Brian Mahardja

Patterns of Population Structure Vary Across the Range of the White Sturgeon

Abstract Critical unknowns surrounding the basic biology of White Sturgeon Acipenser transmontanus have hindered management and conservation efforts. Population genetic data may be used to address some of these uncertainties, but previous examinations of population structure in White Sturgeon have been limited by the highly duplicated nature of the species’ genome. We report results from an analysis of White Sturgeon population structure within and among drainages using 13 polysomic microsatellite loci. Genetic diversity levels varied widely among regions, and the lowest levels were observed in the endangered Kootenai River Distinct Population Segment and the highest levels were detected in regions with access to estuarine and marine habitat. Patterns of within-drainage population structure varied, and no structure was detected in the Sacramento–San Joaquin drainage and a complex pattern of isolation by distance was revealed in the Columbia–Snake River drainage. These results contrast a previously publish...

Interannual variation in connectivity and comparison of effective population size between two splittail (Pogonichthys macrolepidotus) populations in the San Francisco Estuary

The discovery of two genetically distinct splittail populations within the San Francisco Estuary, one which spawns in the rivers of the Central Valley and another in the Petaluma and Napa Rivers of the San Pablo Bay, prompted the need to evaluate their degree of connectivity and relative sizes. We genotyped multiple age-0 splittail cohorts using 19 microsatellite loci to assess any spatiotemporal changes in the distribution of the two populations and estimate their effective population sizes (Ne). Genetic population assignments demonstrated that while age-0 splittail are predominantly spatially segregated by populations, substantial geographical overlap may occur during years of high precipitation. However, despite this periodic range overlap, the original observed population structure has persisted for nearly a decade which has included a similarly wet year. This suggests that the present population structure will likely persist in the future due to strong philopatry and/or adaptive differences. We also found that Ne estimates were generally lower for the San Pablo Bay population than the Central Valley population, which is consistent with the relative amount of habitat availability in the two locations and genetic diversity indices. The relative isolation and apparent lower Ne of the San Pablo Bay splittail population indicates a higher vulnerability to extinction. A more consistent monitoring effort of splittail in the Petaluma and Napa Rivers may be necessary in order to better understand the future viability of this less studied population.

Characterization of 36 additional microsatellite loci in splittail (Pogonichthys macrolepidotus) and cross-amplification in five other native Californian cyprinid species

We characterized 36 new microsatellite markers for splittail (Pogonichthys macrolepidotus), an estuarine fish species endemic to the San Francisco Estuary. Genetic variation was assessed using 25 individuals from the Sacramento River and 16 individuals from the Petaluma River. Number of alleles per locus varies considerably, ranging from 3 to 19. One locus deviated significantly from Hardy–Weinberg equilibrium and a single pair of loci was found to be in linkage disequilibrium. Twenty-four markers successfully cross-amplified and were polymorphic in at least one of the five additional California cyprinid species (Ptychocheilus grandis, Siphateles bicolor, Lavinia exilicauda, Orthodon microlepidotus & Mylopharodon conocephalus) examined in this study.

Inter-population differences in salinity tolerance and osmoregulation of juvenile wild and hatchery-born Sacramento splittail

Genetically-distinct populations of the Sacramento Splittail, a minnow endemic to the San Francisco Estuary, exhibit different physiological responses and tolerances to salinity as juveniles. Population-level responses correspond with known salinity habitat differences suggesting some degree of local adaptation. Further studies are needed to elucidate these differences, but these data suggest a potential need for population-specific conservation and management strategies.

A Conservation Hatchery Population of Delta Smelt Shows Evidence of Genetic Adaptation to Captivity After 9 Generations

Genetic adaptation to captivity is a concern for threatened and endangered species held in conservation hatcheries. Here, we present evidence of genetic adaptation to captivity in a conservation hatchery for the endangered delta smelt (Fish Conservation and Culture Laboratory, University of California Davis; FCCL). The FCCL population is genetically managed with parentage analysis and the addition of wild fish each year. Molecular monitoring indicates little loss of genetic variation and low differentiation between the wild and conservation populations. Yet, we found an increase in offspring survival to reproductive maturity during the subsequent spawning season (recovery rate) in crosses that included one or both cultured parents. Crosses with higher levels of hatchery ancestry tend to produce a greater number of offspring that are recovered the following year. The recovery rate of a cross decreases when offspring are raised in a tank with fish of high levels of hatchery ancestry. We suggest changes in fish rearing practices at the FCCL to reduce genetic adaptation to captivity, as delta smelt numbers in the wild continue to decline and the use of FCCL fish for reintroduction becomes more likely.

Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta

Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, a shift in zooplankton community composition, and a rapid expansion of invasive aquatic vegetation. To evaluate whether major changes have also occurred in the littoral fish community, we analyzed a beach seine survey dataset collected from 1995 to 2015 from 26 sites within the Delta. We examined changes in the Delta fish community at three different ecological scales (species, community, and biomass), using clustering analyses, trend tests, and change-point analyses. We found that the annual catch per effort for many introduced species and some native species have increased since 1995, while few experienced a decline. We also observed a steady pattern of change over time in annual fish community composition, driven primarily by a steady increase in non-native Centrarchid species. Lastly, we found that littoral fish biomass has essentially doubled over the 21-year study period, with Mississippi Silverside Menidia audens and fishes in the Centrarchidae family driving most of this increase. The changes in the catch per effort, fish community composition, and biomass per volume indicate that a shift has occurred in the Delta littoral fish community and that the same factors affecting the Delta’s pelagic food web may have been a key driver of change.