1.
Ali, O.A., O’Rourke, S.M. Amish, S.J., Meek, M.H., Luikart, J., Jeffres, C. & Miller, M.R. (2016) RAD Capture (Rapture): flexible and efficient sequence-based genotyping. Genetics, 202, 389–400. https://doi.org/10.1534/genetics.115.183665
Allendorf, F. (2017) Genetics and the conservation of natural populations: allozymes to genomes. Molecular Ecology, 26, 420–430. https://doi.org/10.1111/mec.13948
Bailey, R.M. & Bond, C.E. (1963) Four new species of freshwater sculpins, genus Cottus, from western North America. Occasional Papers of the Museum of Zoology, University of Michigan, 634, 1–27.
Barnes, M.A. & Turner, C.R. (2016) The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics, 7 (1), 1–17. https://doi.org/10.1007/s10592-015-0775-4
Baumsteiger, J., Kinziger, A.P. & Aguilar, A. (2012) Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach. Molecular Phylogenetics and Evolution, 65, 940–52. https://doi.org/10.1016/j.ympev.2012.08.015
Baumsteiger, J., Kinziger, A.P., Reid., S.B. & Aguilar, A. (2014) Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus). Molecular Ecology, 23, 2602–2618. https://doi.org/10.1111/mec.12758
Baumsteiger, J., Moyle, P.B., Aguilar, A., O’Rourke, S.M. & Miller, M.R. (2017) Genomics clarifies taxonomic boundaries in a difficult species complex. PLoS ONE, 12 (12), e0189417. https://doi.org/10.1371/journal.pone.0189417
Baumsteiger, J. & Moyle, P.B. (2019) A reappraisal of the California Roach/Hitch (Cypriniformes, Cyprinidae, Hesperoleucus/Lavinia) species complex. Zootaxa, 4543 (2), 2221–240. https://doi.org/10.11646/zootaxa.4543.2.3
Baumsteiger, J., Young, M. & Moyle, P.B. (2019) Using the Distinct Population Segment (DPS) concept to protect fishes with low levels of genomic differentiation: conservation of an endemic minnow (Hitch). Transactions of the American Fisheries Society, 148, 406–416. https://doi.org/10.1002/tafs.10144
Belyaeva, M. & Taylor, D.J. (2009) Cryptic species within the Chydorus sphaericus species complex (Crustacea: Cladocera) revealed by molecular markers and sexual stage morphology. Molecular Phylogenetics and Evolution, 50, 534–546. https://doi.org/10.1016/j.ympev.2008.11.007
Bickford, D., Lohman D.J., Sodhi, N.S., Ng, P.K., Meier, R., Winker, K., Ingram, K.K. & Das, I. (2007) Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution, 22,148–155. https://doi.org/10.1016/j.tree.2006.11.004
Chifman, J. & Kubatko, L. (2014) Quartet inference from SNP data under the coalescent model. Bioinformatics, 30, 3317–3324. https://doi.org/10.1093/bioinformatics/btu530
Chifman, J. & Kubatko, L. (2015) Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. Journal of Theoretical Biology, 374, 35–47. https://doi.org/10.1016/j.jtbi.2015.03.006
Copus, J.M., Montgomery, W.L., Forsman, Z.H., Bowen, B.W. & Toonen, R.J. (2018) Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species. PeerJ, Doi10.771/, peerj 5605. https://doi.org/10.7717/peerj.5605
Daniels, R.A. & Moyle, P.B. (1984) Geographic variation and a taxonomic reappraisal of the marbled sculpin, Cottus klamathensis. Copeia, 1984, 949–959. https://doi.org/10.2307/1445339
Egge, J.J.D. & Simons, A.M. (2006) The challenge of truly cryptic diversity: diagnosis and description of a new madtom catfish (Ictaluridae: Noturus). Zoologica Scripta, 35 (6), 581–595. https://doi.org/10.1111/j.1463-6409.2006.00247.x
Evanno, G., Regnaut, S. & Goudet, J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Evermann, B.W. & Clark, H.W. (1931) A distributional list of the species of freshwater fishes known to occur in California. California Division of Fish and Game Fish Bulletin, 35,1–67.
Francis, R.M. (2017) pophelper: an R package and web app to analyze and visualize population structure. Molecular Ecology Resources, 17, 27–32. https://doi.org/10.1111/1755-0998.12509
Freudenstein, J.V., Broe, M.B., Folk, R.A. & Sinn, B.T. (2017) Biodiversity and the species concept—lineages are not enough. Systematic Biology, 66 (4), 644–656. https://doi.org/10.1093/sysbio/syw098
Fumagalli, M., Vieira, F.G., Linderoth, T. & Nielsen, R. (2014) ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics, 30, 1486–1487. https://doi.org/10.1093/bioinformatics/btu041
Girard, C. (1854) Descriptions of new fishes collected by Dr. A. L. Heermann, naturalist attached to the survey of the Pacific railroad route, under Lieut. R. S. Williamson, U. S.A. Proceedings of the Academy of Natural Sciences of Philadelphia, 7, 129–165.
Gudde, E.G. & Bright, W. (1998) California Place Names. University of California Press, Berkeley, 172 pp. https://doi.org/10.1525/9780520920545
Hebert, P.D. & Gregory, T.R. (2005) The promise of DNA barcoding for taxonomy. Systematic Biology, 54, 852–859. https://doi.org/10.1080/10635150500354886
Hoskin, C.J., Higgie, M., McDonald, K.R. & Moritz, C. (2005) Reinforcement drives rapid allopatric speciation. Nature, 437 (7063), 1353. https://doi.org/10.1038/nature04004
Hudson, R.R. & Coyne, J.A. (2002) Mathematical consequences of the genealogical species concept. Evolution, 56,1557–1565. https://doi.org/10.1111/j.0014-3820.2002.tb01467.x
Jordan, D.S. (1896) Notes on fishes little known or new to science. Proceedings of California Academy of Sciences, Series 2, 6, 221–225.
Jordan, D.S. & Evermann, B.W. (1896) Fishes of North and Middle America. Bulletin of US National Museum, 47 (1–4), 1–3705.
Katoh, K. & Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9, 286–298. https://doi.org/10.1093/bib/bbn013
Kinziger, A.P., Hellmair, M., Fong, S.R., Goodman, D.H. & Kelsey, H. (2016) Evolution of rough sculpin (Cottus asperrimus): genetic divergence and late Quaternary displacement on the Hat Creek fault, California, USA. Conservation Genetics, 17 (6),1257–1267. https://doi.org/10.1007/s10592-016-0859-9
Kinziger, A.P, Wood, R.M. & Neely, D.A. (2005) Molecular systematics of the genus Cottus (Scorpaeniformes: Cottidae). Copeia, 2005 (2), 303–311. https://doi.org/10.1643/CI-03-290R1
Kon, T., Yoshino, T., Mukai, T. & Nishida, M. (2007) DNA sequences identify numerous cryptic species of the vertebrate: a lesson from the gobioid fish Schindleria. Molecular Phylogenetics and Evolution, 44, 53–62. https://doi.org/10.1016/j.ympev.2006.12.007
Korneliussen, T.S., Albrechtsen, A. & Nielse, R. (2014) ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics, 15, 356. https://doi.org/10.1186/s12859-014-0356-4
Krejsa, R.J. (1967) The Systematics of the Prickly Sculpin, Cottus asper Richardson, a Polytypic Species: Part I. Synonymy, Nomenclatural History, and Distribution. Ph.D Thesis, University of Washington, 125 pp.
Krishnamurthy, P.K. & Francis, R.A. (2012) A critical review on the utility of DNA barcoding in biodiversity conservation. Biodiversity and Conservation, 21, 1901–1919. https://doi.org/10.1007/s10531-012-0306-2
Lara, A., Ponce de León, J.L., Rodriguez, R., Casane, D., Cote, G., Bernatchez, L. & García‐Machado, E.R. (2010) DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts. Molecular Ecology Resources, 10, 421–430. https://doi.org/10.1111/j.1755-0998.2009.02785.x
Leidy, R.A. (2007) Ecology, Assemblage Structure, Distribution, and Status of Fishes in Streams Tributary to the San Francisco Estuary, California. San Francisco Estuary Institute Contribution 530.
Leidy, R.A. & Moyle, P.B. (2021) Keeping up with the status of freshwater fishes: a California (USA) perspective. Conservation Science and Practice, 3 (8), e474. [10 pp.] https://doi.org/10.1111/csp2.474
Li, H. & Durbin, L.H.R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. & Durbin, R., 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Liu, Z., Chen, G., Zhu, T., Zeng, Z., Lyu, Z., Wang, J., Messenger, K., Greenberg, A.J., Guo, Z., Yang, Z. & Shi, S. (2018) Prevalence of cryptic species in morphologically uniform taxa–Fast speciation and evolutionary radiation in Asian frogs. Molecular Phylogenetics and Evolution, 127, 723–731. https://doi.org/10.1016/j.ympev.2018.06.020
Luikart, G., England, P.R., Tallmon, D., Jordan, S. & Taberlet, P. (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981. https://doi.org/10.1038/nrg1226
Markle, D.F. (2016) A Guide to the Fishes of Oregon. Oregon State University Press, Corvallis, 160 pp.
Moyle, P.B. (2002) Inland Fishes of California. Revised and Expanded. University of California Press, Berkeley, 517 pp.
Moyle, P.B. & Cech, J.J. (2004) Fishes: An Introduction to Ichthyology. Fifth Edition. Prentice Hall, New Jersey, 726 pp.
Moyle, P.B. & Daniels, R.A. (1982) Fishes of the Pit River System, McCloud River System, and Surprise Valley Region. In: Moyle, P.B. (Ed.), Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. University of California Publications in Zoology, 115, 1–82. https://doi.org/10.2307/1444119
Moyle, P.B., Kiernan, J.D., Crain, P.K. & Quiñones, R.M. (2013) Climate change vulnerability of native and alien freshwater fishes of California: a systematic assessment approach. PLoS One, 8(5): e63883. https://doi.org/10.1371/journal.pone.0063883
Moyle, P.B., Katz J.V.E. & Quiñones, R.M. (2011) Rapid decline of California’s native inland fishes: a status assessment. Biological Conservation, 144, 2414–2423. https://doi.org/10.1016/j.biocon.2011.06.002
Moyle, P., Lusardi, R., Samuel, P. & Katz, J. (2017) State of the Salmonids: Status of California’s Emblematic Fishes 2017. Center for Watershed Sciences, University of California, Davis and California Trout, San Francisco, CA, 579 pp. [https://watershed.ucdavis.edu/files/content/news/SOS%20II_Final.pdf]
Page, L.M. & Burr, B.M. (2011) Peterson Field Guide to Freshwater Fishes of North America North of Mexico. Houghton Mifflin Harcourt.
R Core Team. (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
Paradis, E. (2010) “pegas: an R package for population genetics with an integrated–modular approach. Bioinformatics, 26, 419–420. https://doi.org/10.1093/bioinformatics/btp696
Paradis, E. & Schliep, K. (2019) “ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526–528. https://doi.org/10.1093/bioinformatics/bty633
Pickrell, J.K. & Pritchard, J.K. (2012) Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. PLOS Genetics, 8: e1002967 https://doi.org/10.1371/journal.pgen.1002967
Robins, C.R. & Miller, R.R. (1957) Classification, variation, and distribution of sculpins, genus Cottus, inhabiting Pacific waters in California and southern Oregon, with a key to species. California Fish and Game, 43, 213–233.
Rowsey, D.M. & Egge, J.J. (2017) Morphometric analysis of two enigmatic sculpin species, Cottus gulosus and Cottus perplexus (Scorpaeniformes: Cottidae). Northwestern Naturalist, 98, 190–203. https://doi.org/10.1898/NWN16-23.1
Ruby, J.G., Bellare, P. & DeRisi, J.L. (2013) PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3: Genes, Genomes, Genetics, 3, 865–880. https://doi.org/10.1534/g3.113.005967
Rutter, C. (1908) The fishes of the Sacramento-San Joaquin Basin with a study of their distribution and variation. Bulletin of US Bureau of Fisheries, 27, 103–122.
Santos, N.R., Katz, J.V.E., Moyle, P.B. & Viers, J.H. (2013) A programmable information system for management and analysis of aquatic species range data in California. Environmental Modeling & Software, 53, 13–26. https://doi.org/10.1016/j.envsoft.2013.10.024
Shapovalov, L. & Dill, W.A. (1950) A check list of the fresh-water and anadromous fishes of California. California Fish and Game, 36,382–391.
Sloan, D. (2006) Geology of the San Francisco Bay Area. University of California Press, Berkeley, 360 pp.
Smith, J.J. (1982) Fishes of the Pajaro River System. In: Moyle, P.B. (Ed.), Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. University of California Publications in Zoology, 115, 83–170. https://doi.org/10.2307/1444119
Snyder, J.O. (1905) Notes on the fishes of the streams flowing into San Francisco Bay, Report U.S. Bureau of Fisheries for 1904, 5, 327–338.
Snyder, J.O. (1913) The fishes of the streams tributary to San Francisco Bay. Bulletin of the United States Bureau of Fisheries, 32, 49–72.
Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates. https://doi.org/10.1111/j.0014-3820.2002.tb00191.x
Tautz, D., Arctander, P., Minelli, A., Thomas, R.H. & Vogler, A.P. (2003) A plea for DNA taxonomy. Trends in Ecology and Evolution, 18, 70–74. https://doi.org/10.1016/S0169-5347(02)00041-1
Victor, B.C. (2015) How many coral reef fish species are there? Cryptic diversity and the new molecular taxonomy. In: Mora, C. (Ed.), Ecology of Fishes on Coral Reefs. Cambridge University Press, Cambridge, pp. 76–87. https://doi.org/10.1017/CBO9781316105412.010
Westerling, A.L. & Bryant, B.P. (2008) Climate change and wildfire in California. Climatic Change, 87, 231–249. https://doi.org/10.1007/s10584-007-9363-z
Williams, A.P., Cook, E.R., Smerdon, J.E., Cook, B.I., Abatzoglou, J.Y., Bolles, K., Baek, A., Badger, M. & Livineh, B. (2020) Large contribution from anthropogenic warming to an emerging North American megadrought. Science, 368 (6488), 3140318. https://doi.org/10.1126/science.aaz9600
Wilson, C.C. & Bernatchez, L. (1998) The ghost of hybrids past: fixation of arctic charr (Salvelinus alpinus) mitochondrial DNA in an introgressed population of lake trout (S. namaycush). Molecular Ecology, 7, 127–132. https://doi.org/10.1046/j.1365-294x.1998.00302.x
Winterbottom, R., Hanner, R.H., Burridge, M. & Zur, M. (2014) A cornucopia of cryptic species-a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes). ZooKeys, 381,79–111. https://doi.org/10.3897/zookeys.381.6445
Wydoski, R.S. & Whitney, R.R. (2003) Inland Fishes of Washington. 2nd edition. University of Washington Press, Seattle, 384 pp.
Yang, Z. & Rannala, B. (2017) Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses. Molecular Ecology, 26, 3028–3036. https://doi.org/10.1111/mec.14093
Yokoyama, R. & Goto, A. (2005) Evolutionary history of freshwater sculpins, genus Cottus (Teleostei; Cottidae) and related taxa, as inferred from mitochondrial DNA phylogeny. Molecular Phylogenetics and Evolution, 36, 654–668. https://doi.org/10.1016/j.ympev.2005.06.004
Young, M.K., McKelvey, K.S., Pilgrim, K.L. & Schwartz, M.K. (2013) DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams. Molecular Ecology Resources, 13, 83–595. https://doi.org/10.1111/1755-0998.12091
Zúniga-Reinoso, . & Benítez, H.A. (2015) The overrated use of the morphological cryptic species concept: An example with Nyctelia darkbeetles (Coleoptera: Tenebrionidae) using geometric morphometrics. Zoologischer Anzeiger-A Journal of Comparative Zoology, 255, 47–53. https://doi.org/10.1016/j.jcz.2015.01.004
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