59:143-163.

Danabalan, R, MT Monaghan, DJ Ponsonby, Y-M Linton. 2014.
Occurrence and host preference of Maculipennis Group mosquitoes in England and Wales.
Medical and Veterinary Entomology 28:169-178.

Gamboa M, MT Monaghan. 2014.
Association of adult female and male stoneflies (Plecoptera) from an Alpine river using wing morphometrics and mitochondrial DNA.
Aquatic Insects 36:1-8.

Geiger MF F Herder, MT Monaghan, V Almada, R Barbieri, M Bariche, P Berrebi, J Bohlen, M Casal-Lopez, G B Delmastro, GPJ Denys, A Dettai, I Doadrio, E Kalogianni, H Kärst, M Kottelat, M Kovačić, M Laporte, M Lorenzoni, Z Marčić, M Özuluğ, A Perdices, S Perea, H Persat, S Porcelotti, C Puzzi, J Robalo, R Šanda, M Schneider, V Šlechtová, M Stumboudi, S Walter, J Freyhof. 2014.
Spatial heterogeneity in the Mediterranean biodiversity hotspot affects barcoding accuracy of its freshwater fishes.
Molecular Ecology Resources 14:1210-1221.

Hughes JM, DS Finn, MT Monaghan, A Schultheis, BW Sweeney. 2014.
Basic and applied uses of molecular approaches in freshwater ecology.
Freshwater Science 33:168-171.

Pauls SU, M Alp, M Bálint, P Bernabò, F Čiampor Jr, Z Čiamporová-Zat’ovičová, 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.

Yaegashi S, K Watanabe, MT Monaghan, T Omura. 2014.
Fine-scale dispersal in a stream caddisfly inferred from spatial autocorrelation of microsatellite markers.
Freshwater Science 33:172-180.

Watanabe K, S Kazama, T Omura, MT Monaghan. 2014.
Adaptive genetic divergence along narrow environmental gradients in four stream insects.
PLoS ONE 9:e93055.

Baselga, A, T Fujisawa, A Crampton-Platt, J Bergsten, PG Foster, MT Monaghan, AP Vogler. 2013.
Whole-community DNA barcoding reveals a spatiotemporal continuum of biodiversity at species and genetic levels.
Nature Communications 4:1892.

Hilt, S, J Köhler, R Adrian, MT Monaghan, CD Sayer. 2013.
Clear, crashing, turbid and back – long-term macrophyte changes in a shallow lake.
Freshwater Biology 58:2027-2036.

Scharnweber, K, K Watanabe, J Syväranta, T Wanke, MT Monaghan, T Mehner. 2013.
Effects of predation pressure and resource use on morphological divergence in omnivorous prey fish.
BMC Evolutionary Biology 13:132.

Vuataz, L, M Sartori, J-L Gattolliat, MT Monaghan. 2013.
Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections.
Molecular Phylogenetics and Evolution 66:979-991.

Bergsten, J, DT Bilton, T Fujisawa, M Elliott, MT Monaghan, M Balke, L Hendrich, J Geijer, J Herrmann, GN Foster, I Ribera, AN Nilsson, TG Barraclough, AP Vogler. 2012.
The effect of geographical scale of sampling on DNA barcoding.
Systematic Biology 61:851-869.

Dziallas, C, M Allgaier, MT Monaghan, H-P Grossart. 2012.
Act together – implications of symbioses in aquatic ciliates.
Frontiers in Microbiology 3:288.

Gamboa, M, RK Kimbirauskas, RW Merritt, MT Monaghan. 2012.
A molecular approach to identifying the natural prey of the African creeping water bug Naucoris, a potential reservoir of Mycobacterium ulcerans.
Journal of Insect Science 12:2.

Gerecke, R, MT Monaghan. 2012.
Eintagsfliegen (Ephemeroptera).
Schriften des Nationalparks Gesäuse 7:132-141.

Powell, JR, MT Monaghan, M Opik, MC Rillig. 2011.
Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories.
Molecular Ecology 20:655-66.

Vuataz, L, A Wagner, M Sartori, MT Monaghan. 2011.
Toward a DNA Taxonomy of Alpine Rhithrogena (Ephemeroptera: Heptageniidae) using a mixed Yule-coalescent analysis of mitochondrial and nuclear DNA.
PLoS ONE 6:e19728.

Isambert, B, J Bergsten, MT Monaghan, H Andriamizehy, T Ranarilalatiana, M Ratsimbazafy, J-R Andriniainimanana, AP Vogler. 2011.
Contrasting patterns of endemism and evolutionary history in the freshwater biodiversity of Madagascar.
Biological Conservation 144:1902-1909.

Walz N, R Adrian, JJ Gilbert, MT Monaghan, G Weithoff, H Zimmermann-Timm. 2011.
Preface – Rotifera XII.
Hydrobiologia 662:1-4.

Monaghan, MT, SU Pauls, JM Hughes, CT Robinson. 2010.
Evolutionary ecology, systematics, speciation, and phylogeography in benthology – Preface.
Journal of the North American Benthological Society 29:1024-1036.

Mehner, T, K Pohlmann, C Elkin, MT Monaghan, B Nitz, J Freyhof. 2010.
Genetic population structure of sympatric and allopatric populations of Baltic ciscoes Coregonus albula complex, Teleostei, Coregonidae).
BMC Evolutionary Biology 10:85.

Gattolliat J-L, MT Monaghan. 2010.
DNA-based association of adults and larvae in Baetidae (Ephemeroptera) with the description of a new genus Adnoptilum in Madagascar.
Journal of the North American Benthological Society 29:1042-1057.

Watanabe K, MT Monaghan, Y Takemon, T Omura. 2010.
Dispersal ability determines the genetic effects of habitat fragmentation caused by reservoirs in three species of aquatic insect.
Aquatic Conservation – Marine and Freshwater Ecosystems 20:574-579.

Lozan, AI, SA Belokobylskij, C van Achterberg, MT Monaghan. 2010.
Diversity and distribution of Braconidae (Hymenoptera, Ichneumonoidea) in the Central European peatbogs of South Bohemia, Czech Republic.
Journal of Insect Science 10:16.

Monaghan, MT, R Wild, M Elliot, T Fujisawa, M Balke, DJG Inward, DC Lees, R Ranaivosolo, P Eggleton, TG Barraclough, AP Vogler. 2009.
Accelerated species inventory on Madagascar using coalescent-based models of species delineation.
Systematic Biology 58:298-311.

Monaghan, MT, M Sartori. 2009.
Genetic contributions to the study of taxonomy, ecology, and evolution of mayflies (Ephemeroptera): review and future perspectives.
Aquatic Insects 31 Suppl. 1:19-39.

Papadopoulou, A, MT Monaghan, TG Barraclough, AP Vogler. 2009.
Sampling error does not invalidate the Yule-coalescent model for species delimitation. A response to Lohse (2009).
Systematic Biology 58:442-444.

Mehner, T, K Pohlmann, C Elkin, MT Monaghan, J Freyhof. 2009.
Genetic mixing from enhancement stocking in commercially exploited vendace populations.
Journal of Applied Ecology 46:1340-1349.

Gattolliat, J-L, H Barber-James, MT Monaghan 2009.
New species and generic delimitation of the Afrotropical Baetidae (Ephemeroptera) genera Bugilliesia Lugo-Ortiz & McCafferty 1996, Cheleocloeon Wuilot & Gillies 1993 and Delouardus Lugo-Ortiz & McCafferty 1999 (Baetidae; Ephemeroptera).
Aquatic Insects 31:167-186.

Tabacchi, E, J Steiger, D Corenblit, MT Monaghan, A-M. Planty-Tabacchi. 2009.
Implications of biological and physical diversity for resilience and resistance patterns within Highly Dynamic River Systems.
Aquatic Sciences 71:279-289.

Papadapoulou, A, J Bergsten, T Fujisawa, MT Monaghan, TG Barraclough, AP Vogler. 2008.
Speciation and DNA barcodes – testing the effects of dispersal on the formation of discrete sequence clusters.
Philosophical Transactions of the Royal Society of London B Biological Sciences 363:2987-2996.

Watanabe, K, MT Monaghan, Y Takemon, T Omura. 2008.
Biodilution of heavy metals in a stream macroinvertebrate food web: evidence from stable isotope analysis.
Science of the Total Environment 394:57-67.

Lozan, A, MT Monaghan, K Spitzer, J Jaros, M Zurovcova, V Broz. 2008.
Genetic confirmation that the parasitic wasp Cotesia glomerata (L.) (Braconidae, Hymenoptera) is a new threat to endemic butterflies of the Canary Islands.
Conservation Genetics 9:1431-1437.

Shaverdo, H, MT Monaghan, DC Lees, R Ranaivosolo, M Balke. 2008.
A new genus of Malagasy endemic diving beetles and description of a highly unusual species based on morphology and DNA sequence data (Dytiscidae: Copelatinae).
Systematics and Biodiversity 6:43-51.

Gattolliat, J-L, SJ Hughes, MT Monaghan, M Sartori. 2008.
Revision of Madeiran mayflies (Insecta, Ephemeroptera).
Zootaxa 1957:52-68.

Watanabe, K, MT Monaghan, T Omura. 2008.
Longitudinal patterns of genetic diversity and larval density of the riverine caddisfly Hydropsyche orientalis (Trichoptera).
Aquatic Sciences 70:377-387.

Gattolliat, J-L, MT Monaghan, M Sartori, J-M Elouard, H Barber-James, FC deMoor, P Derleth, O Glaizot, AP Vogler. 2008.
A molecular analysis of the Afrotropical Baetidae.
pp 219-232 In International Advances in the Ecology, Zoogeography and Systematics of Mayflies and Stoneflies (eds. FR Hauer, JA Stanford, RL Newell) University of California Press, Berkeley.

Monaghan, MT, DG Inward, T Hunt, AP Vogler. 2007.
A molecular phylogenetic analysis of the Scarabaeinae (dung beetles).
Molecular Phylogenetics and Evolution 45:674-692.

Ahrens, D, MT Monaghan, AP Vogler. 2007.
DNA-based taxonomy for associating adults and larvae in multi-species assemblages of chafers (Coleoptera: Scarabaeidae).
Molecular Phylogenetics and Evolution 44:436-449.

Vogler, AP, MT Monaghan. 2007.
Recent advances in DNA taxonomy.
Journal of Zoological Systematics and Evolutionary Research 45:1-10.

Monaghan, MT, M Balke, J Pons, AP Vogler. 2006.
Beyond barcodes: complex DNA taxonomy of a South Pacific Island radiation.
Proceedings of the Royal Society of London B Biological Sciences 273:887-893.

Monaghan, MT, M Balke, TR Gregory, AP Vogler. 2005.
DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.
Philosophical Transactions of the Royal Society of London B Biological Sciences 360:1925-1933.

Monaghan, MT, J-L Gattolliat, M Sartori, J-M Elouard, H James, P Derleth, O Glaizot, FC de Moor, AP Vogler. 2005.
Trans-oceanic and endemic origins of the small minnow mayflies (Ephemeroptera, Baetidae) of Madagascar.
Proceedings of the Royal Society of London B Biological Sciences 272:1829-1836.

Monaghan, MT, CT Robinson, P Spaak, JV Ward. 2005.
Macroinvertebrate species richness and nestedness in fragmented alpine streams: implications for freshwater conservation.
Aquatic Sciences 67:454-464.

Giller, P, H Hillebrand, U-G Berninger, MO Gessner, S Hawkins, P Inchausti, C Inglis, H Leslie, B Malmqvist, MT Monaghan, PJ Morin, G O’Mullan. 2004.
Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environments.
Oikos 104:423-436.

Gili, M, MT Monaghan, P Spaak. 2004.
Amplified fragment length polymorphism (AFLP) reveals species-specific markers in the Daphnia galeata-hyalina species complex.
Hydrobiologia 526:63-71.

Robinson, CT, U Uehlinger, MT Monaghan 2004.
Stream ecosystem response to multiple experimental floods from a reservoir.
River Research and Applications 20:359-377.

Robinson, CT, U Uehlinger, MT Monaghan 2003.
Effects of a multi-year experimental flood regime on macroinvertebrates downstream of a reservoir.
Aquatic Sciences 65:210-222.

Georgian, T, JD Newbold, SA Thomas, MT Monaghan, GW Minshall, CE Cushing. 2003.
Comparison of corn pollen and natural fine particulate matter transport in streams: can pollen be used as a seston surrogate?
Journal of the North American Benthological Society 22:2-16.

Monaghan, MT, P Spaak, CT Robinson, JV Ward. 2002.
Population genetic structure of 3 Alpine stream insects: influences of gene flow, demographics, and habitat fragmentation.
Journal of the North American Benthological Society 21:114-131.

Monaghan, MT, M Hieber, CT Robinson, P Spaak, JV Ward. 2002.
Spatial patterns of Ephemeroptera, Plecoptera, and Trichoptera species diversity in fragmented alpine streams.
Verh. Internat. Verein. Limnol. (Proceedings of the International Limnological Society) 28:1429-1435.

Monaghan, MT, P Spaak, CT Robinson, JV Ward. 2001.
Genetic differentiation of Baetis alpinus Pictet (Ephemeroptera: Baetidae) in fragmented alpine streams.
Heredity 86:395-403.

Monaghan, MT, SA Thomas, GW Minshall, JD Newbold, CE Cushing. 2001.
The influence of filter-feeding benthic macroinvertebrates on the transport and deposition of particulate organic matter and diatoms in two streams.
Limnology and Oceanography 46:1091-1099.

Thomas, SA, JD Newbold, MT Monaghan, GW Minshall, T Georgian, CE Cushing. 2001.
The influence of particle size on the deposition of seston in streams.
Limnology and Oceanography 46:1415-1424.

Winder, M, MT Monaghan, P Spaak. 2001.
Have human impacts changed alpine zooplankton diversity over the past 100 years?
Arctic, Antarctic, and Alpine Research 33:467-475.

Minshall, GW, SA Thomas, JD Newbold, MT Monaghan, CE Cushing. 2000.
Physical influences on organic particle transport and deposition in streams.
Journal of the North American Benthological Society 19:1-16.

Royer, TV, MT Monaghan, GW Minshall. 1999.
Processing of native and exotic leaf litter in two Idaho (USA) streams.
Hydrobiologia 400:123-128.

*equal contributions