Evolutionary relationships of Fish Lake Valley Tui Chub Siphateles obesus ssp. (Teleostei, Cypriniformes, Leuciscidae) and a new genus of leuciscid minnows from the Alvord Basin, western United States
Authors/Creators
- 1. University of Alaska Museum of the North, Fairbanks, United States of America|University of California, Davis, United States of America
- 2. University of California, Davis, United States of America
- 3. California Department of Fish and Wildlife, Inland Deserts Region, Bishop, United States of America
Description
The Tui Chubs, Siphateles spp., are found widely across the Great Basin and in some adjacent regions. Nearly all diversity of Siphateles has been consolidated under the name S. bicolor and there are numerous isolated populations of Tui Chubs of uncertain taxonomic standing and therefore unclear conservation priority. The Fish Lake Valley Tui Chub (FLVTC) has been recognized informally as S. bicolor ssp. 4 with a limited natural distribution in Fish Lake Valley in southwest Nevada. Considering that a rigorous examination of the phylogenetic relationships of the FLVTC and other Tui Chubs has not been conducted, the FLVTC is placed in a taxonomic framework by first applying a species delimitation method to S. bicolor sensu lato using mitochondrial data and then conducting phylogenetic analyses of genome-wide SNP data. Siphateles bicolor is better characterized by seven species, all with existing names, which here are considered to be valid Siphateles species. Furthermore, the separation of Alvord Basin Siphateles from other Siphateles is apparent as a deeply divergent lineage. As a result, we propose Epizon Campbell & Finger, gen. nov. to contain these fishes. The Fish Lake Valley Tui Chub is found to be the earliest-branching lineage of S. obesus in our SNP data set and are highly differentiated from other S. obesus. These findings are concordant with geologic evidence that indicates that Fish Lake Valley became connected to the broader Lahontan Basin ~2 million years ago, with gene flow possible until ~0.5 million years ago. Based on the geographic distribution and magnitude of genetic divergence, we find the recognition of FLVTC as a subspecies of S. obesus is appropriate.
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References
- Ali OA, O'Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C, Miller MR (2016) RAD Capture (Rapture): Flexible and efficient sequence-based genotyping. Genetics 202(2): 389–400. https://doi.org/10.1534/genetics.115.183665
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25(17): 3389–3402. https://doi.org/10.1093/nar/25.17.3389
- Azevedo-Santos VM, Ottoni FP (2025) Conserving the type locality hotspots. Bioscience 75(8): biaf025. https://doi.org/10.1093/biosci/biaf024
- Brown JH, Lomolino MV (1998) Biogeography, ed. 2. Sinauer Press, Sunderland, Massachusetts, 691 pp.
- Campbell MA, Badger ME, Buckmaster N, Starostka AB, Hawks T, Finger AJ (2023) Molecular phylogenetic and population genetic relationships of a putative species of sucker (Catostomus sp.) from Surprise Valley in the Great Basin, USA. Transactions of the American Fisheries Society 152(3): 273–286. https://doi.org/10.1002/tafs.10407
- Campbell MA, Hammer MP, Adams MB, Unmack PJ (2024) Evolutionary relationships and fine-scale geographic structuring in the temperate percichthyid genus Gadopsis (blackfishes) to support fisheries and conservation management. Molecular Phylogenetics and Evolution 199: 108159. https://doi.org/10.1016/j.ympev.2024.108159
- Cavender TM (1986) Review of the Fossil History of North American Freshwater Fishes. In: Hocutt CH, Wiley EO (Eds) The Zoogeography of North American Fishes. Wiley Interscience, New York, 699–724.
- Chen Y, Parmenter S, May B (2007) Introgression between Lahontan and endangered Owens Tui Chubs, and apparent discovery of a new Tui Chub in the Owens Valley, California. Conservation Genetics 8(1): 221–238. https://doi.org/10.1007/s10592-006-9164-3
- Chen Y, Reid S, May B (2009) Genetic relationships of tui chub populations in the northwestern Great Basin and conservation implications for the Cow Head Tui Chub. Conservation Genetics 10(1): 101–114. https://doi.org/10.1007/s10592-008-9529-x
- Chen Y, Parmenter S, May B (2013) Genetic characterization and managemet of the endangered Mohave tui chub. Conservation Genetics 14(1): 11–20. https://doi.org/10.1007/s10592-012-0410-6
- Chifman J, Kubatko L (2014) Quartet inference from SNP data under the coalescent model. Bioinformatics (Oxford, England) 30(23): 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
- Cucherousset J, Olden JD (2011) Ecological impacts of non-native freshwater fishes. Fisheries (Bethesda, Md. ) 36(5): 215–230. https://doi.org/10.1080/03632415.2011.574578
- Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H (2021) Twelve years of SAMtools and BCFtools. GigaScience 10(2): giab008. https://doi.org/10.1093/gigascience/giab008
- Edwards S, Bensch S (2009) Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008. Molecular Ecology 18(14): 2930–2933. https://doi.org/10.1111/j.1365-294X.2009.04270.x
- Finger AJ, Benjamin A, Crookshanks C, Campbell MA, Saglam IK (2022) Broad- and fine-scale structure across the distribution of the Relict Dace (Relictus solitarius) in the Great Basin Desert, USA. Conservation Science and Practice 4(6): e12672. https://doi.org/10.1111/csp2.12672
- Fricke R, Eschmeyer WN, van der Laan R [Eds] (2025) Eschmeyer's Catalog of Fishes: Genera, Species, References. http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp [accessed 03 March 2025]
- Harris PM (2000) Systematic studies of the genus Siphateles (Ostariophysi: Cyprinidae) from western North America. PhD Thesis, Oregon State University, Corvallis, Oregon, USA. https://doi.org/10.11646/zootaxa.5653.3.8
- Harris PM, Markle DF, Campbell MA (2025) Catostomus murivallis, a new species of sucker (Cypriniformes: Catostomidae) from Wall Canyon Creek, Surprise Valley, in Northwestern Nevada, U.S.A. Zootaxa 5653(3): 429–439.
- Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35(2): 518–522. https://doi.org/10.1093/molbev/msx281
- Houghton SG (1976) A trace of desert waters, The Great Basin story. The Arthur H. Clark Co. , Glendale, California, 283 pp.
- Hubbs CL, Miller RR (1972) Diagnoses of new cyprinid fishes of isolated waters in the Great Basin of western North America. Transactions of the San Diego Society Natural History 17: 101–106.
- Huson DH, Bryant D (2005) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23(2): 254–267. https://doi.org/10.1093/molbev/msj030
- Jenkins CN, Van Houtan KS, Pimm SL, Sexton JO (2015) US protected lands mismatch biodiversity priorities. Proceedings of the National Academy of Sciences of the United States of America 112(16): 5081–5086. https://doi.org/10.1073/pnas.1418034112
- Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods 14(6): 587–589. https://doi.org/10.1038/nmeth.4285
- Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30(4): 772–780. https://doi.org/10.1093/molbev/mst010
- Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9(4): 286–298. https://doi.org/10.1093/bib/bbn013
- Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14): 3059–3066. https://doi.org/10.1093/nar/gkf436
- Korneliussen TS, Albrechtsen A, Nielsen R (2014) ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15(1): 356. https://doi.org/10.1186/s12859-014-0356-4
- Kumar S, Stecher G, Suleski M, Hedges SB (2017) TimeTree: A resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution 34(7): 1812–1819. https://doi.org/10.1093/molbev/msx116
- Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 26(5): 589–595. https://doi.org/10.1093/bioinformatics/btp698
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England) 25(16): 2078–2079. https://doi.org/10.1093/bioinformatics/btp352
- Lubinski PM, Scholz AT (2021) Tui Chub (Siphateles bicolor) are Native to the Columbia River Basin in Washington State. Northwest Science 94(3–4): 243–255. https://doi.org/10.3955/046.094.0303
- Lundberg JG, Kottelat M, Smith GR, Stiassny MLJ, Gill AC (2000) So Many Fishes, So Little Time: An overview of recent ichthyological discovery in continental waters. Annals of the Missouri Botanical Garden 87(1): 26–62. https://doi.org/10.2307/2666207
- Mifflin MD, Wheat MM (1979) Pluvial lakes and estimated pluvial climates of Nevada. Bulletin of the Nevada Bureau of Mines Geology 94, 57 pp.
- Miller RR (1973) Two new fishes, Gila bicolor snyderi and Catostomus fumeiventris, from the Owens River Basin, California. Occasional Papers of the Museum of Zoology University of Michigan No. 667, 19 pp.
- Miller BA (2006) The phylogeography of Prosopium in Western North America. MSc Thesis, Brigham Young University, Provo, Utah, USA.
- Minckley WL (1986) Geography of Western North American Freshwater Fishes: Description and Relationships to Intracontinental Tectonism. In: Hocutt CH, Wiley EO (Eds) Zoogeography of North American Freshwater Fishes. John Wiley & Sons, New York, 519–613.
- Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37(5): 1530–1534. https://doi.org/10.1093/molbev/msaa015
- Mock KE, Evans RP, Crawford M, Cardall BL, Janeckes SU, Miler MP (2006) Rangewide molecular structuring in the Utah sucker (Catostomus ardens). Molecular Ecology 15(8): 2223–2238. https://doi.org/10.1111/j.1365-294X.2006.02932.x
- Moyle PB, Campbell MA (2022) Cryptic dpecies of freshwater sculpin (Cottidae: Cottus) in California. Zootaxa 5154(5): 501–527. https://doi.org/10.11646/zootaxa.5154.5.1
- Moyle PB, Buckmaster N, Su Y (2023) Taxonomy of the Speckled Dace Species Complex (Cypriniformes: Leuciscidae, Rhinichthys) in California, USA. Zootaxa 5249(5): 6. https://doi.org/10.11646/zootaxa.5249.5.1
- Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ (2014) IQ-TREE: A fast and effective stochastic algorithm for estimating Maximum-Likelihood phylogenies. Molecular Biology and Evolution 32(1): 268–274. https://doi.org/10.1093/molbev/msu300
- Orr EL, Orr WN (2012) Oregon geology. Oregon State University Press, Corvallis, 304 pp.
- Ottoni FP, South J, Azevedo-Santos VM, Henschel E, Bragança PHN (2023) Editorial: Freshwater biodiversity crisis: Multdisciplinary approaches as tools for conservation. Frontiers in Environmental Science 11: 1155608. https://doi.org/10.3389/fenvs.2023.1155608
- Ottoni FP, Ândrade M, Henschel E, Azevedo-Santos VM, Pavanelli CS, Albert JS (2025) Editorial: Freshwater biodiversity crisis: multidisciplinary approaches as tools for conservation Volume II. Frontiers in Environmental Science 13: 1613883. https://doi.org/10.3389/fenvs.2025.1613883
- Paradis E (2010) pegas: An R package for population genetics with an integrated–modular approach. Bioinformatics (Oxford, England) 26(3): 419–420. https://doi.org/10.1093/bioinformatics/btp696
- Puillandre N, Brouillet S, Achaz G (2021) ASAP: Assemble species by automatic partitioning. Molecular Ecology Resources 21(2): 609–620. https://doi.org/10.1111/1755-0998.13281
- Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81(3): 559–575. https://doi.org/10.1086/519795
- Rabosky DL, Chang J, Title PO, Cowman PF, Sallan L, Friedman M, Kaschner K, Garilao C, Near TJ, Coll M, Alfaro ME (2018) An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559(7714): 392–395. https://doi.org/10.1038/s41586-018-0273-1
- Reheis M (1999) Highest pluvial-lake shorelines and Pleistocene climate of the western Great Basin. Quaternary Research 52(2): 196–205. https://doi.org/10.1006/qres.1999.2064
- Reheis MC, Slate JL, Sarna-Wojcicki AM, Meyer CE (1991) An early Pleistocene lake in Fish Lake Valley, Nevada California: Ringside resort for the eruption of the bishop tuff. https://data.nbmg.unr.edu/public/Geothermal/GreyLiterature/Reheis_FishLkVlly_PluvialLk_1991.pdf
- Reheis MC, Sarna-Wojcicki AM, Reynolds RL, Repenning CA, Mifflin MD (2002) Pliocene to Middle Pleistocene Lakes in the Western Great Basin: Ages and Connections. In: Hershler R, Madsen DB, Currey DR (Eds) Great Basin Aquatic Systems History. Smithsonian Institution Press, Washington DC, 53–108.
- Remple S (2013) Taxonomy and Systematic Relationships of Tui Chubs (Siphateles: Cyprinidae) from Oregon's Great Basin. MSc Thesis, Oregon State University.
- Scheerer PD, Peterson JT, Clements S (2015) Distribution and abundance of Alvord Chub in Oregon and Nevada. Northwestern Naturalist (Olympia, Wash. ) 96(2): 118–132. https://doi.org/10.1898/1051-1733-96.2.118
- Schonhuth S, Shiozawa DK, Dowling TE, Mayden RL (2012) Molecular systematics of western North American cyprinids (Cypriniformes: Cyprinidae). Zootaxa 3586(1): 281–303. https://doi.org/10.11646/zootaxa.3586.1.27
- Schonhuth S, Perdices A, Lozano-Vilano L, Garcia-de-Leon F, Espinosa H, Mayden RL (2014) [January] Phylogenetic relationships of North American western chubs of the genus Gila (Cyprinidae, Teleostei), with emphasis on southern species. Molecular Phylogenetics and Evolution 70: 210–230. https://doi.org/10.1016/j.ympev.2013.09.021
- Schonhuth S, Vukic J, Sanda R, Yang L, Mayden RL (2018) Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Molecular Phylogenetics and Evolution 127: 781–799. https://doi.org/10.1016/j.ympev.2018.06.026
- Sigler WF, Sigler JW (2014) Fishes of the Great Basin: a natural history. University of Nevada Press, Reno, 448 pp.
- Simons AM, Mayden RL (1998) Phylogenetic relationships of the western North American phoxinins (Actinopterygii: Cyprinidae) as inferred from mitochondrial 12S and 16S ribosomal RNA sequences. Molecular Phylogenetics and Evolution 9(2): 308–329. https://doi.org/10.1006/mpev.1997.0467
- Smith GR, Dowling TE, Gobalet KW, Lugaski T, Shiozawa DK, Evans RP (2002) Biogeography and timing of evolutionary events among Great Basin fishes. In: Hershler R, Madsen DB, Currey DR (Eds) Great Basin Aquatic Systems History, Smithsonian Contributions to Earth Sciences, 175–234.
- Smith CT, Von Bargen J, DeHaan PW, Scheerer P, Meeuwig MH (2019) Genetic structure and history of chub in the Alvord Basin. Conservation Genetics 20(3): 489–501. https://doi.org/10.1007/s10592-019-01148-6
- Soltz DL, Naimain RJ (1978) The Natural History of Native Fishes in the Death Valley System. Serial Publications of the Natural History Museum of Los Angeles County Series 30, 76 pp.
- Su Y, Moyle PB, Campbell MA, Finger AJ, O'Rourke SM, Baumsteiger J, Miller MR (2022) Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California. Transactions of the American Fisheries Society 151(6): 695–710. https://doi.org/10.1002/tafs.10388
- Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts. https://paup.phylosolutions.com/ [accessed 3 March 2025]
- Unmack PJ, Dowling TE, Laitinen NJ, Secor CL, Mayden RL, Shiozawa DK, Smith GR (2014) Influence of introgression and geological processes on phylogenetic relationships of Western North American Mountain Suckers (Pantosteus, Catostomidae). PLOS ONE 9(3): e90061. https://doi.org/10.1371/journal.pone.0090061
- Uyeno T (1961) Osteology and phylogeny of the American cyprinid fishes allied to the genus Gila. PhD Dissertation. University of Michigan Ann Arbor.
- Williams JE, Bond CE (1980) Gila boraxobius, a new species of cyprinid fish from southeastern Oregon with a comparison to G. alvordensis. Proceedings of the Biological Society of Washington 93: 291–298.
- Williams JE, Bond CE (1983) Status and life history notes on the native fishes of the Alvord Basin, Oregon and Nevada. Great Basin Naturalist. 43(3): 409–420. https://scholarsarchive.byu.edu/gbn/vol43/iss3/5
- Williams JE, Williams CD, Bond CE (1980) Fishes of the Sheldon National Wildlife Refuge. In RA Tubb (Principle Investigator): Survey of fishes, amphibians, and reptiles on the Sheldon National Wildlife Refuge, Nevada. US Fish and Wildlife Service, Washington DC, 58 pp.
- Zardoya R, Doadrio I (1998) Phylogenetic relationships of Iberian cyprinids: Systematic and biogeographic implications. Proceedings. Biological Sciences 265(1403): 1365–1372. https://doi.org/10.1098/rspb.1998.0443
- Zink RM, Barrowclough GF (2008) Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology 17(9): 2107–2121. https://doi.org/10.1111/j.1365-294X.2008.03737.x