Molecular Genetics Informs Spatial Segregation of Two Desert Stream <i>Gila</i> Species

Marsh, Paul C.; Clarkson, Robert W.; Dowling, Thomas E.

doi:10.1080/00028487.2016.1227373

Cited by 6 publications

(14 citation statements)

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“…robusta, so while it is possible clade 5 represents a geographically restricted lineage, additional geographical sampling will similarly likely erode the unity of this clade. In any case, whatever the finding with clade 5, our data are consistent with previous studies based on allozyme, mtDNA, and microsatellite markers that likewise failed to find diagnostic characters among these nominal species (DeMarais, 1992;DeMarais et al, 1992;Dowling & DeMarais, 1993;Dowling et al, 2015, Marsh, Clarkson & Dowling, 2017. The average most recent common ancestor of each of the clades resolved in this study is 63kya (51kya to 76 kya 95 HPD interval) with the most recent common ancestor of all populations 119 kya (97 kya to 140 kya 95% HPD interval).…”

Section: Phylogenomics and Hybridizationsupporting

confidence: 92%

“…hybridization producing viable offspring is a common occurrence (Gerber, Tibbets & Dowling, 2001;Marsh, Clarkson & Dowling, 2017). This history, coupled with the cyclical nature of Manuscript to be reviewed glacially driven pluvial periods makes it unlikely that evolutionary forces will induce speciation in the absence of permanent barriers to gene flow.…”

Section: Management Implicationsmentioning

confidence: 99%

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Peer Review #1 of "Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species (v0.1)"

2018

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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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Section: Phylogenomics and Hybridizationsupporting

confidence: 92%

Section: Management Implicationsmentioning

confidence: 99%

Peer Review #1 of "Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species (v0.1)"

2018

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“…These periods of isolation may have promoted an accumulation of ecological divergences that persisted post-contact, and were sufficient to maintain species boundaries despite contemporary sympatric distributions and weak morphological differentiation. This hypothesis is also supported by the non-random mating found among G. robusta and G. nigra, despite anthropogenically-induced contact (Marsh et al 2017).…”

Section: Complex Evolution and Biogeography Of The Colorado Rivermentioning

confidence: 68%

Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta complex) in the Colorado River

Chafin

Douglas

Bangs

et al. 2019

Preprint

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Disclosure statement:Authors have nothing to disclose.Abstract (242/250) Species are an indisputable unit for biodiversity conservation, yet their delimitation is fraught 2 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 4 North America. Three species were originally defined according to subtle morphological differences with weak diagnostic power, with traditional genetic analyses failing to support the 6 nominal species. Consequently, the complex was re-defined as a single polytypic unit, with the proposed 'threatened' status of two putative species withdrawn at the federal level. Here, we 8 utilized dense spatial and genomic sampling (N=387 and >22k loci) to re-evaluate the status of the complex, based on SNP-based coalescent and polymorphism-aware phylogenetic models. In 10 doing so, all three species were supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To understand this discrepancy with past studies, we 12 categorized evolutionary mechanisms driving discordance. We tested (and subsequently rejected) prior hypotheses suggesting that phylogenetic discord in the complex was hybridization-driven. 14 Instead, we found the G. robusta complex to have diverged within the 'anomaly zone' of tree space and, as such, have accumulated inconsistent patterns of diversity which have confounded 16 prior studies. After extending these analyses with phylogeographic modeling, we propose that this is reflective of a rapid radiation promoted by Plio-Pleistocene tectonism. Our results not only 18 support resurrection of the three species as distinct entities, but also offer an empirical example of how phylogenetic discordance can be categorized in other recalcitrant taxa. 20 between G. robusta from the upper and lower basins of the Colorado River ecosystem (Chafin et 130 al. 2019). One species, Gila elegans, is extirpated from the wild, thus samples were provided by the 132 Southwestern Native Aquatic Resources and Recovery Center (Dexter, NM). The genus Ptychocheilus served to root the Gila clade within the broader context of western leuciscids 134 (Schönhuth et al. 2012, 2014, 2018). 8 136 Reduced-representation sequencing Genomic DNA was extracted using either PureGene® or DNeasy® kits (Qiagen Inc.) and 138 quantified via fluorometer (Qubit™; Thermo-Fisher Scientific). Library preparations followed the published ddRAD protocol (Peterson et al. 2012). Restriction enzyme and size-selection 140 ranges were first screened using an in silico procedure (Chafin et al. 2018), with the target fragment sizes further optimized by quantifying digests for 15 representative samples on an 142 Agilent 2200 TapeStation. Final library preparations were double-digested using a high-fidelity PstI (5'-CTGCAG-3') and MspI (5'-CCGG-3') following manufacturer's protocols (New 144 England Biosciences). Digests were purified using bead purification (Ampure XP; Beckman-Coul...

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“…Marsh et al . () consider the Gila robusta complex as three cryptic species and used microsatellites to distinguish between G . robusta and G .…”

Section: Introductionmentioning

confidence: 99%

“…While the conceptual framework of for monophyly of any of the species within the G. robusta species complex using one mitochondrial and several nuclear genes. Marsh et al (2017) consider the Gila robusta complex as three cryptic species and used microsatellites to distinguish between G. robusta and G. nigra, document hybridization and identify the replacement of G. nigra with G. robusta in middle sections of a single stream. The American Fisheries Society and the American Society of Ichthyologists and Herpetologists Joint Committee on the Names of Fishes, however, recently investigated the taxonomic status of species in the robusta complex and, based on preliminary whole-genome sequence data (Copus et al, 2016), determined the available genetic and morphological data supports a single species rather than three (Page et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Can members of the south‐western Gila robusta species complex be distinguished by morphological features?

Moran

O’Neill

Armbruster

et al. 2017

Journal of Fish Biology

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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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Molecular Genetics Informs Spatial Segregation of Two Desert Stream Gila Species

Cited by 6 publications

References 43 publications

Peer Review #1 of "Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species (v0.1)"

Peer Review #1 of "Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species (v0.1)"

Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta complex) in the Colorado River

Can members of the south‐western Gila robusta species complex be distinguished by morphological features?

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