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Suchocki CR, Ka'apu-Lyons C, Copus JM, Walsh CAJ, Lee AM, Carter JM, Johnson EA, Etter PD, Forsman ZH, Bowen BW, Toonen RJ. Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae). Sci Rep 2023; 13:15810. [PMID: 37737242 PMCID: PMC10517014 DOI: 10.1038/s41598-023-41719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
The Gila robusta species complex in the lower reaches of the Colorado River includes three nominal and contested species (G. robusta, G. intermedia, and G. nigra) originally defined by morphological and meristic characters. In subsequent investigations, none of these characters proved diagnostic, and species assignments were based on capture location. Two recent studies applied conservation genomics to assess species boundaries and reached contrasting conclusions: an ezRAD phylogenetic study resolved 5 lineages with poor alignment to species categories and proposed a single species with multiple population partitions. In contrast, a dd-RAD coalescent study concluded that the three nominal species are well-supported evolutionarily lineages. Here we developed a draft genome (~ 1.229 Gbp) to apply genome-wide coverage (10,246 SNPs) with nearly range-wide sampling of specimens (G. robusta N = 266, G. intermedia N = 241, and G. nigra N = 117) to resolve this debate. All three nominal species were polyphyletic, whereas 5 of 8 watersheds were monophyletic. AMOVA partitioned 23.1% of genetic variance among nominal species, 30.9% among watersheds, and the Little Colorado River was highly distinct (FST ranged from 0.79 to 0.88 across analyses). Likewise, DAPC identified watersheds as more distinct than species, with the Little Colorado River having 297 fixed nucleotide differences compared to zero fixed differences among the three nominal species. In every analysis, geography explains more of the observed variance than putative taxonomy, and there are no diagnostic molecular or morphological characters to justify species designation. Our analysis reconciles previous work by showing that species identities based on type location are supported by significant divergence, but natural geographic partitions show consistently greater divergence. Thus, our data confirm Gila robusta as a single polytypic species with roughly a dozen highly isolated geographic populations, providing a strong scientific basis for watershed-based future conservation.
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Affiliation(s)
- Christopher R Suchocki
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cassie Ka'apu-Lyons
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cameron A J Walsh
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Anne M Lee
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Julie Meka Carter
- Arizona Game and Fish Department, 5000 W. Carefree Highway, Phoenix, AZ, 85086, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
- Reefscape Restoration Initiative, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA.
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Chafin TK, Douglas MR, Bangs MR, Martin BT, Mussmann SM, Douglas ME. Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta Complex) in the Colorado River. Genome Biol Evol 2021; 13:evab200. [PMID: 34432005 PMCID: PMC8449829 DOI: 10.1093/gbe/evab200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 12/18/2022] Open
Abstract
Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed "threatened" status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (n = 387 and >22 k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the "anomaly zone" of tree space producing ambiguities that served to confound prior studies. Our results not only support the resurrection of the three species as distinct entities but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species level.
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Affiliation(s)
- Tyler K Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Marlis R Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Max R Bangs
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Bradley T Martin
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Global Campus, University of Arkansas, Fayetteville, Arkansas, USA
| | - Steven M Mussmann
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Michael E Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
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Copus JM, Montgomery WL, Forsman ZH, Bowen BW, Toonen RJ. Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species. PeerJ 2018; 6:e5605. [PMID: 30294509 PMCID: PMC6167970 DOI: 10.7717/peerj.5605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 08/17/2018] [Indexed: 11/20/2022] Open
Abstract
The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions.
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Affiliation(s)
- Joshua M. Copus
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - W. L. Montgomery
- Department of Biology, Northern Arizona University, Flagstaff, AZ, USA
| | - Zac H. Forsman
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Robert J. Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
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Carter JM, Clement MJ, Makinster AS, Crowder CD, Hickerson BT. Classification Success of Species within theGila robustaComplex Using Morphometric and Meristic Characters—A Reexamination. COPEIA 2018. [DOI: 10.1643/cg-17-614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Moran CJ, O'Neill MW, Armbruster JW, Gibb AC. Can members of the south-western Gila robusta species complex be distinguished by morphological features? JOURNAL OF FISH BIOLOGY 2017; 91:302-316. [PMID: 28589694 DOI: 10.1111/jfb.13348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
The goal for this project was to re-examine key morphological characters hypothesized to differentiate Gila intermedia, Gila robusta and Gila nigra and outline methods better suited for making species designations based on morphology. Using a combination of meristic counts, morphological measurements and geometric morphometrics, morphological dissimilarities were quantified among these three putative species. Traditional meristic counts and morphological measurements (i.e. distances between landmarks) were not useful for species identification. Geometric morphometrics, however, identified differences among species, while also suggesting an effect of geographic location on morphological variation. Using canonical variate analysis for the 441 fish sampled in this study, geometric morphometrics accurately predicted true group membership 100% of the time for G. nigra, 97% of the time for G. intermedia and 91% of the time for G. robusta. These results suggest that geometric morphometric analysis is necessary to identify morphological differences among the three species. Geometric morphometric analysis used in this study can be adopted by management officials as a tool to classify unidentified individuals.
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Affiliation(s)
- C J Moran
- College of Arts and Sciences, Fairfield University, 1073 N. Benson Rd, Fairfield, CT, 06824, U.S.A
| | - M W O'Neill
- United States Forest Service Coconino National Forest, 1824 S. Thompson St, Flagstaff, AZ, 86001, U.S.A
| | - J W Armbruster
- Department of Biological Sciences, 101 Rouse Life Sciences Building, Auburn University, Auburn, AL, 36849, U.S.A
| | - A C Gibb
- Department of Biology, Northern Arizona University, 617 S. Beaver St, Flagstaff, AZ, 86011, U.S.A
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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