SEARCH

SEARCH BY CITATION

References

  • Allan J.D. & Castillo M.M. (2010) Stream Ecology: Structure and Function of Running Waters. Springer, Dordrecht.
  • Allendorf F.W., Leary R.F., Spruell P. & Wenburg J.K. (2001) The problems with hybrids: setting conservation guidelines. Trends in Ecology & Evolution, 16, 613622.
  • Alp M., Keller I., Westram A.M. & Robinson C.T. (2012) How river structure and biological traits influence gene flow: a population genetic study of two stream invertebrates with differing dispersal abilities. Freshwater Biology, 57, 969981.
  • Andreou A., Vacquie-Garcia J., Cucherousset J., Blanchet S., Gozlan R.E. & Loot G. (2012) Individual genetic tagging for teleost fishes: an empirical validation and a guideline for ecologists. Journal of Fish Biology, 80, 181194.
  • Andrew R.L., Bernatchez L., Bonin A., Buerkle C.A., Carstens B.C., Emerson B.C. et al. (2013) A road map for molecular ecology. Molecular Ecology, 22, 26052626.
  • Baird D.J. & Hajibabaei M. (2012) Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology, 21, 20392044.
  • Baird D.J. & Sweeney B.W. (2011) Applying DNA barcoding in benthology: the state of the science. Journal of the North American Benthological Society, 30, 122124.
  • Bálint M., Domisch S., Engelhardt C.H.M., Haase P., Lehrian S., Sauer J. et al. (2011) Cryptic biodiversity loss linked to global climate change. Nature Climate Change, 1, 313318.
  • Bálint M., Málnás K., Nowak C., Geismar J., Váncsa É., Polyák L. et al. (2012) Species history masks the effects of human-induced range loss – unexpected genetic diversity in the endangered giant mayfly Palingenia longicauda. PLoS One, 7, e31872.
  • Balkenhol N. & Landguth E.L. (2011) Simulation modelling in landscape genetics: on the need to go further. Molecular Ecology, 20, 667670.
  • Balkenhol N., Waits L.P. & Dezzani R.J. (2009) Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography, 32, 818830.
  • Baselga A., Fujisawa T., Crampton-Platt A., Bergsten J., Foster P.G., Monaghan M.T. et al. (2013) Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels. Nature Communications, 4, 1892.
  • Beaumont M.A., Zhang W.Y. & Balding D.J. (2002) Approximate Bayesian computation in population genetics. Genetics, 162, 20252035.
  • Bergsten J., Bilton D.T., Fujisawa T., Elliott M., Monaghan M.T., Balke M. et al. (2012) The effect of geographical scale of sampling on DNA barcoding. Systematic Biology, 61, 851869.
  • Bernabò P., Rebecchi L., Jousson O., Martinez-Guitarte J.L. & Lencioni V. (2011) Thermotolerance and hsp70 heat shock response in the cold-stenothermal chironomid Pseudodiamesa branickii (NE Italy). Cell Stress & Chaperones, 16, 403410.
  • Blanchet S. (2012) The use of molecular tools in invasion biology: an emphasis on freshwater ecosystems. Fisheries Management and Ecology, 19, 120132.
  • Blanchet S., Rey O., Etienne R., Lek S. & Loot G. (2010) Species-specific responses to landscape fragmentation: implications for management strategies. Evolutionary Applications, 3, 291304.
  • Bonada N., Múrria C., Zamora-Munoz C., El Alami M., Poquet J.M., Punti T. et al. (2009) Using community and population approaches to understand how contemporary and historical factors have shaped species distribution in river ecosystems. Global Ecology and Biogeography, 18, 202213.
  • Braaker S. & Heckel G. (2009) Transalpine colonisation and partial phylogeographic erosion by dispersal in the common vole (Microtus arvalis). Molecular Ecology, 18, 25182531.
  • Brändle M., Heuser R., Marten A. & Brandl R. (2007) Population structure of the freshwater flatworm Crenobia alpina (Dana): old lineages and low gene flow. Journal of Biogeography, 34, 11831192.
  • Bunn S.E. & Hughes J.M. (1997) Dispersal and recruitment in streams: evidence from genetic studies. Journal of the North American Benthological Society, 16, 338346.
  • Carstens B., Lemmon A.R. & Lemmon E.M. (2012) The promises and pitfalls of next-generation sequencing data in phylogeography. Systematic Biology, 61, 713715.
  • Chaput-Bardy A., Fleurant C., Lemaire C. & Secondi J. (2009) Modelling the effect of in-stream and overland dispersal on gene flow in river networks. Ecological Modelling, 220, 35893598.
  • Chikhi L., Sousa V.C., Luisi P., Goossens B. & Beaumont M.A. (2010) The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics, 186, 983995.
  • Čiamporová-Zaťovičová Z. & Čiampor F. (2011) Aquatic beetles of the alpine lakes: diversity, ecology and small-scale population genetics. Knowledge and Management of Aquatic Ecosystems, 402, 110.
  • Colbourne J.K., Pfrender M.E., Gilbert D., Thomas W.K., Tucker A., Oakley T.H. et al. (2011) The ecoresponsive genome of Daphnia pulex. Science, 331, 555561.
  • Cook B.D., Kennard M.J., Real K., Pusey B.J. & Hughes J.M. (2011) Landscape genetic analysis of the tropical freshwater fish Mogurnda mogurnda (Eleotridae) in a monsoonal river basin: importance of hydrographic factors and population history. Freshwater Biology, 56, 812827.
  • Cornuet J.M., Santos F., Beaumont M.A., Robert C.P., Marin J.M., Balding D.J. et al. (2008) Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics, 24, 27132719.
  • Costedoat C., Pech N., Chappaz R. & Gilles A. (2007) Novelties in hybrid zones: crossroads between population genomic and ecological approaches. PLoS One, 2, e357.
  • Csillery K., Blum M.G.B., Gaggiotti O.E. & Francois O. (2010) Approximate Bayesian Computation (ABC) in practice. Trends in Ecology & Evolution, 25, 410418.
  • Davies K.F., Margules C.R. & Lawrence K.F. (2000) Which traits of species predict population declines in experimental forest fragments? Ecology, 81, 14501461.
  • Depraz A., Cordellier M., Hausser J. & Pfenninger M. (2008) Postglacial recolonization at a snail's pace (Trochulus villosus): confronting competing refugia hypotheses using model selection. Molecular Ecology, 17, 24492462.
  • DeWalt R.E. (2011) DNA barcoding: a taxonomic point of view. Journal of the North American Benthological Society, 30, 174181.
  • Dijkstra K.-D.B., Monaghan M.T. & Pauls S.U. (2014) Ecological diversification and the evolution of freshwater insect diversity. Annual Review of Entomology, 59, 143163.
  • Domisch S., Araújo M.B., Bonada N., Pauls S.U., Jähnig S.C. & Haase P. (2013) Modelling distribution in European stream macroinvertebrates under future climates. Global Change Biology, 19, 752762.
  • Dubut V., Grenier R., Meglecz E., Chappaz R., Costedoat C., Danancher D. et al. (2010) Development of 55 novel polymorphic microsatellite loci for the critically endangered Zingel asper L. (Actinopterygii: Perciformes: Percidae) and cross-species amplification in five other percids. European Journal of Wildlife Research, 56, 931938.
  • Elbrecht V.E., Feld C.K., Hering D., Gies M., Sondermann M., Tollrian R. & Leese F. (2014) Genetic diversity and dispersal potential of the stonefly Dinocras cephalotes in a central European low mountain range. Freshwater Science, 33, 181192.
  • Engelhardt C.H.M., Haase P. & Pauls S.U. (2011) From the Western Alps across Central Europe: postglacial recolonisation of the tufa stream specialist Rhyacophila pubescens (Insecta, Trichoptera). Frontiers in Zoology, 8, 114.
  • Estoup A. & Guillemaud T. (2010) Reconstructing routes of invasion using genetic data: why, how and so what? Molecular Ecology, 19, 41134130.
  • Etienne R. & Olff H. (2004) A novel genealogical approach to neutral biodiversity theory. Ecology Letters, 7, 170175.
  • Evanno G., Castella E., Antoine C., Paillat G. & Goudet J. (2009) Parallel changes in genetic diversity and species diversity following a natural disturbance. Molecular Ecology, 18, 11371144.
  • Faubet P. & Gaggiotti O.E. (2008) A new Bayesian method to identify the environmental factors that influence recent migration. Genetics, 178, 14911504.
  • Ficetola G.F., Miaud C., Pompanon F. & Taberlet P. (2008) Species detection using environmental DNA from water samples. Biology Letters, 4, 423425.
  • Finn D.S., Bonada N., Múrria C. & Hughes J.M. (2011) Small but mighty: headwaters are vital to stream network biodiversity at two levels of organization. Journal of the North American Benthological Society, 30, 963980.
  • Finn D.S. & Poff N.L. (2011) Examining spatial concordance of genetic and species diversity patterns to evaluate the role of dispersal limitation in structuring headwater metacommunities. Journal of the North American Benthological Society, 30, 273283.
  • Foll M. & Gaggiotti O. (2006) Identifying the environmental factors that determine the genetic structure of populations. Genetics, 174, 875891.
  • Frankham R. (2010) Challenges and opportunities of genetic approaches to biological conservation. Biological Conservation, 143, 19191927.
  • Gaggiotti O.E. (2010) Preface to the special issue: advances in the analysis of spatial genetic data. Molecular Ecology Resources, 10, 757759.
  • Gamboa M., Kimbirauskas R.K., Merritt R.W. & Monaghan M.T. (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.
  • Gardner M.G., Fitch A.J., Bertozzi T. & Lowe A.J. (2011) Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources, 11, 10931101.
  • Geist J. (2010) Strategies for the conservation of endangered freshwater pearl mussels (Margaritifera margaritifera L.): a synthesis of conservation genetics and ecology. Hydrobiologia, 644, 6988.
  • Geist J. (2011) Integrative freshwater ecology and biodiversity conservation. Ecological Indicators, 11, 15071516.
  • Girod C., Vitalis R., Leblois R. & Freville H. (2011) Inferring population decline and expansion from microsatellite data: a simulation-based evaluation of the Msvar method. Genetics, 188, 165179.
  • Glover K.A., Quintela M., Wennevik V., Besnier F., Sorvik A.G.E. & Skaala O. (2012) Three decades of farmed escapees in the wild: a spatio-temporal analysis of Atlantic salmon population genetic structure throughout Norway. PLoS One, 7, e43129.
  • Glover K.A., Taggart J.B., Skaala Ø. & Teale A.J. (2004) A study of inadvertent domestication selection during start-feeding of brown trout families. Journal of Fish Biology, 64, 11681178.
  • Gomez-Uchida D., Palstra F.P., Knight T.W. & Ruzzante D.E. (2013) Contemporary effective population and metapopulation size (Ne and meta-Ne): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries. Ecology and Evolution, 3, 569580.
  • Gustafson R.G., Waples R.S., Myers J.M., Weitkamp L.A., Bryant G.J., Johnson O.W. et al. (2007) Pacific salmon extinctions: quantifying lost and remaining diversity. Conservation Biology, 21, 10091020.
  • Haap T. & Köhler H.-R. (2009) Cadmium tolerance in seven Daphnia magna clones is associated with reduced hsp70 baseline levels and induction. Aquatic Toxicology, 94, 131137.
  • Haase P., Murray-Bligh J., Lohse S., Pauls S., Sundermann A., Gunn R. et al. (2006) Assessing the impact of errors in sorting and identifying macroinvertebrate samples. Hydrobiologia, 566, 505521.
  • Haase P., Pauls S.U., Schindehutte K. & Sundermann A. (2010) First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results. Journal of the North American Benthological Society, 29, 12791291.
  • Hajibabaei M., Shokralla S., Zhou X., Singer G.A. & Baird D.J. (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One, 6, e17497.
  • Hajibabaei M., Spall J.L., Shokralla S. & van Konynenburg S. (2012) Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecology, 12, 28.
  • Hamilton M.B. (2009) Population Genetics. Wiley-Blackwell, Oxford.
  • Hebert P.D.N., Cywinska A., Ball S.L. & DeWaard J.R. (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society Series B Biological Sciences, 270, 313321.
  • Heilveil J.S. & Berlocher S.H. (2006) Phylogeography of postglacial range expansion in Nigronia serricornis Say (Megaloptera: Corydalidae). Molecular Ecology, 15, 16271641.
  • Hindar K., Fleming I.A., McGinniti P. & Diserund O. (2006) Genetic and ecological effects of salmon farming on wild salmon: modelling from experimental results. ICES Journal of Marine Science, 63, 12341247.
  • Hoban S., Bertorelle G. & Gaggiotti O.E. (2012) Computer simulations: tools for population and evolutionary genetics. Nature Reviews Genetics, 13, 110122.
  • Hodges K.M., Rowell D.M. & Keogh J.S. (2007) Remarkably different phylogeographic structure in two closely related lizard species in a zone of sympatry in south-eastern Australia. Journal of Zoology, 272, 6472.
  • Hoffmann A.A. & Willi Y. (2008) Detecting genetic responses to environmental change. Nature Reviews Genetics, 9, 421432.
  • Holzenthal R.W., Robertson D.R., Pauls S.U. & Mendez P.K. (2010) Taxonomy and systematics: contributions to benthology and J-NABS. Journal of the North American Benthological Society, 29, 147169.
  • Hu X., He F. & Hubbell S. (2006) Neutral theory in macroecology and population genetics. Oikos, 113, 548556.
  • Hughes J.M. (2007) Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams. Freshwater Biology, 52, 616631.
  • Hughes J.M., Huey J.A., McLean A.J. & Baggiano O. (2011) Aquatic insects in Eastern Australia: a window on ecology and evolution of dispersal in streams. Insects, 2, 447461.
  • Hughes J.M., Schmidt D.J. & Finn D.S. (2009) Genes in streams: using DNA to understand the movement of freshwater fauna and their riverine habitat. BioScience, 59, 573583.
  • Isambert B., Bergsten J., Monaghan M.T., Andriamizehy H., Ranarilalatiana T., Ratsimbazafy M. et al. (2011) Contrasting patterns of endemism and evolutionary history in the freshwater biodiversity of Madagascar. Biological Conservation, 144, 19021909.
  • Jerde C.L., Mahon A.R., Chadderton W.L. & Lodge D.M. (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation Letters, 4, 150157.
  • Johnson J.B. & Omland J.S. (2004) Model selection in ecology and evolution. Trends in Ecology & Evolution, 19, 101108.
  • Jones F.C., Grabherr M.G., Chan Y.F., Russell P., Mauceli E., Johnson J. et al. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature Methods, 484, 5561.
  • Kingman J.F.C. (1982) On the genealogy of large populations. Journal of Applied Probability, 19, 2743.
  • Knapp M. & Hofreiter M. (2010) Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes, 1, 227243.
  • Kohout J., Jašková I., Papoušek I., Šedivá A. & Šlechta V. (2012) Effects of stocking on the genetic structure of brown trout, Salmo trutta, in Central Europe inferred from mitochondrial and nuclear DNA markers. Fisheries Management and Ecology, 19, 252263.
  • Krueger D.A. & Dodson S.I. (1981) Embryological induction and predation ecology in Daphnia pulex. Limnology and Oceanography, 26, 219223.
  • Kubow K.B., Robinson C.T., Shama L.N.S. & Jokela J. (2010) Spatial scaling in the phylogeography of an alpine caddisfly, Allogamus uncatus, within the central European Alps. Journal of the North American Benthological Society, 29, 10891099.
  • Kultz D. (2005) Molecular and evolutionary basis of the cellular stress response. Annual Review of Physiology, 67, 225257.
  • Landguth E.L., Muhlfeld C.C. & Luikart G. (2012) CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes. Conservation Genetics Resources, 4, 133136.
  • Latta L.C., Weider L.J., Colbourne J.K. & Pfrender M.E. (2012) The evolution of salinity tolerance in Daphnia: a functional genomics approach. Ecology Letters, 15, 794802.
  • Leclerc E., Mailhot Y., Mingelbier M. & Bernatchez L. (2008) The landscape genetics of yellow perch (Perca flavescens) in a large fluvial ecosystem. Molecular Ecology, 17, 17021717.
  • Lee C.E., Kiergaard M., Gelembiuk G.W., Eads B.D. & Posavi M. (2011) Pumping ions: rapid parallel evolution of ionic regulation following habitat invasions. Evolution, 65, 22292244.
  • Lee C.E., Moss W.E., Olson N., Chau K.F., Chang Y.M. & Johnson K.E. (2013) Feasting in fresh water: impacts of food concentration on freshwater tolerance and the evolution of food X salinity response during the expansion from saline into fresh water habitats. Evolutionary Applications, 6, 673689.
  • Leese F., Brand P., Rozenberg A., Mayer C., Agrawal S., Dambach J. et al. (2012) Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology. PLoS ONE, 7, e49202.
  • Lehrian S., Pauls S.U. & Haase P. (2009) Contrasting patterns of population structure in the montane caddisflies Hydropsyche tenuis and Drusus discolor in the Central European highlands. Freshwater Biology, 54, 283295.
  • Lemmon A.R. & Lemmon E.M. (2012) High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography. Systematic Biology, 61, 745761.
  • Lencioni V., Bernabò P., Cesari M. & Rebecchi L. (2013) Thermal stress induces hsp70 proteins synthesis in larvae of the cold stream non-biting midge Diamesa cinerella Meigen. Archives of Insect Biochemistry and Physiology, 83, 114.
  • Lencioni V., Boschini D. & Rebecchi L. (2009) Expression of the 70 kDa Heat shock protein family in Alpine freshwater chironomids (Diptera, Chironomidae) under natural conditions. Journal of Limnology, 68, 251256.
  • Lopes J.S., Balding D. & Beaumont M.A. (2009) PopABC: a program to infer historical demographic parameters. Bioinformatics, 25, 27472749.
  • López-Maury L., Marguerat S. & Bähler J. (2008) Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nature Reviews Genetics, 10, 583593.
  • Luikart G., Ryman N., Tallmon D.A., Schwartz M.K. & Allendorf F.W. (2010) Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics, 11, 355373.
  • Malausa T., Gilles A., Meglecz E., Blanquart H., Duthoy S., Costedoat C. et al. (2011) High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Molecular Ecology Resources, 11, 638644.
  • Manel S. & Holderegger R. (2013) Ten years of landscape genetics. Trends in Ecology and Evolution, 28, 614621.
  • Miyakawa H., Imai M., Sugimoto N., Ishikawa Y., Ishikawa A., Ishigaki H. et al. (2010) Gene up-regulation in response to predator kairomones in the water flea Daphnia pulex. BMC Developmental Biology, 10, 45.
  • Monaghan M.T., Spaak P., Robinson C.T. & Ward J.V. (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, 114131.
  • Monaghan M.T., Wild R., Elliot M., Fujisawa T., Balke M., Inward D.J.G. et al. (2009) Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology, 58, 298311.
  • Müller R., Seeland A., Jagodzinski L.S., Diogo J.B., Nowak C. & Oehlmann J. (2012) Simulated climate change conditions unveil the toxic potential of the fungicide pyrimethanil on the midge Chironomus riparius: a multigeneration experiment. Ecology and Evolution, 2, 196210.
  • Murdock C.C., Moller-Jacobs L.L. & Thomas M.B. (2013) Complex environmental drivers of immunity and resistance in malaria mosquitoes. Proceedings of the Royal Society B, 280, 20132030.
  • Múrria C., Bonada N., Arnedo M.A., Prat N. & Vogler A.P. (2013) Higher β- and γ-diversity at species and genetic levels in headwaters than in mid-order streams in Hydropsyche (Trichoptera). Freshwater Biology, 58, 22262236.
  • Nemec S., Patel S., Nowak C. & Pfenninger M. (2013) Evolutionary determinants of population differences in population growth rate 3 habitat temperature interactions in Chironomus riparius. Oecologia, 172, 585594.
  • Neuenschwander S. (2006) AQUASPLATCHE: a program to simulate genetic diversity in populations living in linear habitats. Molecular Ecology Notes, 6, 583585.
  • Neuenschwander S., Largiader C.R., Ray N., Currat M., Vonlanthen P. & Excoffier L. (2008) Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit framework. Molecular Ecology, 17, 757772.
  • Nichols R.A. (2001) Gene trees and species trees are not the same. Trends in Ecology & Evolution, 16, 358364.
  • Nolte A.W., Freyhof J., Stemshorn K.C. & Tautz D. (2005) An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups. Proceedings of the Royal Society Series B Biological Sciences, 272, 23792387.
  • Nowak C., Vogt C., Oetken M., Pfenninger M., Schwenk K., Streit B. et al. (2009) Rapid genetic erosion in pollutant-exposed experimental chironomid populations. Environmental Pollution, 157, 881886.
  • O'Bryhim J., Somers C., Lance S.L., Yau M., Boreham D.R., Jones K.L. et al. (2013) Development and characterisation of twenty-two novel microsatellite markers for the mountain whitefish, Prosopium williamsoni and cross-amplification in the round whitefish, P. Cylindraceum, using paired-end Illumina shotgun sequencing. Conservation Genetics Resources, 5, 8991.
  • Olsen J.B., Crane P.A., Flannery B.G., Dunmall K., Templin W.D. & Wenburg J.K. (2011) Comparative landscape genetic analysis of three Pacific salmon species from subarctic North America. Conservation Genetics, 12, 223241.
  • Palstra F.P. & Fraser D.J. (2012) Effective/census population size ratio estimation: a compendium and appraisal. Ecology and Evolution, 2, 23572365.
  • Papadopoulou A., Anastasiou I., Spagopoulou F., Stalimerou M., Terzopoulou S., Legakis A. et al. (2011) Testing the species – genetic diversity correlation in the Aegean archipelago: toward a haplotype-based macroecology? The American Naturalist, 178, 241255.
  • Pauls S.U., Nowak C., Bálint M. & Pfenninger M. (2013) The impact of global climate change on genetic diversity within populations and species. Molecular Ecology, 22, 925946.
  • Paz-Vinas I., Quéméré E., Chikhi L., Loot G. & Blanchet S. (2013a) The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data. Molecular Ecology, 22, 32793291.
  • Paz-Vinas I., Comte L., Chevalier M., Dubut V., Veyssiere C., Grenouillet G. et al. (2013b) Combining genetic and demographic data for prioritizing conservation actions: insights from a threatened fish species. Ecology and Evolution, 3, 26962710.
  • Peña-Castillo L. & Hughes T.R. (2007) Why are there still over 1000 uncharacterized yeast genes? Genetics, 176, 714.
  • Pereira L.H.G., Hanner R., Foresti F. & Oliveira C. (2013) Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genetics, 14, 20.
  • Pernthaler J. (2013) Freshwater microbial communities. In The Prokaryotes (Eds E. Rosenberg, E. Delong, S. Lory, E. Stackebrandt & F. Thompson), pp. 97112. Springer, Berlin Heidelberg.
  • Perrier C., Guyomard R., Bagliniere J.-L., Nikolic N. & Evanno G. (2013) Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency. Ecology and Evolution, 3, 23342349.
  • Perry J.C. & Rowe L. (2011) Rapid microsatellite development for water striders by next-generation sequencing. Journal of Heredity, 102, 125129.
  • Petrusek A., Tollrian R., Schwenk K., Haas A. & Laforsch C. (2009) A “crown of thorns” is an inducible defense that protects Daphnia against an ancient predator. Proceedings of the National Academy of Sciences of the USA, 107, 22482252.
  • Pfenninger M., Bálint M. & Pauls S.U. (2012) Methodological framework for projecting the potential loss of intraspecific genetic diversity due to global climate change. BMC Evolutionary Biology, 12, 224.
  • Pfrender M.E., Hawkins C.P., Bagley M., Courtney G.W., Creutzburg B.R., Epler J.H. et al. (2010) Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches. Quarterly Review of Biology, 85, 319340.
  • Pilgrim E.M., Jackson S.A., Swenson S., Turcsanyi I., Friedman E., Weigt L. et al. (2011) Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls. Journal of the North American Benthological Society, 30, 217231.
  • Roberge C., Einum S., Guderley H. & Bernatchez L. (2006) Rapid parallel evolutionary changes of gene transcription profile in farmed Atlantic salmon. Molecular Ecology, 15, 920.
  • Robinson J.D., Simmons J.W., Williams A.S. & Moyer G.R. (2013) Population structure and genetic diversity in the endangered bluemask darter (Etheostoma akatulo). Conservation Genetics, 14, 7992.
  • Santos M.E. & Salzburger W. (2012) How cichlids diversify. Science, 338, 619621.
  • Schmidt-Kloiber A. & Hering D. (Eds) (2012) The Taxa and Autecology Database for Freshwater Organisms, version 5.0. Accessed online 15 July 2013 at: www.freshwaterecology.info.
  • Schulte P.M. (2004) Changes in gene expression as biochemical adaptations to environmental change: a tribute to Peter Hochachka. Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology, 139, 519529.
  • Schultheis A.S., Booth J.Y., Perlmutter L.R., Bond J.E. & Sheldon A.L. (2012) Phylogeography and species biogeography of montane Great Basin stoneflies. Molecular Ecology, 21, 33253340.
  • Schultheis A.S., Davis N., Page J.T., Fenwick A.M., Bond J.E. & Shiozawa D.K. (2014) Comparative transcriptomics allows for rapid development of population-level nuclear markers in Hesperoperla pacifica (Plecoptera: Perlidae). Freshwater Science, 33, 364.
  • Scoville A.G. & Pfrender M.E. (2010) Phenotypic plasticity facilitates recurrent rapid adaptation to introduced predators. Proceedings of the National Academy of Sciences of the USA, 107, 42604263.
  • Sei M., Lang B.K. & Berg D.J. (2009) Genetic and community similarities are correlated in endemic-rich springs of the northern Chihuahuan Desert. Global Ecology and Biogeography, 18, 192201.
  • Smith P.J., McVeagh S.M. & Collier K.J. (2006) Genetic diversity and historical population structure in the New Zealand mayfly Acanthophlebia cruentata. Freshwater Biology, 51, 1224.
  • Stein E.D., White B.P., Mazor R.D., Miller P.E. & Pilgrim E.M. (2013) Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates. PLoS One, 8, e51273.
  • Stewart J.R., Lister A.M., Barnes I. & Dalen L. (2010) Refugia revisited: individualistic responses of species in space and time. Proceedings of the Royal Society Series B Biological Sciences, 277, 661671.
  • Storz J.F. & Beaumont M.A. (2002) Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution, 56, 154166.
  • Strayer D. & Dudgeon D. (2010) Freshwater biodiversity conservation: recent progress and future challenges. Journal of the North American Benthological Society, 29, 344358.
  • Sweeney B.W., Battle J.M., Jackson J.K. & Dapkey T. (2011) Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? Journal of the North American Benthological Society, 30, 195216.
  • Taberlet P., Coissac E., Hajibabaei M. & Rieseberg L.H. (2012) Environmental DNA. Molecular Ecology, 21, 17891793.
  • Tamura K. & Aotsuka T. (1988) Rapid isolation method of animal mitochondrial DNA by the alkaline lysis procedure. Biochemical Genetics, 26, 815819.
  • Taubmann J., Theissinger K., Feldheim K.A., Laube I., Graf W., Haase P. et al. (2011) Modelling range shifts and assessing genetic diversity distribution of the montane aquatic mayfly Ameletus inopinatus in Europe under climate change scenarios. Conservation Genetics, 12, 503515.
  • Theissinger K., Bálint M., Feldheim K.A., Haase P., Johannesen J., Laube I. et al. (2013) Glacial survival and postglacial recolonization of an arctic-alpine freshwater insect (Arcynopteryx dichroa, Plecoptera, Perlodidae) in Europe. Journal of Biogeography, 40, 236248.
  • Theissinger K., Bálint M., Haase P., Johannesen J., Laube I. & Pauls S.U. (2011) Molecular data and species distribution models reveal the Pleistocene history of the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae). Freshwater Biology, 56, 25542566.
  • Thibault I., Bernatchez L. & Dodson J.J. (2009) The contribution of newly established populations to the dynamics of range expansion in a one-dimensional fluvial-estuarine system: rainbow trout (Oncorhynchus mykiss) in Eastern Quebec. Diversity and Distributions, 15, 10601072.
  • Thomson Reuter (2014) Web of Science, Accessed online 12 February 2014 at: www.webofknowledge.com.
  • Thomsen P.F., Kielgast J., Iversen L.L., Wiuf C., Rasmussen M., Gilbert M.T. et al. (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21, 25652573.
  • Travers S.E., Smith M.D., Bai J., Hulbert S.H., Leach J.E., Schnable P.S. et al. (2007) Ecological genomics: making the leap from model systems in the lab to native populations in the field. Frontiers in Ecology and the Environment, 5, 1924.
  • Ungerer M.C., Johnson L.C. & Herman M.A. (2008) Ecological genomics: understanding gene and genome function in the natural environment. Heredity, 100, 178183.
  • Valiente A.G., Juanes F., Nunez P. & Garcia-Vazquez E. (2010) Brown trout (Salmo trutta) invasiveness: plasticity in life-history is more important than genetic variability. Biological Invasions, 12, 451462.
  • Vellend M. (2005) Species diversity and genetic diversity: parallel processes and correlated patterns. American Naturalist, 166, 199215.
  • Via S., Gomulkiewicz R., De Jong G., Scheiner S.M., Schlichting C.D. & Van Tienderen P.H. (1995) Adaptive phenotypic plasticity: consensus and controversy. Trends in Ecology & Evolution, 10, 212217.
  • Vogt C., Hess M., Nowak C., Diogo J.B., Oehlmann J. & Oetken M. (2010) Effects of cadmium on life-cycle parameters in a multi-generation study with Chironomus riparius following a pre-exposure of populations to two different tributyltin concentrations for several generations. Ecotoxicology, 19, 11741182.
  • Webb J.M., Jacobus L.M., Funk D.H., Zhou X., Kondratieff B., Geraci C.J. et al. (2012) A DNA barcode library for North American Ephemeroptera: progress and prospects. PLoS One, 7, e38063.
  • Wegmann D., Leuenberger C., Neuenschwander S. & Excoffier L. (2010) ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics, 11, 116.
  • Wilcock H.R., Nichols R.A. & Hildrew A.G. (2003) Genetic population structure and neighbourhood population size estimates of the caddisfly Plectrocnemia conspersa. Freshwater Biology, 48, 18131824.
  • Winkler G., Dodson J.J. & Lee C.E. (2008) Heterogeneity within the native range: population genetic analyses of sympatric invasive and noninvasive clades of the freshwater invading copepod Eurytemora affinis. Molecular Ecology, 17, 415430.
  • Wright S. (1938) Size of population and breeding structure in relation to evolution. Science, 87, 430431.
  • Yaegashi S., Watanabe K., Monaghan M.T. & Omura T. (2014) Fine-scale dispersal in a stream caddisfly inferred from spatial autocorrelation of microsatellite markers. Freshwater Science, 33, 172180.
  • Zhou X., Li Y., Liu S., Yang Q., Su X., Zhou L. et al. (2013) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience, 2, 112.
  • Zickovich J.M. & Bohonak A.J. (2007) Dispersal ability and genetic structure in aquatic invertebrates: a comparative study in southern California streams and reservoirs. Freshwater Biology, 52, 19821996.