Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

The delimitation of species-boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life-histories co-distributed in the highly modified Colorado River (i.e., Flannelmouth Sucker, Catostomus latipinnis; Bluehead Sucker, C. Pantosteus discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction-site associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in Bluehead Sucker, supporting elevation of C. P. virescens to species-status, and recognizing C. P. discobolus yarrowi (Zuni Bluehead Sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate Flannelmouth Sucker lineages as ESUs (Evolutionarily Significant Units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the alignment of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.

Long-Term Monitoring of an Endangered Desert Fish and Factors Influencing Population Dynamics

The lower perennial corridor of the Little Colorado River in Grand Canyon, Arizona, is numerically dominated by endemic desert fishes and therefore significant for conservation of these species. From 2000 to 2012, the U.S. Fish and Wildlife Service conducted monitoring of native fishes in the Little Colorado River near its confluence with the Colorado River. The primary focus of these efforts was to estimate the spring and fall abundance of native fishes, especially the federally endangered humpback chub Gila cypha. Because humpback chub in Grand Canyon are influenced by operations of Glen Canyon Dam, our efforts provide managers of the Glen Canyon Dam Adaptive Management Program with abundance estimates and trends of humpback chub in the Little Colorado River, the most important tributary in Grand Canyon for spawning and production of this species. From 2001 to 2006, the spring abundance estimates of humpback chub ≥150 and ≥200 mm remained relatively low (≤3,419 and ≤2,002 fish, respectively), thereafter significantly increasing to highs of 8,083 and 6,250, respectively, by spring 2010. Also from 2000 to 2006, the fall abundance estimates of humpback chub were substantially below those abundances estimated after 2006. In addition, flannelmouth sucker Catostomus latipinnis and bluehead sucker Catostomus discobolus showed post-2006 increases in relative abundance, suggesting a systemwide event occurred that was beneficial to native fishes. Most of the increases of humpback chub occurred during the spring season in the reaches of the Little Colorado River between 5 and 13.57 km upstream from the confluence. Successful production of age 0 year classes of humpback chub may be partially driven by hydrograph dynamics of the Little Colorado River, whereas water temperatures and predation pressures in the mainstem Colorado River likely influence survivorship of native fishes into subadult and adult life stages.

Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques

<em>Abstract</em>.—Our capabilities to address pertinent questions in stream fish ecology, such as population connectivity, biotic homogenization, species invasions, introgression, and effects of habitat alterations on population structure and demography, have been significantly expanded by the development of molecular genetic approaches. A broad spectrum of molecular markers can now be tailored to address specific questions while newer statistical approaches accommodate larger data sets and permit the test of alternative hypotheses. Furthermore, molecular approaches facilitate the evaluation of ecological processes across both spatial and temporal scales, which are often mutually exclusive parameters. Population expansions, declines, and movements can be examined from recent to deep history and scaled from local to continental drainages. The intrinsic properties of stream ecosystems also make them particularly amenable to molecular approaches. The hierarchical order reflected in streams is directly translatable into an expanding spatial scale, from restricted headwaters through entire basins. Additionally, stream habitats are generally linear, and consequently, fish populations are often distributed sequentially, with interactions constrained to neighboring populations. Finally, streams tend to develop vicariant barriers over time, thus isolating populations and promoting local adaptation, a process easily deciphered using molecular markers. The latter have also contributed to the resolution of conservation issues and guided appropriate adaptive management of stream fauna. Molecular approaches in stream fish ecology are far too diverse to be comprehensively reviewed herein. Instead, we illustrate their facility by emphasizing three case studies demonstrating their broad utility: (1) a range-wide analysis of mitochondrial DNA diversity in flannelmouth sucker <em>Catostomus latipinnis</em>, pointing to a population bottleneck likely induced by severe post-Pleistocene drought in the Colorado River basin; (2) single nucleotide polymorphism screening to evaluate hybridization and introgression among native flannelmouth sucker, bluehead sucker <em>C. discobolus </em>(also known as <em>Pantosteus discobolus</em>), and the introduced white sucker <em>C. commersonii </em>in the upper Colorado River basin; and (3) microsatellite DNA analysis to evaluate gene flow and contemporary relationships in the Grand Canyon among populations of an endangered cyprinid fish (the humpback chub <em>Gila cypha</em>). In an appendix, we outline several recent molecular approaches that have expanded our opportunities to study stream fish ecology. We review relevant literature by emphasizing new statistical approaches and potential pitfalls of marker selection and data, rather than by delving into abstruse technical details regarding protocol development.