Jack E. Williams

Pacific Salmon at the Crossroads: Stocks at Risk from California, Oregon, Idaho, and Washington

Abstract The American Fisheries Society herein provides a list of depleted Pacific salmon, steelhead, and sea-run cutthroat stocks from California, Oregon, Idaho, and Washington, to accompany the list of rare inland fishes reported by Williams et al. (1989). The list includes 214 native naturally-spawning stocks: 101 at high risk of extinction, 58 at moderate risk of extinction, 54 of special concern, and one classified as threatened under the Endangered Species Act of 1973 and as endangered by the state of California. The decline in native salmon, steelhead, and sea-run cutthroat populations has resulted from habitat loss and damage, and inadequate passage and flows caused by hydropower, agriculture, logging, and other developments; overfishing, primarily of weaker stocks in mixed-stock fisheries; and negative interactions with other fishes, including nonnative hatchery salmon and steelhead. While some attempts at remedying these threats have been made, they have not been enough to prevent the broad decl...

Fishes of North America Endangered, Threatened, or of Special Concern: 1989

Abstract The American Fisheries Society herein provides an update of their now decade-old list of rare North American fishes. The 1989 list adds 139 new taxa to the list developed by Deacon et al. (1979) of 251 fishes and removes 26 for a total of 364 fishes in Canada, United States, and Mexico that warrant protection because of their rarity. The 26 taxa removed from the 1979 list include 16 removed because of better information on their taxonomy or status and 10 because they have become extinct. Not a single fish warranted removal from the list because of successful recovery efforts. In addition, 49 fishes have changed in status but remain on the list: 7 have improved in status, 24 have declined, and 18 have been reclassified because new information revealed that they were either more common or rarer than was earlier believed and, therefore, were incorrectly classified in 1979. Comparison of the 1979 and 1989 lists indicates that recovery efforts have been locally effective for some species, but are clea...

Extinctions of North American Fishes During the past Century

Abstract Extinctions of 3 genera, 27 species, and 13 subspecies of fishes from North America are documented during the past 100 years. Extinctions are recorded from all areas except northern Canada and Alaska. Regions suffering the greatest loss are the Great Lakes, Great Basin, Rio Grande, Valley of Mexico, and Parras Valley in Mexico. More than one factor contributed to the decline and extinction of 82% of the fishes. Physical habitat alteration was the most frequently cited causal factor (73%). Detrimental effects of introduced species also were cited in 68% of the extinctions. Chemical habitat alteration (including pollution) and hybridization each were cited in 38% of the extinctions, and overharvesting adversely affected 15% of the fishes. This unfortunate and unprecedented rate of loss of the fishery resource is expected to increase as more of the native fauna of North America becomes endangered or threatened.

Flow regime, temperature, and biotic interactions drive differential declines of trout species under climate change

Broad-scale studies of climate change effects on freshwater species have focused mainly on temperature, ignoring critical drivers such as flow regime and biotic interactions. We use downscaled outputs from general circulation models coupled with a hydrologic model to forecast the effects of altered flows and increased temperatures on four interacting species of trout across the interior western United States (1.01 million km2), based on empirical statistical models built from fish surveys at 9,890 sites. Projections under the 2080s A1B emissions scenario forecast a mean 47% decline in total suitable habitat for all trout, a group of fishes of major socioeconomic and ecological significance. We project that native cutthroat trout Oncorhynchus clarkii, already excluded from much of its potential range by nonnative species, will lose a further 58% of habitat due to an increase in temperatures beyond the species’ physiological optima and continued negative biotic interactions. Habitat for nonnative brook trout Salvelinus fontinalis and brown trout Salmo trutta is predicted to decline by 77% and 48%, respectively, driven by increases in temperature and winter flood frequency caused by warmer, rainier winters. Habitat for rainbow trout, Oncorhynchus mykiss, is projected to decline the least (35%) because negative temperature effects are partly offset by flow regime shifts that benefit the species. These results illustrate how drivers other than temperature influence species response to climate change. Despite some uncertainty, large declines in trout habitat are likely, but our findings point to opportunities for strategic targeting of mitigation efforts to appropriate stressors and locations.

Majority of divergence between closely related DNA samples is due to indels

It was recently shown that indels are responsible for more than twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is ≈1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The ratio (Ru) of unpaired nucleotides attributable to indels to those attributable to substitutions is 3.0 for this 2 million-nt chimp DNA sample compared with human. There is similar evidence of a large value of Ru for sea urchins from the polymorphism of a sample of Strongylocentrotus purpuratus DNA (Ru = 3–4). Other work indicates that similarly, per nucleotide affected, large differences are seen for indels in the DNA polymorphism of the plant Arabidopsis thaliana (Ru = 51). For the insect Drosophila melanogaster a high value of Ru (4.5) has been determined. For the nematode Caenorhabditis elegans the polymorphism data are incomplete but high values of Ru are likely. Comparison of two strains of Escherichia coli O157:H7 shows a preponderance of indels. Because these six examples are from very distant systematic groups the implication is that in general, for alignments of closely related DNA, indels are responsible for many more unmatched nucleotides than are base substitutions. Human genetic evidence suggests that indels are a major source of gene defects, indicating that indels are a significant source of evolutionary change.

Fueling Population Growth in Las Vegas: How Large-scale Groundwater Withdrawal Could Burn Regional Biodiversity

ABSTRACT Explosive growth in Las Vegas, Nevada, has stimulated demand for additional water supplies. To meet these needs, local officials hope to obtain rights to about 200,000 acre-feet (246.70 million cubic meters [m3]) per year from a regional groundwater aquifer extending from Salt Lake City, Utah, to Death Valley, California. Officials from satellite communities are pursuing rights to an additional 870,487 acre-feet (1.07 billion m3) per year. If granted, these new permits would trigger declines in groundwater across at least 78 basins covering nearly 130,000 square kilometers. Water-rights decisions have historically interpreted economic development as a more compelling public interest than maintenance of natural systems. If economic development continues to drive allocation decisions, consequent declines in the water table, spring discharge, wetland area, and streamflow will adversely affect 20 federally listed species, 137 other water-dependent endemic species, and thousands of rural domestic and agricultural water users in the region. Reducing consumption and implementing cost-effective technologies, such as recovery of urban runoff and shallow saline groundwater, indirect reuse of potable water, and desalinization, offer ways to meet metropolitan and ecological needs within the limits of the resource.

Stream Restoration: Is Fisheries Biology Enough?

Abstract The fisheries profession is playing a key role in planning and implementing stream restoration projects throughout the world. To date, however, few examples exist of effective stream restoration programs or projects. One of the primary reasons stream restoration projects have not succeeded has been that projects are implemented on a small-scale, site-specific basis. We suggest that stream restoration would have a greater chance of succeeding if planned and implemented at a watershed scale. To do this, stream restoration projects must be expanded beyond instream work to include modification of upslope and riparian conditions that causes stream habitats to decline. In addition, planning for stream restoration at the watershed scale must include other disciplines that better understand these upslope watershed processes.

Native fish conservation areas: A vision for large-scale conservation of native fish communities

Abstract The status of freshwater fishes continues to decline despite substantial conservation efforts to reverse this trend and recover threatened and endangered aquatic species. Lack of success is partially due to working at smaller spatial scales and focusing on habitats and species that are already degraded. Protecting entire watersheds and aquatic communities, which we term “native fish conservation areas” (NFCAs), would complement existing conservation efforts by protecting intact aquatic communities while allowing compatible uses. Four critical elements need to be met within a NFCA: (1) maintain processes that create habitat complexity, diversity, and connectivity; (2) nurture all of the life history stages of the fishes being protected; (3) include a long-term enough watershed to provide long-term persistence of native fish populations; and (4) provide management that is sustainable over time. We describe how a network of protected watersheds could be created that would anchor aquatic conservation...

Conserving Peripheral Trout Populations: the Values and Risks of Life on the Edge

Abstract Peripheral populations—generally defined as those at the geographic edge of the range—often have increased conservation value due to their potential to maximize within-species biodiversity, retain important evolutionary legacies, and provide the fodder for future adaptation. However, there has been little exploration of their conservation value in aquatic systems. Inland cutthroat trout (Oncorhynchus clarkii) subspecies provide a unique opportunity to evaluate the distribution of peripheral populations and patterns of persistence across a wide range of environmental conditions. Our assessment analyzed range-wide losses of peripheral and core populations since the 1800s, and evaluated the likelihood of persistence for remaining populations of five cutthroat trout subspecies: Bonneville, Colorado River, Yellowstone, Rio Grande, and westslope. For all five, we found that core and peripheral populations have declined substantially, but the amounts of habitat occupied by peripheral populations general...

The Conservation Success Index: Synthesizing and Communicating Salmonid Condition and Management Needs

Abstract Increasing our ability to synthesize and compare fisheries assessment data among species and across geographic boundaries should facilitate a better understanding of the broad-scale condition of fish resources and necessary management strategies. We describe the Conservation Success Index (CSI), a new tool to analyze the status of native salmonids and facilitate protection, restoration, reintroduction, and monitoring efforts. The CSI provides a framework to evaluate indicators of population integrity, habitat integrity, and future security within native salmonids across all subwatersheds within their historic range. To date, the CSI has been completed for seven native trout and char species with summary status maps, data sheets, spatial analyses of management needs, and analysis of climate change and energy development impacts available at http://tucsi.spatialdynamics.com. Additional species are added annually. Case studies using Bonneville cutthroat trout and brook trout illustrate how the CSI p...