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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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Ross ST, Modde TC, Ross DG, Camak D. Comparison of Aging Structures and Life History of a Historical Population of Roundtail Chub (Cyprinidae) in the Yampa River, Colorado. WEST N AM NATURALIST 2020. [DOI: 10.3398/064.080.0310] [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)
- Stephen T. Ross
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131
| | | | | | - David Camak
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131
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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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