Almodóvar A, Nicola GG, Ayllón D, Elvira B (2012) Global warming threatens the persistence of Mediterranean brown trout. Glob Chang Biol 18:1549–1560
Google Scholar
Arscott DB, Tockner K, Ward JV (2001) Thermal heterogeneity along a braided floodplain river (Tagliamento River, northeastern Italy). Can J Fish Aquat Sci 58:2359–2373
Google Scholar
Baker DJ, Garnett ST, O’Connor J, Ehmke G, Clarke RH, Woinarski JCZ et al. (2019) Conserving the abundance of nonthreatened species. Conserv Biol 33:319–328
Google Scholar
Blanchet S, Prunier JG, Paz-Vinas I, Saint-Pe K, Rey O, Raffard A et al. (2020) A river runs through it: the causes, consequences, and management of intraspecific diversity in river networks. Evol Appl 13:1195–1213
Google Scholar
Blondel L, Paterson IG, Bentzen P, Hendry AP (2021) Resistance and resilience of genetic and phenotypic diversity to “black swan” flood events: a retrospective analysis with historical samples of guppies. Mol Ecol 30:1017–1028
Google Scholar
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Google Scholar
Brown LE, Milner AM, Hannah DM (2007) Groundwater influence on alpine stream ecosystems. Freshw Biol 52:878–890
Google Scholar
Caissie D (2006) The thermal regime of rivers: a review. Freshw Biol 51:1389–1406
Google Scholar
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140
Google Scholar
Dennenmoser S, Rogers SM, Vamosi SM (2014) Genetic population structure in prickly sculpin (Cottus asper) reflects isolation-by-environment between two life-history ecotypes. Biol J Linn Soc 113:943–957
Google Scholar
Diniz-Filho JAF, De Campos Telles MP (2002) Spatial autocorrelation analysis and the identification of operational units for conservation in continuous populations. Conserv Biol 16:924–935
Google Scholar
Diniz-Filho JAF, Soares TN, Lima JS, Dobrovolski R, Landeiro VL, Telles MP, de C et al. (2013) Mantel test in population genetics. Genet Mol Biol 36:475–485
Google Scholar
Dray S, Bauman D, Blanchet G, Borcard D, Clappe S, Guenard G et al. (2020) adespatial: Multivariate Multiscale Spatial Analysis. R package version 0.3-8. https://CRAN.R-project.org/package=adespatial
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361
Google Scholar
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
Google Scholar
Gilbert B, Bennett JR (2010) Partitioning variation in ecological communities: do the numbers add up? J Appl Ecol 47:1071–1082
Google Scholar
Gilbert B, Lechowicz MJ (2004) Neutrality, niches, and dispersal in a temperate forest understory. Proc Natl Acad Sci USA 101:7651–7656
Google Scholar
Goslee S, Urban D (2007) The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 22:1–19
Google Scholar
Goto A (1998) Life-history variations in the fluvial sculpin, Cottus nozawae (Cottidae), along the course of a small mountain stream. Environ Biol Fishes 52:203–212
Google Scholar
Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486
Google Scholar
Griffith DA, Peres-Neto PR (2006) Spatial modeling in ecology: the flexibility of eigenfunction spatial analyses. Ecology 87:2603–2613
Google Scholar
Guillot G, Rousset F (2013) Dismantling the Mantel tests. Methods Ecol Evol 4:336–344
Google Scholar
Hänfling B, Weetman D (2006) Concordant genetic estimators of migration reveal anthropogenically enhanced source-sink population structure in the river sculpin, Cottus gobio. Genetics 173:1487–1501
Google Scholar
Harmon LJ, Glor RE (2010) Poor statistical performance of the mantel test in phylogenetic comparative analyses. Evolution 64:2173–2178
Google Scholar
Heino J, Grönroos M, Ilmonen J, Karhu T, Niva M, Paasivirta L (2013) Environmental heterogeneity and β diversity of stream macroinvertebrate communities at intermediate spatial scales. Freshw Sci 32:142–154
Google Scholar
Hohenlohe PA, Funk WC, Rajora OP (2021) Population genomics for wildlife conservation and management. Mol Ecol 30:62–82
Google Scholar
Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332
Google Scholar
Iles DT, Williams NM, Crone EE (2018) Source-sink dynamics of bumblebees in rapidly changing landscapes. J Appl Ecol 55:2802–2811
Google Scholar
Ito N, Gotoh RO, Shirakuma T, Araki Y, Hanzawa N (2018) Genetic structure of glacial-relict populations of a freshwater sculpin, Cottus nozawae, in Yamagata area of the Tohoku district. Biogeography 20:96–102
Junker J, Peter A, Wagner CE, Mwaiko S, Germann B, Seehausen O et al. (2012) River fragmentation increases localized population genetic structure and enhances asymmetry of dispersal in bullhead (Cottus gobio). Conserv Genet 13:545–556
Google Scholar
Kanno Y, Vokoun JC, Letcher BH (2011) Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks. Mol Ecol 20:3711–3729
Google Scholar
Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7:1225–1241
Google Scholar
Koizumi I (2011) Integration of ecology, demography and genetics to reveal population structure and persistence: a mini review and case study of stream-dwelling Dolly Varden. Ecol Freshw Fish 20:352–363
Google Scholar
Koizumi I, Maekawa K (2004) Metapopulation structure of stream-dwelling Dolly Varden charr inferred from patterns of occurrence in the Sorachi River basin, Hokkaido, Japan. Freshw Biol 49:973–981
Google Scholar
Koizumi I, Yamamoto S, Maekawa K (2006) Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr. Mol Ecol 15:3175–3189
Google Scholar
Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across. K Mol Ecol Resour 15:1179–1191
Google Scholar
Lamphere BA, Blum MJ (2012) Genetic estimates of population structure and dispersal in a benthic stream fish. Ecol Freshw Fish 21:75–86
Google Scholar
Legendre P, Fortin MJ, Borcard D (2015) Should the Mantel test be used in spatial analysis? Methods Ecol Evol 6:1239–1247
Google Scholar
Legendre P, Legendre L (2012) Numerical Ecology, 3rd edn. Elsevier, Amsterdam
Lichstein JW (2007) Multiple regression on distance matrices: a multivariate spatial analysis tool. Plant Ecol 188:117–131
Google Scholar
Lucek K, Keller I, Nolte AW, Seehausen O (2018) Distinct colonization waves underlie the diversification of the freshwater sculpin (Cottus gobio) in the Central European Alpine region. J Evol Biol 31:1254–1267
Google Scholar
Meirmans PG (2012) The trouble with isolation by distance. Mol Ecol 21:2839–2846
Google Scholar
Meirmans PG (2014) Nonconvergence in Bayesian estimation of migration rates. Mol Ecol Resour 14:726–733
Google Scholar
Meirmans PG (2015) Seven common mistakes in population genetics and how to avoid them. Mol Ecol 24:3223–3231
Google Scholar
Middaugh CR, Kessinger B, Magoulick DD (2018) Climate-induced seasonal changes in smallmouth bass growth rate potential at the southern range extent. Ecol Freshw Fish 27:19–29
Google Scholar
Ministry of the Environment Government of Japan (2020) Red List of Japan. http://www.env.go.jp/press/107905.html. (In Japanese)
Mussmann SM, Douglas MR, Chafin TK, Douglas ME (2019) BA3-SNPs: contemporary migration reconfigured in BayesAss for next-generation sequence data. Methods Ecol Evol 10:1808–1813
Google Scholar
Myers EA, Xue AT, Gehara M, Cox CL, Davis Rabosky AR, Lemos-Espinal J et al. (2019) Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes. Mol Ecol 28:4535–4548
Google Scholar
Nagasaka A, Sugiyama S (2010) Factors affecting the summer maximum stream temperature of small streams in northern Japan. Bull Hokkaido Res Inst 47:35–43. (In Japanese with English abstract)
Nakajima S, Hirota SK, Matsuo A, Suyama Y, Nakamura F (2020) Genetic structure and population demography of white-spotted charr in the upstream watershed of a large dam. Water 12:2406
Google Scholar
Nakamura F, Yamada H (2005) Effects of pasture development on the ecological functions of riparian forests in Hokkaido in northern Japan. Ecol Eng 24:539–550
Google Scholar
Natsumeda T (2003) Effects of a severe flood on the movements of Japanese fluvial sculpin. Environ Biol Fishes 68:417–424
Google Scholar
Nosil P, Vines TH, Funk DJ (2005) Perspective: reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution 59:705–719
Google Scholar
Oksanen JF, Blanchet G, Friendly M, Kindt R, Legendre P, McGlinn D et al. (2019) vegan: Community Ecology Package. R package version 2.5-6. https://CRAN.R-project.org/package=vegan
Okumura N, Goto A (1996) Genetic variation and differentiation of the two river sculpins, Cottus nozawae and C. amblystomopsis, deduced from allozyme and restriction enzyme-digested mtDNA fragment length polymorphism analyses. Ichthyol Res 43:399–416
Google Scholar
Olden JD, Naiman RJ (2010) Incorporating thermal regimes into environmental flows assessments: modifying dam operations to restore freshwater ecosystem integrity. Freshw Biol 55:86–107
Google Scholar
Orsini L, Vanoverbeke J, Swillen I, Mergeay J, De Meester L (2013) Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol Ecol 22:5983–5999
Google Scholar
Paris JR, Stevens JR, Catchen JM (2017) Lost in parameter space: a road map for STACKS. Methods Ecol Evol 8:1360–1373
Google Scholar
Peacock MM, Gustin MS, Kirchoff VS, Robinson ML, Hekkala E, Pizzarro-Barraza C et al. (2016) Native fishes in the Truckee River: are in-stream structures and patterns of population genetic structure related? Sci Total Environ 563–564:221–236
Google Scholar
Peakall R, Smouse PE (2012) GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539
Google Scholar
Poff NL, Richter BD, Arthington AH, Bunn SE, Naiman RJ, Kendy E et al. (2010) The ecological limits of hydrologic alteration (ELOHA): A new framework for developing regional environmental flow standards. Freshw Biol 55:147–170
Google Scholar
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Google Scholar
Raufaste N, Francois R (2001) Are partial Mantel tests adequate? Evolution 55:1703–1705
Google Scholar
Richardson JL, Brady SP, Wang IJ, Spear SF (2016) Navigating the pitfalls and promise of landscape genetics. Mol Ecol 25:849–864
Google Scholar
R Core Team (2019) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
Rousset F (2002) Partial Mantel tests: reply to Castellano and Balletto. Evolution 56:1874–1875
Google Scholar
Ruppert JLW, James PMA, Taylor EB, Rudolfsen T, Veillard M, Davis CS et al. (2017) Riverscape genetic structure of a threatened and dispersal limited freshwater species, the Rocky Mountain Sculpin (Cottus sp.). Conserv Genet 18:925–937
Google Scholar
Sexton JP, Hangartner SB, Hoffmann AA (2014) Genetic isolation by environment or distance: Which pattern of gene flow is most common? Evolution 68:1–15
Google Scholar
Sexton JP, Hufford MB, Bateman AC, Lowry DB, Meimberg H, Strauss SY et al. (2016) Climate structures genetic variation across a species’ elevation range: a test of range limits hypotheses. Mol Ecol 25:911–928
Google Scholar
Suyama Y, Matsuki Y (2015) MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Sci Rep. 5:1–12
Google Scholar
Suzuki K, Ishiyama N, Koizumi I, Nakamura F (2021) Combined effects of summer water temperature and current velocity on the distribution of a cold-water-adapted scupin (Cottus nozawae). Water 13:975
Google Scholar
Tague CL, Farrell M, Grant G, Lewis S, Rey S (2007) Hydrogeologic controls on summer stream temperatures in the McKenzie River basin, Oregon. Hydrol Process 21:3288–3300
Google Scholar
Thomaz AT, Christie MR, Knowles LL (2016) The architecture of river networks can drive the evolutionary dynamics of aquatic populations. Evolution 70:731–739
Google Scholar
Thorpe RS, Surget-Groba Y, Johansson H (2008) The relative importance of ecology and geographic isolation for speciation in anoles. Philos Trans R Soc B Biol Sci 363:3071–3081
Google Scholar
Tsuda Y, Nakao K, Ide Y, Tsumura Y (2015) The population demography of Betula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: Its admixture-like genetic structure is the result of simple population splitting not admixing. Mol Ecol 24:1403–1418
Google Scholar
Uno H (2016) Stream thermal heterogeneity prolongs aquatic-terrestrial subsidy and enhances riparian spider growth. Ecology 97:2547–2553
Google Scholar
Wang IJ, Bradburd GS (2014) Isolation by environment. Mol Ecol 23:5649–5662
Google Scholar
Wang IJ, Summers K (2010) Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog. Mol Ecol 19:447–458
Google Scholar
Watz J, Otsuki Y, Nagatsuka K, Hasegawa K, Koizumi I (2019) Temperature-dependent competition between juvenile salmonids in small streams. Freshw Biol 64:1534–1541
Google Scholar
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
Google Scholar
White SL, Hanks EM, Wagner T (2020) A novel quantitative framework for riverscape genetics. Ecol Appl 30:e02147
Google Scholar
Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177–1191
Google Scholar
Wright S (1943) Isolation by Distance. Genetics 28:114–138
Google Scholar
Yagami T, Goto A (2000) Patchy distribution of a fluvial sculpin, Cottus nozawae, in the Gakko River system at the southern margin of its native range. Ichthyol Res 47:277–286
Google Scholar
Zeileis A, Hothorn T (2002) Diagnostic checking in regression relationships. R News 2:7–10
Zeller KA, Creech TG, Millette KL, Crowhurst RS, Long RA, Wagner HH et al. (2016) Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow. Ecol Evol 6:4115–4128
Google Scholar
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