The red-backed salamander (Plethodon cinereus) has long-served as a model system in ecology, evolution, and behavior, and studies surveying molecular variation in this species have become increasingly common over the past decade. However, difficulties are commonly encountered when extending microsatellite markers to populations that are unstudied from a genetic perspective due to high levels of genetic differentiation across this species’ range. To ameliorate this issue, we used 454 pyrosequencing to identify hundreds of microsatellite loci. We then screened 40 of our top candidate loci in populations in Virginia, Pennsylvania, and Ohio—including an isolated island population ~ 4.5 km off the shore of Lake Erie (South Bass Island). We identified 25 loci that are polymorphic in a well-studied region of Virginia and 11 of these loci were polymorphic in populations located in the genetically unstudied regions of Ohio and Pennsylvania. Use of these loci to examine patterns of variation within populations revealed that South Bass Island has low diversity in comparison to other sites. However, neither South Bass Island nor isolated populations around Cleveland are inbred. Assessment of variation between populations revealed three well defined genetic clusters corresponding to Virginia, mainland Ohio/Pennsylvania, and South Bass Island. Comparisons of our results to those of others working in various parts of the range are consistent with the idea that differentiation is lower in regions that were once glaciated. However, these comparisons also suggest that well differentiated isolated populations in the formerly glaciated portion of the range are not uncommon. This work provides novel genetic resources that will facilitate population genetic studies in a part of the red-backed salamander’s range that has not previously been studied in this manner. Moreover, this work refines our understanding of how neutral variation is distributed in this ecologically important organism.

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Animal colour is a complex trait shaped by multiple selection pressures that can vary across geography. The thermal melanism hypothesis predicts that darker coloration is beneficial to animals in colder regions because it allows for more rapid solar absorption. Here, we use community science images of three closely related species of North American ratsnakes (genus Pantherophis ) to examine if climate predicts colour variation across range-wide scales. We predicted that darker individuals are found in colder regions and higher elevations, in accordance with the thermal melanism hypothesis. Using an unprecedented dataset of over 8000 images, we found strong support for temperature as a key predictor of darker colour, supporting thermal melanism. We also found that elevation and precipitation are predictive of colour, but the direction and magnitude of these effects were more variable across species. Our study is the first to quantify colour variation in Pantherophis ratsnakes, highlighting the value of community science images for studying range-wide colour variation.

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North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here we present two chromosome-scale reference genome assemblies Spikedace (Meda fulgida) and Loach Minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for Spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb and L75 = 18. The complete assembly for Loach Minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for Spikedace and ∼98% for Loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58% and 29.04% of Spikedace and Loach Minnow total genome lengths to be comprised of protein coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions and evidence of positive selection in both genomes.

Understanding trade‐offs associated with occupying various aquatic habitats provides a mechanistic understanding of habitat needs that can be used to evaluate the consequences of habitat loss or alteration. We used instream enclosures and field observations to identify how velocity affects the growth rates of four native species in the upper Gila River basin: longfin dace (Agosia chrysogaster) and speckled dace (Rhinichthys osculus), two species of no conservation concern, and loach minnow (Tiaroga cobitis) and spikedace (Meda fulgida), two federally endangered species. Elevated velocity was predicted to increase food delivery through drift or stimulation of benthic primary production. Energetic costs of high‐velocity habitat were predicted to vary with morphology and behaviour and be lowest for speckled dace and loach minnow because they are adapted to occupy interstitial spaces of the substrate in riffles. Spikedace and longfin dace should perform best in moderate velocities, where the trade‐off between exposure to drifting macroinvertebrates outweighs the energetic costs of maintaining position in the water column. Growth rates of loach minnow and speckled dace increased in higher velocities, but contrary to our initial predictions, spikedace growth rates also increased in high‐velocity habitats while longfin dace grew fastest in low‐velocity habitats; similar to the locations these species occupied based on field observations. These results indicate that for spikedace, the increased abundance of drifting macroinvetebrates in high‐velocity habitats outweighs the energy expenditure, but for longfin dace the energetic costs of occupying moderate to high‐velocity habitats outweigh the benefit to increased food availability. Our experiment provides a mechanistic understanding of habitat requirements across species and may inform predictions on how modifications or restoration of riverine ecosystems influence native fish diversity.

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