Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi.

The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat.

Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river.

Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as 1 of 10 hybrid classes using 30 "diagnostic" single-nucleotide polymorphisms positioned on 26 separate chromosomes.

KNEMIDOKOPTES MITES AND THEIR EFFECTS ON THE GRIPPING POSITION OF THE FEET OF STELLER'S JAYS (CYANOCITTA STELLERI).

Steller's Jays (Cyanocitta stelleri) with swollen legs and feet resembling the signs of scaly leg have been commonly seen around Arcata, California, US. The clinical signs are thought to be caused by knemidokoptic mites, a group of parasites specialized on avian hosts. Between February 2019 and March 2020, we analyzed the long-term database of Steller's Jays collected by Humboldt State University for trends in the prevalence of signs of scaly leg, compared the gripping position in the feet of Steller's Jays with variable signs of this condition as an index of their ability to perch, identified the mites using a partial sequence of the cytochrome oxidase subunit I gene, and examined genetic distances between mites collected from different host species both sequenced in this study and from GenBank.

Recent, small beginnings: genetic analysis suggests Catostomus rimiculus (Klamath smallscale sucker) in the Smith River, California, are introduced.

Identification of introduced species can be important to understanding ecological systems and meeting conservation and management goals, but the process can be surprisingly challenging. The Klamath smallscale sucker Catostomus rimiculus seems likely to be native to the Smith River because the drainage separates two basins believed to be within the fish's native range, the Rogue and Klamath rivers. Further, C.

A complex phenotype in salmon controlled by a simple change in migratory timing.

Differentiation between ecotypes is usually presumed to be complex and polygenic. Seasonal patterns of life history in salmon are used to categorize them into ecotypes, which are often considered "distinct" animals. Using whole-genome sequencing and tribal fishery sampling of Chinook salmon, we show that a single, small genomic region is nearly perfectly associated with spawning migration timing but not with adiposity or sexual maturity, traits long perceived as central to salmon ecotypes.

Using environmental DNA and occupancy modelling to estimate rangewide metapopulation dynamics.

We demonstrate the power of combining two emergent tools for resolving rangewide metapopulation dynamics. First, we employed environmental DNA (eDNA) surveys to efficiently generate multiseason rangewide site occupancy histories. Second, we developed a novel dynamic, spatial multiscale occupancy model to estimate metapopulation dynamics.

Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey.

High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e.

Evidence for the genetic basis and epistatic interactions underlying ocean- and river-maturing ecotypes of Pacific Lamprey (Entosphenus tridentatus) returning to the Klamath River, California.

Surveys of genomic variation have improved our understanding of the relationship between fitness-related phenotypes and their underlying genetic basis. In some cases, single large-effect genes have been found to underlie important traits; however, complex traits are expected to be under polygenic control and elucidation of multiple gene interactions may be required to fully understand the genetic basis of the trait. In this study, we investigated the genetic basis of the ocean- and river-maturing ecotypes in anadromous Pacific lamprey (Entosphenus tridentatus).

Novel Concordance Between Geographic, Environmental, and Genetic Structure in the Ecological Generalist Prickly Sculpin (Cottus asper) in California.

Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California.

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.

Temporal genetic analysis of the endangered tidewater goby: extinction-colonization dynamics or drift in isolation?

Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction-colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California.

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.

Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus).

Species ranges that span different geographic landscapes frequently contain cryptic species- or population-level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However, comparisons suffer if previous studies are limited to a particular group or habitat type.

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.

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.

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.

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.

A narrow hybrid zone between two Cottus species in Wills Creek, Potomac drainage.

We describe a narrow hybrid zone between the mottled sculpin (Cottus b. bairdi) and the Blue Ridge sculpin (C. caeruleomentum).