Freshwater systems across North America and Eurasia are home to inconspicuous species of fish known as sculpins (genus Cottus). As generally small, benthic species, sculpins have largely been ignored by humans. One lineage in particular, Cottopsis, is endemic to the west coast of North America and inhabits diverse geographic areas and ecological conditions. Such complexity is the perfect setting for understanding issues related to speciation, divergence, population structure, gene flow, and phylogeography of freshwater fishes. Comprehensive phylogenetic work using multiple nuclear and mitochondrial markers generated species trees and delimitations which varied slightly by technique and statistical approach, but which revealed a number of cryptic lineages and relationships within the clade. Three species groups in particular showed remarkable variation in California, riffle (C. gulosus) and Pit (C. pitensis) sculpin, and prickly sculpin (C. asper). Following an extensive distributional sampling, a number of phylogeographic breaks, cryptic lineages, and speciation mechanisms were discovered. Within C. gulosus and C. pitensis, the Sacramento River proved to be distinctive showing potential historical hybridization, complete C. pitensis mitochondrial introgression, and restricted contemporary population structure. Consistent with other studies, a phylogeographic break along the Sacramento/San Joaquin River Delta led to the prospective divergence of C. pitensis into the Sacramento/Pit River basin and C. gulosus into the San Joaquin River basin; with different measures of isolation by distance and intra-population structure. A similar break and population structure was seen in inland C. asper populations. Estimated to have diverged from amphidromous coastal populations 110,000 years ago, inland C. asper represent incipient speciation, as evident by poor phylogenetic distinctiveness. Low measures of gene flow and hybridization in the narrow connective corridor between coastal and inland populations, along with no sign of physical barriers suggest inland C. asper are diverging by way of parapatric speciation. A novel lineage of C. asper in Clear Lake is also well-supported, originating from coastal, not inland populations. Overall, results clearly signify sculpin are a complex species group, with structure reflective of their historical hydrology, and worthy of intensive conservation and management strategies.

The overbite clam (Potamocorbula amurensis) is a major invasive species in the San Francisco Estuary, California, and has been implicated in the decline of pelagic productivity and native fish species. Little is known of its impact on Suisun Marsh, a large brackish tidal region of the estuary. We looked at the abundance and spatial distribution of clams in the marsh, including examining the influence of water quality, using long-term (1988–2015) otter trawl surveys. Temporal trends indicated that overbite clam abundance has been increasing, but adult clams were spatially restricted to a single large slough (Suisun). Clams were absent from most interior channels, limiting their overall effect on the marsh aquatic ecosystem. Abiotic variables, particularly salinity, proved important predictors of overbite clam abundance, although the variables examined alone could not explain overbite clam distributions. We propose that connectivity, detritus loads, and/or predation pressure may work in conjunction with abiotic variables to cause poor survival rates for recruits in interior marsh sites, keeping the distribution limited. Overall results are encouraging for restoration projects in brackish tidal marshes that need to deal with overbite clams.