Diversity and dispersal of aquatic invertebrate species from surface and groundwater: Development and application of microsatellite markers for the detection of hydrological exchange processes

Asmyhr, 2014, Fine-scale genetics of subterranean syncarids, Freshw. Biol., 59, 1, 10.1111/fwb.12239 Asmyhr, 2014, Systematic conservation planning for groundwater ecosystems using phylogenetic diversity, PLOS One, 9, 10.1371/journal.pone.0115132 Asmyhr, 2012, The first set of microsatellite markers developed for the ancient Parabathynellidae (Syncarida, Malacostraca) and their utility for other groundwater fauna, Conserv. Genet. Resour., 4, 587, 10.1007/s12686-011-9598-x Austin, 2011, Permanent genetic resources added to molecular ecology resources database 1 February 2011-31 March 2011, Mol. Ecol. Resour., 11, 757, 10.1111/j.1755-0998.2011.03028.x Balázs, 2020, A new non-invasive in situ underwater DNA sampling method for estimating genetic diversity, Evol. Ecol., 34, 633, 10.1007/s10682-020-10053-1 Bauzà-Ribot, 2011, Islands beneath islands: phylogeography of a groundwater amphipod crustacean in the Balearic archipelago, Evol. Biol., 11, 1 Bradford, 2010, DNA barcoding of stygofauna uncovers cryptic amphipod diversity in a calcrete aquifer in Western Australia's arid zone, Mol. Ecol. Resour., 10, 41, 10.1111/j.1755-0998.2009.02706.x Brede, 2006, Microsatellite markers for European Daphnia, Mol. Ecol. Notes, 6, 536, 10.1111/j.1471-8286.2005.01218.x Buhay, 2005, Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes, Mol. Ecol., 14, 4259, 10.1111/j.1365-294X.2005.02755.x Capderrey, 2013, Microsatellite development and first population size estimates for the groundwater isopod Proasellus walteri, PLOS One, 8, e76213, 10.1371/journal.pone.0076213 Cook, 2000 De Meester, 2002, The Monopolization Hypothesis and the dispersal-gene flow paradox in aquatic organisms, Acta Oecol., 23, 121, 10.1016/S1146-609X(02)01145-1 Di Lorenzo, 2019, Recommendations for ecotoxicity testing with stygobiotic species in the framework of groundwater environmental risk assessment, Sci. Total Environ., 681, 292, 10.1016/j.scitotenv.2019.05.030 Einsle, 1985, A further criterion for the identification of species in the genus Cyclops s. str. (Copepoda, Cyclopoida), Crustaceana, 49, 299, 10.1163/156854085X00611 Eme, 2018, Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants, Ecography, 41, 424, 10.1111/ecog.02683 Finston, 2009, Characterisation of microsatellite loci in the groundwater amphipod Chydaekata sP. (Malacostraca: paramelitidae), Conserv. Genet. Resour., 2, 237, 10.1007/s12686-009-9152-2 Gibson, 2019, Shedding light on the hidden world of subterranean fauna: a transdisciplinary research approach, Sci. Total Environ., 684, 381, 10.1016/j.scitotenv.2019.05.316 Green, 2005, Recent advances in the study of long-distance dispersal of aquatic invertebrates via birds, Divers. Distrib., 11, 149, 10.1111/j.1366-9516.2005.00147.x Gudmundsdóttir, 2020, Comparison of the gut microbiota in the groundwater amphipod Crangonyx islandicus Svavarsson & Kristjánsson, 2006 (Amphipoda: crangonyctidae) to biofilms in its spring-source habitat, J. Crustacean Biol., 40, 657, 10.1093/jcbiol/ruaa065 Guzik, 2021, Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia, Genome, 64, 181, 10.1139/gen-2019-0199 Hahn, 2009, Distribution patterns of groundwater communities across aquifer types in south-western Germany, Freshw. Biol., 54, 848, 10.1111/j.1365-2427.2008.02132.x Huys, 1991, 1 James, 2000, The use of temperature and the isotopes of O, H, C, and noble gases to determine the pattern and spatial extent of groundwater flow, J. Hydrol., 237, 100, 10.1016/S0022-1694(00)00303-6 Jombart, 2008, Adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, 24, 1403, 10.1093/bioinformatics/btn129 Jombart, 2010, Discriminant analysis of principal components: a new method for the analysis of genetically structured populations, BMC genetics, 11, 1, 10.1186/1471-2156-11-94 Jordan, 2020, Genomic data reveal similar genetic differentiation in aquifer species with different dispersal capabilities and life histories, Biol. J. Linn. Soc., 129, 315, 10.1093/biolinnean/blz173 Kamvar, 2014, Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction, PeerJ, 2, e281, 10.7717/peerj.281 Karanovic, 2016, Cryptic species or inadequate taxonomy? Implementation of 2D geometric morphometrics based on integumental organs as landmarks for delimitation and description of copepod taxa, Syst. Biol., 65, 304, 10.1093/sysbio/syv088 Karaytug, 1998, The Paracyclops fimbriatus-complex (Copepoda, Cyclopoida): a revision, Zoosystema, 20, 563 Konec, 2016, DNA barcoding sheds light on hidden subterranean boundary between Adriatic and Danubian drainage basins, Ecohydrology, 9, 1304, 10.1002/eco.1727 Konec, 2015, Parallels between two geographically and ecologically disparate cave invasions by the same species, Asellus aquaticus (Isopoda, Crustacea), J. Evol. Biol., 28, 864, 10.1111/jeb.12610 Malard, 2017, Geomorphic influence on intraspecific genetic differentiation and diversity along hyporheic corridors, Freshw. Biol., 62, 1955, 10.1111/fwb.13040 Mammola, 2020, Fundamental research questions in subterranean biology, Biol. Rev. Camb. Philos. Soc., 95, 1855, 10.1111/brv.12642 Mammola, 2019, Scientists' warning on the conservation of subterranean ecosystems, Bioscience, 69, 641, 10.1093/biosci/biz064 Matthews, 2020, Scratching the surface of subterranean biodiversity: molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia, Mol. Phylogenet. Evol., 142, 10.1016/j.ympev.2019.106643 Meleg, 2013, Can environment predict cryptic diversity? The case of Niphargus inhabiting Western Carpathian groundwater, PLOS One, 8, e76760, 10.1371/journal.pone.0076760 Murphy, 2010, The influence of landscape on population structure of four invertebrates in groundwater springs, Freshw. Biol., 55, 2499, 10.1111/j.1365-2427.2010.02479.x Négrel, 2011, Understanding groundwater systems and their functioning through the study of stable water isotopes in a hard-rock aquifer (Maheshwaram watershed, India), J. Hydrol., 397, 55, 10.1016/j.jhydrol.2010.11.033 Niemiller, 2017, Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae), Conserv. Genet. Resour., 10, 247, 10.1007/s12686-017-0785-2 Janetzky, W., 1996. Crustacea: Copepoda: Gelyelloida und Harpacticoida. Süsswasserfauna von Mitteleuropa. Gustav Fischer Verlag, Stuttgart, ISBN 3-437-30741-X, 228 p. Oksanen, J., Guillaume Blanchet, F., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O'Hara, R.B., Simpson, G.L., Solymos, P., Henry, M., Stevens, H., Szoecs, E., Wagner, H. 2020. Vegan: community ecology package. R package version 2.5-6.2019. Orsini, 2013, Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization, Mol. Ecol., 22, 5983, 10.1111/mec.12561 Paetkau, 2004, Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power, Mol. Ecol. Notes, 13, 55, 10.1046/j.1365-294X.2004.02008.x Palandačić, 2012, Molecular data as a possible tool for tracing groundwater flow in karst environment: example of Delminichthys adspersusin Dinaric karst system, Ecohydrology, 5, 791, 10.1002/eco.269 Palandačić, 2012, Fish migrate underground: the example of Delminichthys adspersus (Cyprinidae), Mol. Ecol. Notes, 21, 1658, 10.1111/j.1365-294X.2012.05507.x Paradis, 2010, Pegas: an R package for population genetics with an integrated-modular approach, Bioinformatics, 26, 419, 10.1093/bioinformatics/btp696 Peakall, 2012, GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research–an update, Bioinformatics, 28, 2537, 10.1093/bioinformatics/bts460 Pfenninger, 2007, Cryptic animal species are homogeneously distributed among taxa and biogeographical regions, BMC Evol. Biol., 7, 1 Piry, 2004, GENECLASS2: a software for genetic assignment and first-generation migrant detection, J. Hered., 95, 536, 10.1093/jhered/esh074 Pospisil, 1999, Two new species of the Diacyclops languidoides-group (Copepoda, Cyclopoida) from groundwaters of Austria, Hydrobiologia, 412, 165, 10.1023/A:1003839301339 Rannala, 1997, Detecting immigration by using multilocus genotypes, Proc. Natl. Acad. Sci. U.S.A., 94, 9197, 10.1073/pnas.94.17.9197 R Core Team, R., 2008. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Sacco, M., 2020. Functional ecology of calcrete aquifers in arid zone Western Australia. Ph.D. Thesis, Curtin University, School of Earth and Planetary Sciences. URL http://hdl.handle.net/20.500.11937/80356. Sarkar, 2008, Lattice: Multivariate Data Visualization with R Schminke, 2007, 1 Schwenk, 1998, Genetic markers, genealogies and biogeographic patterns in the cladocera, Aquat. Ecol., 32, 37, 10.1023/A:1009939901198 Stein, 2012, Stygoregions a promising approach to a bioregional classification of groundwater systems, Sci. Rep., 2, 1, 10.1038/srep00673 Tilzer, 1967, Acanthocyclops (Rhenocyclops) sensitivus (Graeter & Chappuis 1914) (Crustacea, Copepoda) aus dem hyporheischen Interstitial des Lech (Tirol), Ber. Nat. Med. Ver. Innsbr., 55, 175 Trontelj, 2009, A molecular test for cryptic diversity in ground water: how large are the ranges of macro-stygobionts?, Freshw. Biol., 54, 727, 10.1111/j.1365-2427.2007.01877.x van den Berg-Stein, 2019, StygoTracing – ein biologisches Tracerverfahren für Grund- und Trinkwasser, KW Korresp. Wasserwirtsch., 12, 217 Van Oosterhout, 2004, Micro-checker: software for identifying and correcting genotyping errors in microsatellite data, Mol. Ecol. Notes, 4, 535, 10.1111/j.1471-8286.2004.00684.x Verovnik, 2004, Phylogeography of subterranean and surface populations of water lice Asellus aquaticus (Crustacea: isopoda), Mol. Ecol., 13, 1519, 10.1111/j.1365-294X.2004.02171.x Waterkeyn, 2010, Unintentional dispersal of aquatic invertebrates via footwear and motor vehicles in a Mediterranean wetland area, Aquat. Conserv. Mar. Freshw. Ecosyst., 20, 580, 10.1002/aqc.1122 White, 2014, Comparison of four species-delimitation methods applied to a DNA barcode data set of insect larvae for use in routine bioassessment, Freshw. Sci., 33, 338, 10.1086/674982 White, 1994, Electrode arrays for measuring groundwater flow direction and velocity, Geophysics, 59, 176, 10.1190/1.1443581