Andrew P. Kinziger

Molecular Systematics of the Genus Cottus (Scorpaeniformes: Cottidae)

Abstract To evaluate the monophyly of Cottus and to identify species groups within the genus we generated a data set of 1914 base pairs of mitochondrial DNA (cytochrome b and ATPase 8 and 6) for 87 individuals representing 36 of the 42 currently recognized species of the genus. Both parsimony and Bayesian analyses consistently supported non-monophyly of Cottus with respect to the Baikalian sculpins and the genus Leptocottus. Analyses also supported recognition of five clades within the genus Cottus. These are referred to herein as the Cottopsis, Uranidea, Baikalian, Cottus, and Cephalocottus clades. These clades encompass all but ten recognized Cottus species, nine whose placement was uncertain in our analyses and one not included in our analyses. Lastly, we recognize a freshwater sculpin clade comprising the most speciose freshwater component of the family Cottidae.

Using occupancy modelling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species

Environmental DNA (eDNA) monitoring approaches promise to greatly improve detection of rare, endangered and invasive species in comparison with traditional field approaches. Herein, eDNA approaches and traditional seining methods were applied at 29 research locations to compare method‐specific estimates of detection and occupancy probabilities for endangered tidewater goby (Eucyclogobius newberryi). At each location, multiple paired seine hauls and water samples for eDNA analysis were taken, ranging from two to 23 samples per site, depending upon habitat size. Analysis using a multimethod occupancy modelling framework indicated that the probability of detection using eDNA was nearly double (0.74) the rate of detection for seining (0.39). The higher detection rates afforded by eDNA allowed determination of tidewater goby occupancy at two locations where they have not been previously detected and at one location considered to be locally extirpated. Additionally, eDNA concentration was positively related to tidewater goby catch per unit effort, suggesting eDNA could potentially be used as a proxy for local tidewater goby abundance. Compared to traditional field sampling, eDNA provided improved occupancy parameter estimates and can be applied to increase management efficiency across a broad spatial range and within a diversity of habitats.

Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus)

Molecular evaluations of successful invaders are common, however studies of introduced species that have had limited invasion success, or have died out completely, are rare. We studied an introduced population of speckled dace (Rhinichthys osculus) from northern California, USA that has rapidly increased in abundance but remained restricted to a 25-km stretch of river since its introduction in the mid-1980s. Field and laboratory analyses indicate that invasion success of speckled dace is constrained by the combined effects of multiple predators. The role of bottleneck effects associated with the introduction has not been studied. We assayed variation in seven microsatellite loci and one mitochondrial DNA gene in the introduced population and nine putative source populations to identify the source population and evaluate bottleneck effects. The Trinity River system was supported as the source owing to its genetic similarity and geographic proximity to the introduced population. Consistent with a bottleneck, the introduced population exhibited reduced allelic and haplotype richness in comparison to source populations. Estimates of the genetically effective number of individuals founding the introduced population using nuclear coalescent analyses and a mitochondrial simulation procedure were highly concordant in suggesting that the initial colonizing group was comprised of about 10 individuals. A bottleneck effect in an exotic species exhibiting limited invasion success has rarely been documented and thus introduction of speckled dace represents an important model system for future investigation. Establishing a relationship between genetic diversity and factors limiting invasion success in this system (e.g., predator avoidance) will help determine the extent to which genetic diversity loss has constrained invasion success in speckled dace.

Rampant drift in artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi)

Habitat fragmentation and its genetic consequences are a critically important issue in evaluating the evolutionary penalties of human habitat modification. Here, we examine the genetic structure and diversity in naturally subdivided and artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi), a small fish restricted to discrete coastal lagoons and estuaries in California, USA. We use five naturally fragmented coastal populations from a 300‐ km spatial scale as a standard to assess migration and drift relative to eight artificially fragmented bay populations from a 30‐ km spatial scale. Using nine microsatellite loci in 621 individuals, and a 522‐base fragment of mitochondrial DNA control region from 103 individuals, we found striking differences in the relative influences of migration and drift on genetic variation at these two scales. Overall, the artificially fragmented populations exhibited a consistent pattern of higher genetic differentiation and significantly lower genetic diversity relative to the naturally fragmented populations. Thus, even in a species characterized by habitat isolation and subdivision, further artificial fragmentation appears to result in substantial population genetic consequences and may not be sustainable.

Mitochondrial DNA Variation in the Ozark Highland Members of the Banded Sculpin Cottus carolinae Complex

Abstract The goal of this study was to determine whether variation in mitochondrial DNA (mtDNA) sequence data is concordant with morphological divergence in the five Ozark Highlands members of the complex of banded sculpin Cottus carolinae: Eyelash sculpin, fringehead sculpin, Black River race, grotto sculpin, and midlands race. We generated a phylogenetic hypothesis for the banded sculpin complex based on a data set composed of 841 base pairs of mtDNA (ATPase-8 and ATPase-6) for 58 individuals representing all banded sculpin complex members that occur in the Ozark Highlands and comparative material collected outside of the highlands. Divergence in mtDNA was found to be generally concordant with morphological distinctiveness in the fringehead sculpin, eyelash sculpin, Black River race, and grotto sculpin; however, genetic divergence of these taxa was generally low (sequence divergence maximum = 0.2-1.4%) relative to the marked morphological distinctness exhibited by these taxa. In contrast, the midlands r...

Systematics of Etheostoma tippecanoe and Etheostoma denoncourti (Perciformes: Percidae)

Abstract Recently, populations of Etheostoma tippecanoe from the Tennessee River drainage were described as a new species, Etheostoma denoncourti. Although populations of E. tippecanoe from the lower Tennessee River (Duck and Buffalo Rivers) were assigned to the new taxon, the species description did not contain an analysis of specimens from these rivers. To evaluate the phylogenetic placement of these unanalyzed populations with respect to all other populations of E. tippecanoe and E. denoncourti, we assembled a dataset composed of DNA sequences (complete cytochrome b) from 32 individuals representing all known populations of these species. Parsimony analysis of these populations, 11 other darter taxa, and five outgroup taxa resulted in 3868 equally most-parsimonous trees at 1687 steps. Populations from the Duck and Buffalo Rivers were always resolved as members of the newly described taxon, E. denoncourti, consistent with the original description. Further, E. tippecanoe and E. denoncourti were resolved as monophyletic sister taxa in all most-parsimonious trees. The amount of cytochrome b sequence divergence separating these two taxa (5.63%) is within the range observed for cytochrome b variation between other species of darters.

Increased extinction potential of insular fish populations with reduced life history variation and low genetic diversity.

Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi), show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species.

A NEW MICROSPORIDIAN INFECTING THE MUSCULATURE OF THE ENDANGERED TIDEWATER GOBY (GOBIIDAE)

A previously unrecognized microsporidian (Kabatana newberryi n. sp.) is described from the musculature of Eucyclogobius newberryi (Gobiidae) in Big Lagoon, Humboldt County, California. Spores are ovoid, ranging in size from 2.8 ± 0.3 μm in total length and 1.9 ± 0.4 μm in width (measurements of 30 spores made by calculation from micrograph). The polar filament has 9–10 coils in 1–2 rows. Development occurs in direct contact with host muscle cell cytoplasm, without xenoma or sporophorous vesicle. Phylogenetic analysis of the new species and of 35 other microsporidians known to infect fish using 1,115 base pairs of aligned 16S rRNA gene indicate the new species is most closely related to Kabatana takedai. However, the new species differs by 11% sequence divergence from K. takedai. Divergence in morphology and genetic data allow for diagnosis from all other fish-infecting microsporidia and supports recognition of a new species of microsporidian, Kabatana newberryi n. sp., presently known only from a suspected specific host, the endangered tidewater goby Eucyclogobius newberryi.

Molecular Systematics of the Polytypic Species Cottus hypselurus (Teleostei: Cottidae)

Abstract Phylogenetic analyses of cytochrome b sequences support the prior hypothesis from genetic and meristic data that the Ozark Plateau endemic, Cottus hypselurus, is polytypic. These results support recognition of two species, C. hypselurus (Osage, Gasconade and Black Rivers) and Cottus sp. cf. hypselurus (Current, Eleven Point, Spring, and White rivers).

Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach.

The west coast of North America contains a number of biogeographic freshwater provinces which reflect an ever-changing aquatic landscape. Clues to understanding this complex structure are often encapsulated genetically in the ichthyofauna, though frequently as unresolved evolutionary relationships and putative cryptic species. Advances in molecular phylogenetics through species tree analyses now allow for improved exploration of these relationships. Using a comprehensive approach, we analyzed two mitochondrial and nine nuclear loci for a group of endemic freshwater fish (sculpin-Cottus) known for a wide ranging distribution and complex species structure in this region. Species delimitation techniques identified three novel cryptic lineages, all well supported by phylogenetic analyses. Comparative phylogenetic analyses consistently found five distinct clades reflecting a number of unique biogeographic provinces. Some internal node relationships varied by species tree reconstruction method, and were associated with either Bayesian or maximum likelihood statistical approaches or between mitochondrial, nuclear, and combined datasets. Limited cases of mitochondrial capture were also evident, suggestive of putative ancestral hybridization between species. Biogeographic diversification was associated with four major regions and revealed historical faunal exchanges across regions. Mapping of an important life-history character (amphidromy) revealed two separate instances of trait evolution, a transition that has occurred repeatedly in Cottus. This study demonstrates the power of current phylogenetic methods, the need for a comprehensive phylogenetic approach, and the potential for sculpin to serve as an indicator of biogeographic history for native ichthyofauna in the region.