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Young MK, Smith R, Pilgrim KL, Isaak DJ, McKelvey KS, Parkes S, Egge J, Schwartz MK. A Molecular Taxonomy of Cottus in western North America. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Michael K. Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Rebecca Smith
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Kristine L. Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Daniel J. Isaak
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Kevin S. McKelvey
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Sharon Parkes
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Jacob Egge
- Department of Biology, Pacific Lutheran University, Tacoma, WA 98447
| | - Michael K. Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
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Buser TJ, Finnegan DL, Summers AP, Kolmann MA. Have Niche, Will Travel. New Means of Linking Diet and Ecomorphology Reveals Niche Conservatism in Freshwater Cottoid Fishes. Integr Org Biol 2019; 1:obz023. [PMID: 33791537 PMCID: PMC7671106 DOI: 10.1093/iob/obz023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evolutionary transitions between habitats have been catalysts for some of the most stunning examples of adaptive diversification, with novel niches and new resources providing ecological opportunity for such radiations. In aquatic animals, transitions from saltwater to freshwater habitats are rare, but occur often enough that in the Neotropics for example, marine-derived fishes contribute noticeably to regional ichthyofaunal diversity. Here, we investigate how morphology has evolved in a group of temperate fishes that contain a marine to freshwater transition: the sculpins (Percomorpha; Cottoidea). We devised a novel method for classifying dietary niche and relating functional aspects of prey to their predators. Coupled with functional measurements of the jaw apparatus in cottoids, we explored whether freshwater sculpins have fundamentally changed their niche after invading freshwater (niche lability) or if they retain a niche similar to their marine cousins (niche conservatism). Freshwater sculpins exhibit both phylogeographical and ecological signals of phylogenetic niche conservatism, meaning that regardless of habitat, sculpins fill similar niche roles in either saltwater or freshwater. Rather than competition guiding niche conservatism in freshwater cottoids, we argue that strong intrinsic constraints on morphological and ecological evolution are at play, contra to other studies of diversification in marine-derived freshwater fishes. However, several intertidal and subtidal sculpins as well as several pelagic freshwater species from Lake Baikal show remarkable departures from the typical sculpin bauplan. Our method of prey categorization provides an explicit, quantitative means of classifying dietary niche for macroevolutionary studies, rather than relying on somewhat arbitrary means used in previous literature.
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Affiliation(s)
- T J Buser
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97321, USA
| | - D L Finnegan
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - A P Summers
- Department of Biology and SAFS, University of Washington s Friday Harbor Laboratories, Friday Harbor, WA 98250, USA
| | - M A Kolmann
- Department of Biology and SAFS, University of Washington s Friday Harbor Laboratories, Friday Harbor, WA 98250, USA
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA
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Baumsteiger J, Moyle PB, Aguilar A, O’Rourke SM, Miller MR. Genomics clarifies taxonomic boundaries in a difficult species complex. PLoS One 2017; 12:e0189417. [PMID: 29232403 PMCID: PMC5726641 DOI: 10.1371/journal.pone.0189417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/24/2017] [Indexed: 11/19/2022] Open
Abstract
Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors.
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Affiliation(s)
- Jason Baumsteiger
- Center for Watershed Sciences, University of California, Davis, United States of America
- Department of Animal Sciences, University of California, Davis, United States of America
- * E-mail: (JB); (MM)
| | - Peter B. Moyle
- Center for Watershed Sciences, University of California, Davis, United States of America
- Department of Wildlife, Fisheries, and Conservation Biology, University of California, Davis, United States of America
| | - Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, United States of America
| | - Sean M. O’Rourke
- Department of Animal Sciences, University of California, Davis, United States of America
| | - Michael R. Miller
- Center for Watershed Sciences, University of California, Davis, United States of America
- Department of Animal Sciences, University of California, Davis, United States of America
- * E-mail: (JB); (MM)
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Balakirev ES, Saveliev PA, Ayala FJ. Complete mitochondrial genome of the Amur sculpin Cottus szanaga (Cottoidei: Cottidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:737-738. [PMID: 33644381 PMCID: PMC7871824 DOI: 10.1080/23802359.2016.1233470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The complete mitochondrial genome was sequenced in two individuals of the Amur sculpin Cottus szanaga. The genome sequences are 16,518 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin genomes published previously. The low level of sequence divergence detected between the genome of C. szanaga and the GenBank complete mitochondrial genome of the Cherskii's sculpin Cottus czerskii (KJ956027) may likely be due to recent divergence, historical hybridization, or presence of a new unrecognized taxonomic unit close to C. szanaga but erroneously identified as C. czerskii.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.,A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch, Russian Academy of Science, Vladivostok, Russia.,Far Eastern Federal University, School of Natural Sciences, Vladivostok, Russia
| | - Pavel A Saveliev
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch, Russian Academy of Science, Vladivostok, Russia
| | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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Baumsteiger J, Kinziger AP, Aguilar A. Novel Concordance Between Geographic, Environmental, and Genetic Structure in the Ecological Generalist Prickly Sculpin (Cottus asper) in California. J Hered 2016; 107:504-17. [PMID: 27489253 DOI: 10.1093/jhered/esw045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/16/2016] [Indexed: 11/14/2022] Open
Abstract
Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California. We then incorporated genetic and GIS data into ecological niche models to assess ecological conditions within identified groups. Though not reciprocally monophyletic, unique mtDNA haplotypes, microsatellite clustering, and measures of isolation by distance (Coastal: r = 0.960, P < 0.001; Inland: r = 0.277, P = 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained to Great Central Valley). Divergence estimates of 41-191 kya combined with the regional biogeographic history suggest geographic barriers are absent between groups since divergence, but ecological niche modeling revealed significant environmental differences (t = 10.84, P < 0.001). Introgressed individuals were also discovered between groups in an ecologically and geographically intermediate region. Population structure was limited, predominately found in tributaries of the San Joaquin basin in the Inland group. Overall, C. asper exhibited substantial genetic diversity, despite its ecological generality, reflecting California's historically unique and complex hydrology. More broadly, this study illustrates variable environments within the range of a generalist species may mask genetic divergences and should not be overlooked in biodiversity assessments.
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Affiliation(s)
- Jason Baumsteiger
- From the School of Natural Sciences and Sierra Nevada Research Institute, University of California Merced, 5200N. Lake Road, Merced, CA 95344 (Baumsteiger, Aguilar); Department of Fisheries Biology, Humboldt State University, 1 Harpst Street, Arcata, CA 95521 (Kinziger). Baumsteiger is now at the Center for Watershed Sciences, University of California Davis, One Shields Avenue, Davis, CA 95616; and Aguilar is now at Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032-8530.
| | - Andrew P Kinziger
- From the School of Natural Sciences and Sierra Nevada Research Institute, University of California Merced, 5200N. Lake Road, Merced, CA 95344 (Baumsteiger, Aguilar); Department of Fisheries Biology, Humboldt State University, 1 Harpst Street, Arcata, CA 95521 (Kinziger). Baumsteiger is now at the Center for Watershed Sciences, University of California Davis, One Shields Avenue, Davis, CA 95616; and Aguilar is now at Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032-8530
| | - Andres Aguilar
- From the School of Natural Sciences and Sierra Nevada Research Institute, University of California Merced, 5200N. Lake Road, Merced, CA 95344 (Baumsteiger, Aguilar); Department of Fisheries Biology, Humboldt State University, 1 Harpst Street, Arcata, CA 95521 (Kinziger). Baumsteiger is now at the Center for Watershed Sciences, University of California Davis, One Shields Avenue, Davis, CA 95616; and Aguilar is now at Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032-8530
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Evolution of rough sculpin (Cottus asperrimus) genetic divergence and late Quaternary displacement on the Hat Creek fault, California, USA. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0859-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Craig CA, Kollaus KA, Behen KPK, Bonner TH. Relationships among spring flow, habitats, and fishes within evolutionary refugia of the Edwards Plateau. Ecosphere 2016. [DOI: 10.1002/ecs2.1205] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Cody A. Craig
- Department of Biology/Aquatic Station; Texas State University - San Marcos; 601 University Drive San Marcos Texas 78666 USA
| | - Kristy A. Kollaus
- The Meadows Center for Water and the Environment; Texas State University - San Marcos; 601 University Drive San Marcos Texas 78666 USA
| | - Kenneth P. K. Behen
- Washington Department of Fish and Wildlife Fish Program Fish Management Division; Olympia Washington 98501 USA
| | - Timothy H. Bonner
- Department of Biology/Aquatic Station; Texas State University - San Marcos; 601 University Drive San Marcos Texas 78666 USA
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