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.

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. Distinct migration timing does not prevent interbreeding between ecotypes, which are the result of a simple, ancient polymorphism segregating within a diverse population. Our finding that a complex migratory phenotype results from a single gene region will facilitate conservation and restoration of this iconic fish.

Mitochondrial DNA variation among 1246 individuals of Pacific lamprey (Entosphenus tridentatus) from 81 populations spanning 2600 km from the Skeena River, British Columbia, to the Ventura River, California, was surveyed using five restriction enzymes. A total of 29 composite haplotypes was detected in two gene fragments (ND2 and ND5). The three most common haplotypes, occurring in 91% of all samples, were present at similar frequencies in all regions. Samples were divided into six biogeographic regions based on sample distribution and geographical landmarks to assess geographic genetic structure. Analysis of molecular variance indicated that 99% of the genetic variation was explained by variability within drainages. The lack of geographical population structure is likely related to a life-history pattern that includes a prolonged larval freshwater stage, migration to oceanic feeding and return to fresh water to spawn. The lack of strong natal homing apparently promotes gene flow among drainages and regions.

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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.

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.

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