Foothill yellow-legged frog breeding biology in a semiregulated river, Humboldt County, CA

River-breeding foothill yellow-legged frogs (Rana boylii) are endemic to California and Oregon. Across this wide geographic range, many populations have declined due habitat loss, non-native competitors and predators (e.g., American bullfrogs [Lithobates catesbeianus], Centrarchid fish), and disrupted water flow due to dams. Even when flow conditions are not extensively regulated, managers still require basic and region-specific information about the breeding biology of this species to prevent further decline. To document spatiotemporal dynamics of reproductive output during drought and high flow years, we surveyed a 13.5 km reach of the lower Mad River, Humboldt County, CA approximately 70 km downstream of Matthews Dam. We found relatively high densities of egg masses (39 to 59 masses / km). Egg masses were generally laid on small cobbles (mean ±SE diameter = 11 ± 0.24 cm) at depths between 0 and 20 cm, and 95% of egg masses were laid within 6 m of the wetted edge. Egg masses were disproportionately found in the tailouts of fast runs and glides, and found less often than expected in side arms, runs, and riffles than would be expected by chance. Breeding timing appeared to be more related to rapid decreases in stream flow variance than air temperature. Taken with previous information about the species, our results suggest that R. boylii rely on multiple cues to initiate breeding. Our results can be used to help inform breeding timing and habitat use by R. boylii breeding under natural flow regimes in Northern California. Our recommendations for future research include further investigating upland habitat use by post-metamorphic life stages factors that influence breeding site selection.

Flow modification associated with reduced genetic health of a river-breeding frog, Rana boylii

River regulation or flow modification—the hydrological alteration of flow by dams and diversions—has been implicated as a cause of fundamental change to downstream aquatic ecosystems. Flow modification changes the patterns and functionality of the natural flow regime, and has the potential to restrict population connectivity and gene flow in river-dependent organisms. Since population connectivity and the maintenance of genetic diversity are fundamental drivers of long-term persistence, understanding the extent flow modification impacts these critical attributes of genetic health is an important goal for long-term conservation. Foothill yellow-legged frogs (Rana boylii) were historically abundant throughout many western rivers but have declined since the onset of regulation. However, the extent to which R. boylii populations in rivers with altered flow regimes are maintaining connectivity and genetic diversity is unknown. Here we use genetic methods to investigate the impacts of flow alteration on R. boylii to explore their potential for long-term persistence under continued flow modification. We found R. boylii in rivers with flow modification showed striking patterns of isolation and trajectories of genetic diversity loss relative to unregulated rivers. For example, flow modification explained the greatest amount of variance in population genetic differentiation compared with other covariates including geographic distance. Importantly, patterns of connectivity and genetic diversity loss were observed regardless of flow alteration level but were most prominent in locations with the greatest flow modification intensity. Although our results do not bode well for long-term persistence of R. boylii populations under current flow regulation regimes, they do highlight the power of genetic monitoring for assessing population health in aquatic organisms.

Population Genomics of the Foothill Yellow-Legged Frog (Rana boylii) and RADseq Parameter Choice for Large-Genome Organisms

Genomic data are useful for attaining high resolution in population genetic studies and have become increasingly available for answering questions in biological conservation. We analyzed RADseq data for the protected foothill yellow-legged frog (Rana boylii) throughout its native range in California and Oregon, including many of the same localities included in an earlier study based on mitochondrial DNA. We recovered five primary clades that correspond to geographic regions within California and Oregon, with better resolution and more spatially consistent patterns than the previous study, confirming the increased resolving power of genomic approaches compared to single-locus analyses. Bayesian clustering, PCA and population differentiation with admixture analyses all indicated that approximately half the range of R. boylii consists of a single, relatively uniform population, while regions in the Sierra Nevada and Central Coast Range of California are deeply differentiated genetically. Additionally, a major methodological challenge for large genome organisms, including many amphibians, is deciding on sequence similarity clustering thresholds for population genetic analyses using RADseq data, and we develop a novel set of metrics that allow researchers to set a sequence similarity threshold that maximizes the separation of paralogous regions while minimizing the oversplitting of naturally occurring allelic variation within loci.

Modeling potential river management conflicts between frogs and salmonids

Management of regulated rivers for yellow-legged frogs (Rana boylii) and salmonids exemplifies potential conflicts among species adapted to different parts of the natural flow and temperature regimes. Yellow-legged frogs oviposit in rivers in spring and depend on declining flows and warming temperatures for egg and tadpole survival and growth, whereas salmonid management can include high spring flows and low-temperature reservoir releases. We built a model of how flow and temperature affect frog breeding success. Its mechanisms include adults selecting oviposition sites to balance risks of egg dewatering by decreasing flow versus scouring by high flow, temperature effects on development, habitat selection by tadpoles, and mortality via dewatering and scouring. In simulations of a regulated river managed primarily for salmonids, below-natural temperatures delayed tadpole metamorphosis into froglets, which can reduce overwinter survival. However, mitigating this impact via higher temperatures was predicted to cause adults to oviposit before spring flow releases for salmonids, which then scoured the egg masses. The relative timing of frog oviposition and high flow releases appears critical in determining conflicts between salmonid and frog management.