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Do you have a science question about the Delta you would like answered?

To have your question considered by Science News, e-mail the editor, Laura Walker at

Pick Our Brain - August 2010

Pick our Brain: What is the difference between a steelhead and a rainbow trout?

Images copyright Joseph Tomelleri
Rainbow trout
Images copyright Joseph Tomelleri
Images copyright Joseph Tomelleri

A steelhead is an anadromous rainbow trout, that is, one that migrates from freshwater to the ocean and back. The rainbow trout, Oncorhynchus mykiss, is one of the most widely distributed and common freshwater fish in California and it has been introduced to cold fresh waters all over the world. The anadromous variety (steelhead) in many parts of California, however, is considered threatened.

Steelhead behave like salmon, maturing in the ocean and returning to their home streams to spawn. Unlike salmon, however, steelhead may spawn more than once and spend varying amounts of time in freshwater and the ocean. Many do not leave their home streams at all but become "resident" rainbow trout. In the Central Valley fewer and fewer are managing to find their way to the ocean and back. Many Central Valley rivers and streams with access to the sea have abundant rainbow trout populations but few migrate to the ocean to become steelhead. They seem to be shifting to a “resident” life history strategy, presumably finding more success staying in freshwater. The exact genetic and environmental factors that cause a rainbow trout to go to sea and become a steelhead are not completely understood and are the subject of ongoing research.

One characteristic of steelhead vs. resident rainbow trout is their larger size. Resident rainbow trout in most streams rarely exceed 15 inches in length while steelhead from the same stream can reach 30 inches or more. Steelhead fresh from the ocean are usually silvery with bluish gray backs and heads—this is thought to be the source of their common name. Their large size and legendary fighting ability make them one of the state’s most sought after sport fish. Steelhead are sometimes called “the fish of a thousand casts” because of the effort it sometimes takes to catch one.


Pick Our Brain - June 2010

Pick our Brain: What is the percentage of native fish in the Delta?

Image courtesy of ...
Native and Non-native Fish Species

About half of all fish species in the upper estuary (Suisun Bay/Marsh and the Delta) are non-native species, according to sampling and calculations by Dr. Peter Moyle, Professor of Biology at the University of California, Davis. Moyle has more than four decades of experience working on fish in Suisun Marsh and the Delta.

According to Moyle, non-native fish species make up about 60 percent of the species in the Delta, 45 percent in Suisun Marsh and 20 percent in San Francisco Bay.

Pick Our Brain - April 2010

Pick our Brain: What are a California floater and a western pearshell?

The California floater (Anodonta californiensis) and the western pearshell (Margaritifera falcate) are two of several species of freshwater mussels native to California. In addition to the Anodonta species and the western pearshell, the western ridged mussel (Gonidea angulata) is also found in California. Although these native mussels are currently uncommon, a recent search by Jeannette Howard of The Nature Conservancy found them in about half of the California locations where they were reported historically. Often looking like stones or buried in bottom sediments, they are easily overlooked, but these fascinating native organisms have been here for thousands of years.

Interest in native mussels has been renewed recently because the Environmental Protection Agency has proposed new ammonia criteria that are contingent on the presence or absence of native freshwater mussels.

Image courtesy of Clifton Adams, 1931, National Geographic Society and Gary Andrashko, Illinois State Museum
Button-punched mussel shells and mussel buttons. (Images courtesy of Clifton Adams, 1931, National Geographic Society and Gary Andrashko, Illinois State Museum).

Interesting Facts About Freshwater Mussels

Freshwater mussels are a little-known component of California streams and rivers. The recent documentation of their widespread presence in our freshwater ecosystems is an important finding since these mussels are important indicators of water quality.

Pick Our Brain - February 2010

Pick Our Brain: The heavy storms in California recently increased the snowpack and brought it up to normal, so does that mean the drought is over?


The storms that have pummeled California over recent weeks have caused many to ask if the drought of the past three years is over. As discussed in an earlier issue of Science News (April 2009) drought comes in varied forms. Drought can be meteorological, hydrological, agricultural, and socioeconomic. The recent storms have greatly ameliorated the meteorological drought and are making a dent in the hydrological drought. The degree to which the hydrological drought is eased come April will be an important indicator of whether the agricultural and socioeconomic drought is easing or over.

One way to address the effects of the recent storms on the California drought is to compare the conditions one year ago to today. The U.S. Drought Monitor ( produces weekly drought summaries for the United States. The Jan. 27, 2009 drought monitor had 16 percent of California in extreme drought (particularly in north-central California), 33 percent in severe drought, 39 percent in moderate drought, 11 percent abnormally dry, and 1 percent without drought (the far northwestern part of California). The Jan. 26, 2010 drought monitor, after the series of major storms had hit California, has 0 percent of California in extreme drought, 2 percent in severe drought, 17 percent in moderate drought, 38 percent abnormally dry, and 43 percent without drought. This is a significant improvement from this time last year.

An important measure of the status of the hydrological drought in California will be the snowpack on April 1, 2010. Snowpack estimates near the end of January find the southern Sierra Nevada snowpack at about 126 percent of normal, the northern Sierra Nevada snowpack at 117 percent of normal and the overall statewide snowpack at about 107 percent of normal. This is encouraging, but the April 1, 2010 is the estimate that is particularly important because this estimate provides the best estimate of spring runoff and agricultural water supply. If the next two months bring ample precipitation and a significantly above normal snowpack come April 1, then, we can truly speak of the drought being over.

Source images courtesy of the U.S. Drought Monitor
Comparison of California drought conditions courtesy of the U.S. Drought Monitor

Pick Our Brain - December 2009

Pick Our Brain: How did the El Niño and La Niña climate phenomena get their names? Are there other climate systems important to California water and ecosystems?


El Niño translates as “the little boy” or “the Christ child” in Spanish. The name was given to unusually warm water in the eastern tropical Pacific by fishermen off the coast of South America. The tendency of the phenomenon to arrive around Christmas was the origin of the name. This climate phenomenon is now understood to have global implications that extend far from the western coast of South America. The flip side of the El Niño phenomenon is a cooling of the waters in the eastern tropical Pacific. Early on this was called an “anti-El Niño,” but the literal translation of “anti-Christ” made the preferred name become La Niña or “the little girl.” La Niña too has global weather affects. In California, El Niño generally produces wetter winter and spring conditions and La Niña brings drier winter and spring conditions, particularly in southern California.

There are other sources of climate variability that are important to California. The Pacific Decadal Oscillation (PDO) is a measure of temperature variability in the north Pacific with variations in the northeast Pacific particularly important to the strength of salmon runs in northern California, the Pacific Northwest, and Alaska. This climate system generally operates at longer time periods than El Niño and La Niña and has effects on the time scale of decades as the name suggests. Another new identified pattern of climate variability is the North Pacific Gyre Oscillation (NPGO). This system appears to have a significant effect on the salinity, nutrients, and algae of coastal California. The fluctuations reflect changes in the intensity of circulations in the North Pacific gyre. Recent research has shown a strong link between the status of NPGO and fish and crab populations in San Francisco Bay.

Changing climate patterns in the Pacific Ocean have clear effects on California precipitation and our aquatic ecosystems. Tracking these climate systems has become an important tool in forecasting seasonal weather conditions and the population dynamics of many of our fish, birds, and marine mammals.

source image courtesy of NOAA
Sea surface temperatures in the Southern Pacific - graphic courtesy of NOAA

Pick Our Brain - October 2009

Pick Our Brain: What are the forms of mercury in the Delta and where did they come from? How dangerous is mercury to humans, fish and wildlife and what can be done about it? – Mary McTaggart, Delta resident

source image courtesy of the USGS
USGS schematic diagram showing transport and fate of mercury in an estuary. Hg(0)=elemental mercury; Hg(II)=ionic mercury (mercuric ion); CH3Hg+=methylmercury
Click here to enlarge image

The forms of mercury in the Delta are elemental mercury (the silvery metal in thermometers), ionic mercury and methyl mercury – associated with sediments (most) dissolved in water (minor). Mercury is a naturally occurring metal that is now much more widespread in rivers and streams as a legacy of California’s Gold Rush days. When aquatic conditions are right, mercury can convert to a highly toxic form known as methyl mercury that readily accumulates in the food chain. Mercury is transformed into methyl mercury by certain types of bacteria, and that change can be accelerated by low-oxygen environments such as wetland sediments.

High concentrations of methyl mercury can cause neurological damage in humans, particularly children. It also impairs reproductive ability of some fish and wildlife. The primary human concern is consumption of relatively long-lived sport fish that accumulate the highest concentrations of mercury by women of child-bearing age. Many wildlife species and lower food web organisms can have methyl mercury within their bodies without adverse effect. Dissolved mercury is at such low levels that it is not a concern for drinking water.

Factors affecting toxic effects of methyl mercury

Formation of methyl mercury from elemental mercury occurs in areas where conditions promote this bacteriological process. These tend to be wetland and floodplain sediments where mercury is present and where there are periods of wetting and drying.

Exposure of food web organisms to methyl mercury

Methyl mercury is a problem only when food web organisms important to susceptible species are exposed to it for a long enough time period to be taken up by those organisms. Methyl mercury may be produced in a certain location, but could stay within that local area and not reach the food chain important to wildlife that are adversely affected by it or to sport fish (where it is an issue for humans). Methyl mercury also may be transformed back to elemental mercury (“demethylated”) or transported away before higher level food web organisms are exposed to it.

What can be done about it?

For humans:

source image courtesy of OEHHA
Fish Consumption Health Advisory Poster
Click here to enlarge image

Fortunately, humans have an easier time than fish and wildlife in reducing their exposure to methyl mercury through following these advisories.

For fish and wildlife:

*Methylation is the attachment or substitution of a methyl group on various substrates.

For further information on mercury, please read our Science Action mercury issue here:

Pick Our Brain, August 2009

What is the difference between native, non-native, endemic, and invasive species?

Source images courtesy Rene Reyes and Cindy Brown

Pick Our Brain, June 2009

Question: People talk about ‘wasted’ water ‘lost’ to evaporation from irrigated crops, lawns, etc. Where does this lost water go? Isn't much of it carried eastward during the warm seasons, eventually condensing into additional rain over the western slopes of the Sierras or the Rocky Mountains? --Robert Meagher, Sacramento

Water that is returned to the atmosphere through evapotranspiration (the combined processes of evaporation and transpiration) is a major component of the hydrologic cycle. The global average residence time for water vapor in the atmosphere is eight to nine days. In high humidity areas of the world, this process makes for efficient local recycling of water. For example, it is estimated that the water transported from the Atlantic Ocean to the Amazon Basin is recycled (precipitation, evapotranspiration and reprecipitation) four times as you move from the eastern to western portion of the Amazon Basin. In areas where humidity is commonly lower, like much of California, the evapotranspired water is carried much further before conditions allow for condensation and precipitation. Where this occurs is dictated by a complex mix of wind speed and direction, humidity and temperature.

Some of the water vapor coming from irrigated crops and lawns in California does condense over the mountains and return as rain. However, climatologists and meteorologists think this is a relatively small fraction of summertime precipitation in arid and semi-arid regions of the Western United States. Summertime precipitation in the West derives mainly from the Gulf of California, Gulf of Mexico and the Pacific Ocean. Most of the evapotranspiration from California is transported eastward, where the moisture interacts with water vapor from additional evapotranspiration from other parts of the continental United States and moist air from the Gulf of Mexico. These processes can generate precipitation or the water vapor can be transported in the atmosphere to the Atlantic Ocean.

Pick Our Brain, April 2009

Question: How much of the snow and rain that falls ends up running off into rivers and reservoirs?

There is a common misconception that 100 percent of snow and rain makes it into rivers and reservoirs. Several contributing factors, however, affect the percentage of runoff out of each watershed, so that there will never be 100 percent yield. These factors include evaporation, transpiration (plant release of water), sublimation (conversion of snow and ice directly to water vapor), added soil moisture, groundwater recharge, and human use, mainly for agriculture.

The rates of these factors that keep precipitation from reaching rivers and reservoirs vary depending upon the geographic location. Climate plays an important role in these differences. The more arid the area, the more these factors intensify.

Location of the river basin in California has a major impact on percent runoff. In general, the farther north in California the river is located, the greater percentage of precipitation will be converted to runoff. The farther south in California the river is, the lower the percentage of precipitation that will become runoff. Human modification of the river basins through the building of dams and irrigated agriculture also affect the percent of runoff. California rivers range from more than half of the precipitation running off as river water (Russian River) to only two percent running off as river water (Santa Ana River).

River % Runoff
San Joaquin
Santa Margarita
Santa Ana

Pick Our Brain, March 2009

Question: What’s the difference between ammonia and ammonium?

Recent CALFED Science Program and Interagency Ecological Program (IEP) funded research has shown that ammonium and ammonia may contribute to some of the ecological problems in the Delta. Most articles refer to ammonia in the waters of the Delta, but care needs to be taken to accurately present what is actually in the water. Ammonia is a gas that is dissolved in water much like the gases oxygen and nitrogen dissolve in water. Ammonia is quite toxic to animals living in water. The chemical formula for ammonia is NH3. Because ammonia is a gas, it is very hard to measure unless procedures for measuring gases are used.

Ammonium is an important nutrient for plants and algae and a source of energy for some bacteria. Ammonium is dissolved in water like a salt dissolves in water. The chemical formula for ammonium is NH4, and this form has a positive charge. The chemical methods used on water samples measure mainly ammonium because the water samples are filtered before analysis and the gaseous ammonia escapes to the atmosphere. It is more accurate to refer to the ammonium concentration of a water sample because this is what is measured.

Collectively, ammonium and ammonia are often referred to as total ammonia, or simply (but somewhat misleadingly) ammonia. In practice, total ammonia is rarely measured. Both ammonium and ammonia are often present in high concentrations in effluent from wastewater treatment plants that employ secondary treatment methods and in some types of agricultural run-off. It is important to be clear on the form (ammonia and ammonium) when reporting concentrations or studying toxicity.

Pick Our Brain, January 2009

Question: What are some of the expected effects of climate change on fish in the Delta?

There are numerous types of effects to consider. One is the direct effect of rising temperatures. Water temperatures are known to correlate closely with air temperatures. Therefore, warming of the climate by 2 degrees C will have a similar effect on water temperatures. This is of concern when water temperatures reach levels that are stressful or lethal to fish. There are studies that point to stressful or lethal temperatures being reached for salmon and delta smelt with this level of warming. These effects could be exacerbated by heat waves and low flows.

Other effects are much more difficult to evaluate. For example, climate change is very likely to deliver more water to California as rain versus snow and peak runoff from our rivers will occur earlier in the spring or winter. The effects of a change in the timing of high flows on Delta fish are less clearly understood. Major life cycle process like fish migration and reproduction are keyed to flow. It is unclear whether fish of the Delta can adapt or if they will be severely by these changes. Another example of an indirect effect is the strong likelihood that extreme weather conditions will accompany climate change. Extreme droughts and floods are predicted to become more common. The effects of these extreme events on the fish of the Delta are not well known, but are likely to place further stress on fish species. The direct effects of climate change are very likely to be important, but the additional effects that we can and cannot forecast may well be even more significant.

Pick Our Brain, December 2008

Question: Why does it matter if male fish become feminized?

Answer: Fish, like people, go through an elaborate developmental process that lets them become male or female. Which sex they become is generally prescribed by their genes, and carried out by hormones – the same process we humans go through. Unlike people, however, the sex of fish can change throughout their life – naturally – or because of an external influence. The natural sex changes appear to have evolved as an adaptation that helps certain fish populations survive. But sex changes induced by unnatural factors – like estrogens from birth control pills that pass through wastewater treatment plants into rivers, lakes, and oceans – likely imperil populations. (Other substances can also do this, including a variety of pesticides and substance in cosmetics, plastics, etc. They can all act like hormones.)

A recent study showed that a continuous exposure of small minnows to low levels of a synthetic estrogen in a lake caused the lake’s entire minnow population to crash after only two years because so many male minnows turned into females that they could not produce enough offspring anymore. If this happens in many places, or if an exposed species has a very limited range (e.g. delta smelt), this could lead to major population declines, or even, extinction.

Pick Our Brain, October 2008

Question: How do scientists know if a salmon was born in a hatchery?

Answer: Hatchery-born salmon can differ from their wild counterparts in ways obvious and not so obvious. Let’s start with the most obvious difference. Tags identifying when and where salmon were spawned are sometimes placed inside hatchery fish. Central Valley hatcheries most commonly use a small piece of wire known as a coded wire tag. Injected into a salmon’s snout when it is very young, this tag has a microscopic code etched on it. To alert scientists to the presence of the tags, hatcheries typically remove a young salmon’s adipose fin—a small, fleshy fin between the dorsal fin and tail— after inserting a tag into the fish. In this way, the presence of a tag can be detected without sacrificing the fish. Unfortunately, a fish must be sacrificed to remove and read the tags.

Now for the less obvious distinction. A salmon’s otolith or earbone can be cut and read like tree rings. In fact, an otolith adds a new ring each day of a salmon’s life. Because the otolith of a hatchery salmon differs from that of a wild salmon in several ways, scientists can examine these features to learn if a salmon was born in a hatchery. For instance, the spacing between the rings on hatchery salmon otoliths is typically larger than on wild salmon otoliths. However, the length of the otolith’s center region, or nucleus, is usually longer in wild salmon. Also, the point at which salmon started feeding is usually more clearly visible on the otoliths of hatchery salmon than on those of wild salmon.

Pick Our Brain, August 2008

Question: If there has been no earthquake in the Delta for 100 years why is the current prediction of earthquake risk so high?

Answer: Scientists have identified at least five major faults near the Delta that are capable of producing large earthquakes. When seismologists and geologists study faults, they estimate how large an earthquake a fault is capable of generating. This is called an earthquake’s “magnitude.” They also estimate how frequently both large and small earthquakes might occur on that fault. This is called an earthquake’s “frequency.” When scientists predict the frequency of a given earthquake magnitude, say, “100 years,” they do not mean that this earthquake will occur exactly every 100 years. Earthquakes are random. Sometimes it will be more than 100 years between two similar earthquakes, and sometimes it will be less.

Consider a fault that is seismically active and has yielded large earthquakes in the past, but has not produced a large earthquake in the past 100 years. Seismologists believe that the chance of such a large earthquake occurring will increase with time. In other words, the more time that passes, the greater the chance of an earthquake occurring because the stresses are building without relief.

Pick Our Brain, November 2007

Question: What caused (or what set of environmental conditions resulted in) the abundance increases of Delta smelt and young striped bass that were observed in the late 1990s — early 2000s? What did we learn from this short-duration boost that can be applied to the current abundance crisis?

Answer: We really do not know the answer to this question. It seems likely that the sustained period of high flows in the latter 1990s improved conditions for Delta smelt and striped bass. The period between 1995 and 2000 was one of pretty consistent wet weather in both winter and spring. Wet weather results in high river flows, which historically have enhanced the survival and abundance of many of the estuary’s key species. High freshwater flows may do many positive things for the estuary’s fishes, like improve their habitat suitability, decrease the concentrations of contaminants in the water, and reduce the numbers of young fish lost to water diversions in the Delta. Other factors may well play a role and there is no obvious “fix” for the recent declines. Research continues and we hope to have a clearer answer to this question in the future.

Pick Our Brain, September 2007

Question: What is the historic spawning habitat for Delta smelt? How far up each tributary do they now spawn and how does that compare to the historic spawning habitat?

Answer: We really do not know the historic or current range of spawning habitat for Delta smelt. We do know that Delta smelt prefer to live in brackish water but spawn in freshwater. Spawning occurs between February and August each year and is most active from mid-August through May. Actual spawning locations are not known and must be guessed at from the locations where spawned-out adults or very young larvae are captured. In dry years the fish spawn in the Sacramento River, particularly around Prospect Island, and in Barker and Lindsey sloughs. In wet years their spawning distribution is broader, including most of the Delta, Suisun Marsh, and the Napa River. The eggs are adhesive and are probably stuck to rocks or gravel until they hatch. Eggs hatch in about 10 days at 60 degrees. The distribution of spawning is governed mainly by salinity in the Delta and upper estuary so that changes in freshwater flows into the Delta influence where smelt spawn.

Pick Our Brain, August 2007

How Do We Know How Old Fish Are?

There are many ways to determine the age of a fish: scales, bones, and fin rays have all been used. However, it is the otolith, the ear bone of fish, that offers the most accurate means of determining a fish’s age. These ear bones frequently show daily, seasonal and annual rings or layers that can be counted much like the rings on a tree. However, the rings on ear bones are much less clear, and much, much smaller; especially if considering the tiny larvae of the delta smelt. High resolution microscopes and specialized computer imaging helps, but accurate age determination of fish using otoliths still requires a lot of experience.

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