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2018 and In press
 Haase, P., F. Pilotto, F. Li, A. Sundermann, A. W. Lorenz, J. D. Tonkin, and S. Stoll. (In press). Moderate warming over the past 25 years has already reorganized stream invertebrate communities. Science of the Total Environment.
 Van Looy, K., J. D. Tonkin, M. Floury, C. Leigh, J. Soininen, S. Larsen, J. Heino, N. L. Poff, M. Delong, S. C. Jähnig, T. Datry, N. Bonada, J. Rosebery, A. Jamoneau, S. J. Ormerod, K. J. Collier, and C. Wolter. (In press). The three Rs of river ecosystem resilience: Resources, Recruitment and Refugia. River Research and Applications.
 Tiegs, S. D., et al. (incl. J. D. Tonkin). (In press). Global patterns and drivers of ecosystem functioning in rivers and riparian zones. Science Advances.
 Jourdan, J., M. Plath, J. D. Tonkin, M. Ceylan, A. C. Dumeier, G. Gellert, W. Graf, C. P. Hawkins, E. Kiel, A. Lorenz, C. Matthaei, P. Verdonschot, R. Verdonschot, and P. Haase. 2018. Reintroduction of freshwater macroinvertebrates: challenges and opportunities. Biological Reviews DOI:10.1111/brv.12458.
 Pilotto, F., J. D. Tonkin, K. Januschke, A. W. Lorenz, J. Jourdan, V. Baranov, A. Sundermann, D. Hering, S. Stoll, and P. Haase. 2018. Diverging response patterns of terrestrial and aquatic species to hydromorphological restoration. Conservation Biology DOI:10.1111/cobi.13176.
 Li, F., J. D. Tonkin, and P. Haase. 2018. Dispersal capacity and broad-scale landscape structure shape communities along stream networks. Limnologica 71:68-74.
 Tonkin, J. D., R. G. Death, T. Muotka, A. Astorga, and D. A. Lytle. 2018. Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities? PeerJ 6:e4898.
 Dalu, T., M. L. Magoro, J. D. Tonkin, L. R. D. Human, R. Perissinotto, S. H. P. Deyzel, J. B. Adams, and A. K. Whitfield. 2018. Assessing phytoplankton composition and structure within micro-estuaries and micro-outlets: A community analysis approach. Hydrobiologia 818:177–191.
 Wetzel, F. T., H. Bingham, Q. Groom, P. Haase, U. Köljalg, M. Kuhlmann, C. S. Martin, L. Penev, T. Robertson, H. Saarenmaa, D. S. Schmeller, S. Stoll, J. D. Tonkin, and C. Häuser. 2018. Unlocking biodiversity data - Prioritization and filling the gaps in biodiversity observation data in Europe. Biological Conservation 221:78-85.
 Jourdan, J, R. B. O’Hara, R. Bottarin, T. Hiura, K. Huttunen, M. Kuemmerlen, D. Monteith, T. Muotka, T. Ohta, R. Paavola, F. Pilotto, G. Springe, S. Stoll, A. Sundermann, J. D. Tonkin, and P. Haase. 2018. Effects of changing climate on European stream invertebrate communities: a long-term data analysis. Science of the Total Environment 621:588-599.
 Tonkin, J. D., J. D. Olden, D. M. Merritt, L. V. Reynolds, and D. A. Lytle. 2018. Flow regime alteration degrades ecological networks in riparian ecosystems. Nature Ecology & Evolution 2:86-93.
 Tonkin, J. D., F. Altermatt, D. Finn, J. Heino, J. D. Olden, S. U. Pauls, and D. A. Lytle. 2018. The role of dispersal in river network metacommunities: patterns, processes, and pathways. Freshwater Biology 63:141–163.
 Haase, P.*, J. D Tonkin*, S. Stoll*, B. Burkhard, M. Frenzel, I. R. Geijzendorffer, C. Haeuser, S. Klotz, I. Kühn, W. H. McDowell, M. Mirtl, F. Müller, M. Musche, J. Penner, S. Zacharias, and D. S. Schmeller. 2018. The next generation of site-based long-term ecological monitoring: Linking Essential Biodiversity Variables and Ecosystem Integrity. Science of the Total Environment 613–614:1376-1384. * Contributed equally
 McMullen, L. E., P. DeLeenheer, J. D. Tonkin, and D. A. Lytle. 2017. High mortality and enhanced recovery: modeling the countervailing effects of disturbance on population dynamics. Ecology Letters DOI:10.1111/ele.12866.
 Dalu, T., R. J. Wasserman, J. D. Tonkin, T. Mwedzi, M. Magoro, and O. L. F Weyl. 2017. Water or sediment? Partitioning the role of water column and sediment chemistry as drivers of macroinvertebrate communities in an austral South African stream. Science of the Total Environment 607-608:317-325.
 Dalu, T., R. J. Wasserman, M. E. Alexander, J. D. Tonkin, S. N. Motitsoe, M. T. B. Sachikonye, K. I. Manungo, O. Bepe, and T. Dube. 2017. Assessing drivers of benthic macroinvertebrate community structure in African highlands: an exploration using multivariate analysis. Science of the Total Environment 601-602:1340-1348.
 Jähnig, S. C., J. D. Tonkin, M. Gies, S. Domisch, D. Hering, and P. Haase. 2017. Severity multipliers as a methodology to explore potential effects of climate change on stream bioassessment programs. Water 9:188.
 Höckendorff, S., J. D. Tonkin, P. Haase, M. Bunzel-Drüke, O. Zimball, M. Scharf, and S. Stoll. (In press). Characterizing fish responses to a river restoration based on 21 years of sampling: the role of time and species traits. Conservation Biology DOI:10.1111/cobi.12908.
 Lytle, D. A., D. M. Merritt, J. D. Tonkin, J. D. Olden, and L. V. Reynolds. 2017. Linking river flow regimes to riparian plant guilds: a community-wide modeling approach. Ecological Applications DOI:10.1002/eap.1528.
 Tonkin, J. D., M. T. Bogan, N. Bonada, B. Rios-Touma, and D. A. Lytle. 2017. Seasonality and predictability shape temporal species diversity. Ecology DOI:10.1002/ecy.1761.
 Tonkin, J. D., R. D. T. Shah, D. N. Shah, F. Hoppeler, S. C. Jähnig, and S. U. Pauls. 2017. Metacommunity structuring in Himalayan streams over large elevational gradients: the role of dispersal routes and niche characteristics. Journal of Biogeography DOI:10.1111/jbi.12895.
 Stoll, S., N. Hormel, D. Früh, and J. D. Tonkin. 2017. Effects of Chaetogaster limnaei limnaei on freshwater snail communities. Hydrobiologia DOI:10.1007/s10750-016-2909-1.
 Hoppeler, F., R. D. T. Shah, D. N. Shah, S. C. Jähnig , J. D. Tonkin, S. Sharma, and S. U. Pauls. 2016. Environmental and spatial characterisation of an unknown fauna using DNA sequencing – An example with Himalayan Hydropsychidae (Insecta: Trichoptera). Freshwater Biology DOI:10.1111/fwb.12824.
 Tonkin, J. D., F. O. Arimoro, and P. Haase. 2016. Exploring stream communities in a tropical biodiversity hotspot: biodiversity, regional occupancy, niche characteristics and environmental correlates. Biodiversity and Conservation 25:975–993.
 Leps, M., A. Sundermann, J. D. Tonkin, A. W. Lorenz, and P. Haase. 2016. Time is no healer: increasing restoration age does not lead to improved benthic invertebrate communities in restored rivers. Science of the Total Environment 557–558:722–732.
 Stoll, S., P. Breyer, J. D. Tonkin, D. Früh, and P. Haase. 2016. Scale-dependent effects of river habitat quality on benthic invertebrate communities - implications for stream restoration practice. Science of the Total Environment 553:495–503.
 Tonkin, J. D., J. Heino, A. Sundermann, P. Haase, and S. C. Jähnig. 2016. Context dependency in biodiversity patterns of central German stream metacommunities. Freshwater Biology DOI:10.1111/fwb.12728.
 Tonkin, J. D., S. Stoll, S. C. Jähnig, and P. Haase. 2016. Elements of metacommunity structure of river and riparian assemblages: communities, taxonomic groups and deconstructed trait groups. Ecological Complexity 25:35-43.
 Tonkin, J. D., S. Stoll, S. C. Jähnig, and P. Haase. 2016. Anthropogenic land use stress alters community concordance at the river-riparian interface. Ecological Indicators DOI:10.1016/j.ecolind.2015.08.037.
 Tonkin, J. D., S. Stoll, S. C. Jähnig, and P. Haase. 2016. Contrasting metacommunity structure and beta diversity in a river-floodplain system. Oikos DOI:10.1111/oik.02717.
 Shah, D. N., J. D. Tonkin, P. Haase, and S. C. Jähnig. 2015. Latitudinal patterns and large-scale environmental determinants of stream insect richness across Europe. Limnologica 55:33-43.
 Tonkin, J. D., A. Sundermann, S. C. Jähnig, and P. Haase. 2015. Environmental controls on river assemblages at the regional scale: an application of the Elements of Metacommunity Structure framework. PLOS ONE 10(8): e0135450.
 Leps, M., J. D. Tonkin, V. Dahm, D. Hering, P. Haase, and A. Sundermann. 2015. Disentangling environmental drivers of benthic invertebrate assemblages: the role of spatial scale and riverscape heterogeneity in a multiple stressor environment. Science of the Total Environment.
 Jähnig, S. C., D. N. Shah, R. D. T. Shah, F. Li, Q. Cai, A. Sundermann, J. D. Tonkin, and S. Stendera. 2015. Community-environment relationships of riverine invertebrate communities in central Chinese streams. Environmental Earth Sciences.
 Tonkin, J. D., D. N. Shah, M. Kuemmerlen, F. Li, Q. H. Cai, P. Haase, and S. C. Jähnig. 2015. Climatic and catchment-scale predictors of Chinese stream insect richness differ between taxonomic groups. PLOS ONE 10:e0123250.
 Tonkin, J. D., A. Brown, and E. M. Chappell. 2015. Small-scale patch complexity, benthic invertebrate colonisation and leaf breakdown in three headwater streams in Bay of Plenty, New Zealand. New Zealand Journal of Marine and Freshwater Research.
 Chappell, E. M., D. S. Webb, A. J. Brown, and J. D. Tonkin. 2015. A preliminary survey of altitudinal variation in two ground weta species, Hemiandrus maculifrons and H. pallitaris (Walker) (Orthoptera: Anostostomatidae). New Zealand Entomologist 38:1-6.
 Tonkin, J. D. 2014. Drivers of macroinvertebrate community structure in unmodified streams. PeerJ 2:e465.
 Tonkin, J. D., S. C. Jähnig, and P. Haase. 2014. The rise of riverine flow-ecology and environmental flow research. Environmental Processes 1:323-330.
 Tonkin, J. D., R. G. Death, and J. Barquin. 2014. Periphyton control on stream invertebrate communities: is periphyton architecture more important than biomass? Marine and Freshwater Research 65:818-829.
 Tonkin, J. D., S. Stoll, A. Sundermann, and P. Haase. 2014. Dispersal distance and the pool of taxa, but not barriers, determine the colonisation of restored river reaches by benthic invertebrates. Freshwater Biology 59:1843-1855.
 Chappell, E. M., D. S. Webb, and J. D. Tonkin. 2014. Notes on sexual size dimorphism, sex ratio and movement of ground weta Hemiandrus maculifrons (Walker) (Orthoptera: Anostostomatidae) in Otanewainuku Forest, Bay of Plenty, New Zealand. New Zealand Entomologist 37:3-92.
 David, B. O., J. D. Tonkin, K. W. T. Taipeti and H. Hokianga. 2014. Learning the ropes: mussel spat ropes improve fish and shrimp passage through culverts. Journal of Applied Ecology 51:214-223.
 Tonkin, J. D., and R. G. Death. 2014. The combined effects of flow regulation and an artificial flow release on a regulated river. River Research and Applications 30:329-337.
 Tonkin, J. D., and R. G. Death. 2013. Scale dependent effects of productivity and disturbance on diversity in streams. Fundamental and Applied Limnology 182:283-295. Editor’s Choice
 Tonkin, J. D., and R. G. Death. 2013. Macroinvertebrate drift-benthos trends in a regulated river. Fundamental and Applied Limnology 182:231-245.
 Tonkin, J. D., R. G. Death, and J. Barquin. 2013. Productivity-diversity relationships for stream invertebrates differ geographically. Aquatic Ecology 47:109-121.
 Tonkin, J. D., R. G. Death, and K. J. Collier. 2013. Do productivity and disturbance interact to modulate macroinvertebrate diversity in streams? Hydrobiologia 701:159-172.
2012 and earlier
 Tonkin, J. D., and R. G. Death. 2012. Consistent effects of productivity and disturbance on diversity between landscapes. Ecosphere 3:art108.
 Tonkin, J. D., L. A. H. Wright, and B. O. David. 2012. Mussel spat ropes assist redfin bully (Gobiomorphus huttoni) passage through experimental culverts with hydrological barriers. Water 4:683-689.
 Schwendel, A. C., R. G. Death, I. C. Fuller, and J. D. Tonkin. 2012. A new approach to assess bed stability relevant for invertebrate communities in upland streams. River Research and Applications 28:1726-1739.
 Collier, K. J., B. Aldridge, B. J. Hicks, J. Kelly, A. Macdonald, B. J. Smith, and J. Tonkin. 2009. Ecological values of Hamilton urban streams (North Island, New Zealand): constraints and opportunities for restoration. New Zealand Journal of Ecology 33:177-189.
 Tonkin, J. D., R. G. Death, and M. K. Joy. 2009. Invertebrate drift patterns in a regulated river: dams, periphyton biomass or longitudinal patterns? River Research and Applications 25:1219-1231.
Tonkin, J. D., J. Heino, and F. Altermatt. 2018. Editorial: Metacommunities in river networks: the importance of network structure and connectivity on patterns and processes. Freshwater Biology 63:1-5.
Tonkin, J. D. 2011. The effects of productivity and disturbance on diversity in stream communities. PhD thesis, Massey University, New Zealand.
Tonkin, J. D. 2006. The effects of flow regulation on macroinvertebrate drift in the Tongariro River, New Zealand. Unpublished Honours thesis, Massey University, Palmerston North.
David, B., M. Hamer, J. Tonkin, and C. Bourke. 2014. Appropriate use of mussel spat ropes to facilitate passage for stream organisms. Waikato Regional Council Technical Report 2014/29, Hamilton, New Zealand.
Tonkin, J. D., A. M. F. Macdonald, and M. K. Joy. 2004. Manawatu-Wanganui brown mudfish (Neochanna apoda) survey Report to horizons.mw.
Tonkin J. D., R. G. Death, and F. Death. 2005. Freshwater fish survey of the lowland Manawatu-Wanganui region Report to horizons.mw.
Tonkin, J. D. 2008. Makino Stream Tributary Fish Survey. Report to Rangitikei District Council, Massey University, Palmerston North.
Tonkin J. D. 2008. Reporoa Stream Fish Survey. Report to Rangitikei District Council, Massey University, Palmerston North.