A grizzly bear in British Columbia. Its California cousin,
Ursus horribilis californicus, is long extinct.
(Photo: Charlesjsharp)

Earlier this month, California’s beleaguered salmon fishing industry finally got a break. After the catastrophic collapse of Central Valley’s fall Chinook run in 2008-2009, hundreds of thousands of fish may be on their way back to Sacramento riverbeds.

With a forecast of 820,000 Chinook now at sea, commercial salmon boats, rendered irrelevant for two straight seasons and set loose for just eight days in 2010, can return to business as usual this summer. And though the apparent rebound is good news for salmon, the fall Chinook’s future is far from secure.

The disheartening run of 2008 followed a lean spawning year (which biologists call “escapement,” after the number of fish that elude fishermen to reproduce), with just under 88,000 survivors returning to streams or hatcheries in 2007.

California has four seasonal salmon runs, each with distinct behavioral and genetic traits. Conservation biologists like to compare genetic diversity to a diversified stock portfolio. More diversity means a better chance of weathering tough times. (See, for example, "Irish potato famine.") And while the National Marine Fisheries Service cited poor ocean conditions as the “proximate cause” for the dismal runs (because freshwater habitat, though degraded, was no worse than usual), the agency also noted several other factors, including heavy reliance on hatchery fish, which homogenized the fall Chinook’s historically diverse genetic portfolio.

Fall Chinook once thrived in every major river in the Central Valley. Biologists suspect the runs rivaled the storied San Joaquin spring runs. Documents from 1870 unearthed by historian Paul Vandor described salmon returning in “such shoals” that “restful sleep was disturbed because myriads of them can be heard nightly splashing over the sand bars in the river opposite town.”

Chinook Salmon on the Lower Stanislaus River. (Photo: USFWS)

Spring run Chinook are long gone from the San Joaquin watershed. Just 3,802 fish made the Sacramento run in 2009.

Pacific fisheries managers monitor Chinook take to allow 122,000-180,000 fish to escape capture and swim upriver. In 2008, just 66,000 fish made it back. Fewer than 40,000 returned in 2009 (close to 54,000 counting hatchery fish), the worst run on record.

(The runs in 2010 barely made it above the minimum target, with close to 40,000 returning to hatcheries and about 86,000 returning to wild streams.)

This season’s good news notwithstanding, the grim returns of the past few years didn’t affect just fishermen and salmon consumers. Biologists have long known that ecosystems suffer when managers value economics over ecosystems and allow overfishing.

But cutting back on harvests to let more salmon spawn in rivers and creeks will not only help safeguard their ecological role, argues a study published last week in PLoS Biology, but will help commercial fishers and consumers by ensuring a future for salmon.

When salmon thrive, so does everything else, says Taal Levi, a PhD candidate in environmental studies at UC Santa Cruz, who led the study. “Abundance matters in ecosystems.”

The study supports a growing literature linking abundant salmon to positive ecological effects, Levi says. “It suggests we should be letting more salmon into rivers.”

Letting more salmon return to coastal streams
to spawn will benefit bears, ecosystems,
and eventually the offshore salmon catch.
(Photo: Jennifer Allen)

Salmon are the ultimate mobile nutrient-delivery system. They spread the wealth wherever they go, from streams to sea and back again. Healthy salmon runs boost primary productivity in coastal lakes (by providing nutrients for algae), fuel vegetative growth along streams, creating better habitat for salmon hatchlings and leading to higher densities of diverse insects and songbirds. They also feed all manner of predators and scavengers, from orcas to raptors and—in the places they still exist—grizzly bears.

Hundreds of thousands of salmon once injected massive seasonal pulses of nutrients from the sea to Pacific coastal and riparian ecosystems. Commercial harvests deprive ecosystems of this historic recharge. But restricting harvests cuts into fishery profits. Levi and his colleagues developed a model to help fishery managers weigh the costs and benefits to commercial fishers and ecosystems of allowing more spawning, using grizzly bears as a proxy for salmon’s ecosystem benefits.

Studies show that spawning and dead salmon are the single most important fall resource to grizzlies preparing for hibernation and cub-rearing on Alaska’s Kenai Peninsula. In this study, the authors show that grizzlies are good indicators of salmon’s ecosystem services because bear densities are so closely tied to salmon abundance.

The authors used fishing records to model increased escapement across various management options for six sockeye salmon stocks in Alaska and British Columbia to determine how bear numbers and income from fishing change with the number of fish harvested. For each stock, more spawning meant more bears. And for sockeye stocks that breed in streams alongside other salmon species, both long-term fishing yields and bears benefited from higher escapement.

Conservation and economic interests conflicted only where grizzlies are threatened and eat primarily sockeye, because reducing harvests would cut into profits. But the tradeoffs would be clear, and managers could estimate the costs of protecting salmon runs and endangered bears. It’s conceivable that managers could even find ways to help fisheries recoup their losses in the name of conservation.

The fishing industry in California doesn’t dominate the state economy as it does in Alaska. But Levi argues that having more salmon in streams would also have economic benefits from better wildlife viewing opportunities.

Increased salmon abundance would surely help California’s bald eagles. “We don’t have abundant bald eagle populations anymore but we have a nesting pair at Pinto Lake in Watsonville,” Levi says. (There’s another pair in San Mateo now.) More salmon would be a boon to the state’s recovering eagle population.

More salmon would also increase black bear populations, he says, which is good for both hunters and wildlife observers.

Black bears often move in when grizzlies go extinct, serving a similar ecological role. In fact, biologists say, black bears eat more salmon than grizzlies because they’re more widely distributed.

But there’s no reason that restoring California’s salmon runs couldn’t go hand in hand with restoring the state’s grizzly population, Levi says: California and Oregon have millions of acres of contiguous protected land, more than enough to support grizzlies.

In the 1970s, grizzlies survived on only 4 million acres in the Greater Yellowstone Ecosystem, he points out. Protected areas in six national forests from Klamath to Mendocino provide nearly 9 million acres of contiguous habitat, not counting available habitat along the coast range from Humboldt down to Point Reyes.

Grizzly bear (Photo: Eric Sambol/www.raincoast.org)

Grizzlies once inhabited nearly every part of the state. In the 1800s, there were so many in the Santa Cruz Mountains where Levi lives that a Spanish missionary said they prowled about “in herds like hogs on a farm.”

Even as late as the 1850s, grizzlies roamed San Mateo and Santa Cruz counties. By the 1870s, they were gone because, as legendary naturalist Joseph Grinnell wrote, “Great numbers of people…have been alert to seize any and every opportunity to kill bears.”

Levi admits the prospect for reintroducing grizzlies could be “politically insurmountable,” but adds wistfully, “this would be ambitious wildlife conservation.”

“It is not at all crazy to think that grizzlies could have a viable population in California," he says. "The question is just whether we want them back.”

Kyla, a female mountain lion rescued as a kitten after
poachers killed her mother, now lives at Sonoma County
Wildlife Rescue in Petaluma. (Photo: Liza Gross)

Should the head of an agency charged with regulating California’s natural resources stay on after flaunting his delight in killing one of the state’s most iconic species? That’s the question on many minds since a photo surfaced showing California Fish and Game Commission President Dan Richards grinning ear to ear, clutching a massive, lifeless mountain lion against his chest.

It’s not that the hunt itself was illegal. Hunting mountain lions, or cougars as they’re commonly known, is legal in Idaho, where Richards bagged his trophy, as it is in every other state where they're found—except California.

Richards killed the lion, a 115-pound, three-year-old male, after an eight-hour hound hunt left the weary animal stranded, an easy target, in the tall reaches of a Douglas fir.

The hunt happened on the Flying B Ranch, which charges $6,800 for the privilege. But Richards didn’t pay $6,800. A manager on the ranch told the Associated Press that the commissioner paid $3,200 to hunt birds. California law bars officials from accepting gifts exceeding $420 in one year, and now Richards faces an ethics complaint, filed with the Fair Political Practices Commission.

Putting aside the question of how shooting a trapped animal constitutes “sport,” lions are “a specially protected mammal” in California. It’s illegal to “take, injure, possess, transport, import, or sell any mountain lion,” unless you can prove possession on June 6, 1990, the day after voters prohibited lion hunting. That means Richards couldn’t legally bring the carcass back into the state. A moot point, anyway, since he says he ate it.

The history of lions in California follows the sorry story of large carnivores across the country. Early (non-indigenous) residents considered predators unacceptable threats to livestock and game and, in 1907, the state hired bounty hunters to exterminate them. There’s no doubt extermination was the goal: Females commanded a higher price. By the time the bounty ended in 1963, more than 25,000 lions were dead.

As public attitudes softened, the state reclassified the lion, first as a non-protected mammal in 1963, and then again as a game animal in 1969. But it wasn’t until the early ’70s, when Napa Democrat John Dunlap, backed by 52 conservation groups and thousands of concerned voters, managed to pass a four-year moratorium on trophy hunting, with the goal of conservation, not killing, in mind.

Dunlap’s moratorium was extended until 1986, when then-Gov. Deukmejian vetoed reauthorization, placing lions legally in hunters’ sights once again. But public outcry, followed by legal action, upheld the moratorium, which became permanent in 1990, when voters approved Prop. 117, the California Wildlife Protection Act. (It’s still legal to kill lions considered a threat to life or livestock.)

The last major push to repeal the ban was rejected in 1996.

Mountain lions are notoriously shy and prefer to avoid humans if possible. (Photo: US FWS)

Still, campaigns to reinstate hunting continue, most recently led by farmers and ranchers in San Benito County asserting (without basis) that a growing lion population places residents and livestock in jeopardy. Wildlife biologists, meanwhile, worry that humans pose the bigger threat, by developing prime lion habitat.

It’s against this backdrop that Richards, a San Bernardino County commercial real estate developer and National Rifle Association life member, traveled to Idaho, killed the young lion, sent his celebratory photo to a hunting web site, and then fired off a defiant letter to California Assemblyman Ben Hueso, one of 40 legislators asking him to resign, essentially telling him to bug off.

Richards then took his case to talk radio, calling his critics “well-funded enviro terrorists” and “lawsuit machines,” singling out the Humane Society as the “primary culprit in this deal.” He charged the society, and environmental groups, with trying “to infiltrate the department” to stifle debate. “Not only do I challenge them on a daily basis,” Richards asserted, “but it’s more insidious than that, because if they can get a toehold in there…they have the long-term handle. We’ve just done some of that with this MLPA process.”

Richards was referring to the Marine Life Protection Act, a landmark science-based initiative to conserve ocean life and habitat that some sport fishers view as a threat to jobs and fishing rights. The radio show host said the Legislature would be “pretty sick” to pursue Richards’ ouster.

Aiming to prevent that, the NRA and Keep America Fishing urged their members to support their ally in Riverside when the Fish and Game Commission met on March 7. In a press release, Keep America Fishing thanked the commissioner for “being a voice of reason throughout the Marine Life Protection initiative.”

By "reason," they meant Richards’ votes against implementing the MLPA.

Richards also voted against renewed efforts to protect California condors from lead ammunition, despite solid evidence that it’s poisoning the critically endangered birds. In 2011 alone, Richards voted against moves to protect several native species, including the black-backed woodpecker, Cedars buckwheat, American pika, and steelhead salmon.

OR-11, a male pup (born spring 2011) from the Walla Walla pack in Oregon, waking up from anesthesia after being radio-collared on Oct. 25, 2011. (Photo: ODFW )

I won’t guess how he’ll vote on a petition before the commission to list the gray wolf under the California Endangered Species Act, sparked by the appearance of OR-7, the dispersing male from Oregon. Gray wolves receive protection under the federal ESA, except in Idaho (and Montana) after a surprise move by Congress last year. When Idaho’s Fish and Game Commission met in March, its wolf management plan considered five ways to kill them.

And, yes, Flying B Ranch offers wolf hunts, which you can learn about on the Idaho commission’s web site.

Given Richards’ background, his actions shouldn’t be surprising. Officials, says the commission’s web site, have “expertise in various wildlife-related fields,” though it’s unclear how real estate qualifies as a wildlife-related field. But then only one of the five commissioners, all political appointees, has a background in biology. All the rest have careers in business, labor and farming.

Research over the past decade suggests that predators help maintain plant communities by regulating herbivores. Reintroducing wolves in Yellowstone in the mid-1990s, led to a rebound of cottonwoods, willows and other riparian species by keeping elk numbers down, and provided more habitat for songbirds.

Mountain lions, it seems, offer a similar service. A 2008 study showed that after lions disappeared from Yosemite in the 1920s, mule deer populations expanded only to decimate black oak stands by eating up all the tasty shoots before they could take hold, paving the way for other species like pines and firs to fill the void.

Biologists are also finding evidence that hunting can drive evolutionary changes in target species, selecting for smaller body size and earlier sexual maturity. But it’s unlikely the current commission would care about these studies.

It’s no wonder that hunters and sport fishers want the commission to protect their interests. Their license fees pay the bulk of state wildlife agency budgets. If the commission is serious about deflecting charges that it favors the interests of hunters and fishers and is concerned only with consuming wildlife resources, why not appoint biologists, rather than businessmen, as wildlife officials?

Prop. 117 allocated $30 million a year to protect, restore and acquire habitat for lions and other native species. If Californians really want to protect our wild heritage, we’ll have to do better than that.

Recent discoveries of a Lilliputian lizard and elfin amphibian, fascinating in their own right, highlight one of the most enduring questions in biology: what controls the evolution of body size? Why do some taxa grow smaller and smaller, while others grow larger and larger, as if they’d tumbled down the rabbit hole with Alice and devoured all the curious potions and cakes she found there?

The question endures in large part because body size affects nearly every aspect of an organism’s existence, from physiology (temperature regulation and metabolism) to ecology (life history and foraging strategies) and evolution (reproductive success over time).

For more than a century, biologists thought evolutionary taxa, or lineages, grew larger and larger over time, a phenomenon known as Cope’s Rule, illustrated most often by horse evolution. Modern equids, scientists believe, evolved from the diminutive Hyracotherium (commonly known as eohippus, or “dawn horse”), which appeared in the fossil record some 55 million years ago. Many textbooks mistakenly liken Hydracotherium to a fox terrier (think Asta of The Thin Man movies), but the ancestral horse was more Lassie than Asta, as Stephen Jay Gould famously explained in his essay "The Case of the Creeping Fox Terrier Clone."

A replica skeleton of Hydracotherium vasacciensis, the putative ancestral horse, at the Museum of Natural History in Washington, D.C. (Photo: Jeff Kubina)

In 1997, though, David Jablonski showed that (as usual) biology rarely follows hard and fast rules. In a 10-year review of fossils covering 16 million years and 1,000 species from 191 lineages of bivalves (clams and scallops) and gastropods (snails and slugs), Jablonski found that just as many taxa decreased in body size over time as increased. And even the horse example has come under fire. A 2004 study analyzed horse fossils in light of recently resolved relationships among evolutionary groups and showed that while the lineage that gave rise to the modern horse grew larger, others shrank.

Still, examples of lineages evolving toward larger body size abound, with evidence linking greater size to higher fitness (better survival and mating success for individuals). If you’re big (say, a lion or other large carnivore), it’s easier to catch prey, avoid predation (though elephants, like mammoths before them, may perish at the hands of human hunters), survive tough conditions, attract mates (silverback gorillas claim exclusive breeding rights to females), and claim more resources than your competitors.

Given the advantages of size, one might think the tiny frog and chameleon are simply freaks, outliers among a field of giants. But the fossil record offers plenty of examples of large animals shrinking over millennia (known as “phyletic dwarfism”), often after winding up on islands or other restricted ranges.

Until about 10,000 years ago, dwarf elephants inhabited Crete and other Mediterranean islands, which favored smaller, nimbler forms that could survive on less food and manage the rocky terrain. Even dwarf mammoths (the oxymoron notwithstanding), dinosaurs, and hominids (Homo floresiensis) once inhabited isolated islands.

If you’re small, you might reproduce quickly, offer too little reward for a predator’s effort, and maybe even prove too hard to see.

Paedophryne amauensis, a minute frog found in Papua New Guinea, may be the smallest vertebrate on Earth. (Photo: PLoS ONE. doi:10.1371/journal.pone.0029797)

That seems to be the case for a pint-sized amphibian found, through no small effort, in the forests of Papua New Guinea, which its discoverers claimed as the “world’s smallest vertebrate.” Because the largest vertebrate, the blue whale, and (previously) smallest, a fish, are aquatic species, some biologists thought a water-based lifestyle may facilitate the evolution of extreme size. But, as the scientists argue in the paper describing the frog, this doesn’t explain how extreme miniaturization evolved at least 11 times in terrestrial frogs.

The 7-8 millimeter frog, named Paedophryne amauensis, is active mostly at dawn and dusk, sounding more like a cricket than a frog when it calls out to potential mates from the leafy detritus of the forest floor. (The authors dubbed the species “amauensis” after the region near Amau Village where it was found.) Leaf litter in tropical forests stays moist throughout the year, keeping the minute amphibian safe from desiccation and likely explaining the evolution of its life history: offspring bypass the tadpole stage, emerging fully formed, though even tinier, avoiding fish, insects, and other aquatic predators. Of course, teeny adults would be at higher risk from predators if they lived in the water, too, which might explain why the species carved out a niche in upland areas with a lower diversity of such threats.

Brookesia micra, one of four dwarf leaf chameleon species found in Madagascar. (Photo: PLoS ONE. doi:10.1371/journal.pone.0031314)

And just last month, another group of researchers reported their discovery of four new species of dwarf chameleons, one so small it can balance on the tip of a match head. The mini chameleon, Brookesia micra, measures a smidgen over an inch from snout to tail, and seems restricted to Nosy Hara, a small (naturally) island off the coast of Madagascar. An extensive survey of Nosy Hara and adjacent islands in 2007 failed to spot the little lizard, which scampers around limestone rocks and dry forest leaf litter during the day and roosts on low-lying branches a few inches above the ground at night.

Unlike their amphibian counterparts, the minuscule reptiles inhabit relatively dry tropical areas. Because small body size carries a higher risk of desiccation from the proportionally higher body surface area, it’s surprising the lizards live in a dry environment, the scientists explain in their report. It’s possible they’ve adapted to certain features of the landscape that retain moisture, like leaf-filled fissures in limestone.

The tiny frog and chameleons may or may not win the title for smallest of their kind, but the distinction is beside the point. The discovery of these new species offers a rare ray of hope amid ongoing reports of devastating declines in amphibian and reptile populations around the world, mostly due to habitat destruction. These dwarf species have likely benefited from minimal space and resource requirements, and being too tiny to spot. And for me, it’s no small comfort to know that we can still find wonders, both beautiful and strange, on this side of the looking glass.

Dusky-capped flycatcher (credit: mdf)

Most people know the Philadelphia suburbs for cheesesteaks and unruly sports fans. But it’s no wonder that John James Audubon started his lifelong affair with birds just 25 miles northwest of Center City, and a 20-minute drive from my natal stomping grounds. The dense, rolling woodlands of Pennsylvania’s Montgomery County where I grew up offered prime habitat for cardinals, chickadees, blue jays, wrens, and countless other species my mom loved to point out to us kids. I didn’t realize it at the time, but my mom’s avian affinities taught me not just to pay attention to the biology in my backyard but, ultimately, to consider which species lived there and why.

This weekend, novice Bay Area wildlife watchers get the chance to play field biologist in their own backyards and join forces with expert birders and scientists to gather data on the incidence, abundance, and distribution of birds. Between February 17 and 20, the 15th annual Great Backyard Bird Count invites people of all ages and experience to spend as little as 15 minutes (or as long as you like) counting birds wherever you are.

The event is a joint project of the Cornell Lab of Ornithology, Audubon, and Bird Studies Canada, leading bird conservation organizations that provide a wealth of resources for participants, including tips for getting started,
regional checklists, and tools for resolving tricky identifications.

“The Great Backyard Bird Count is an excellent introductory citizen science project for any level of birder,” says Brian Sullivan, an expert on North American birds and project leader of Cornell’s online resource for birders around the world, eBird.

“You can just count the birds you see in your backyard or go to your local park and count what you see there. The idea is to get a weekend snapshot of late-winter bird distribution across the United States and to make things really simple so just about anyone can participate.”

Sullivan, who has 1,669 species on his life list, says lucky birders could see “mega-rarities” like an Iceland gull, “a very rare bird in California” spotted near Sausalito in early February, or maybe the dusky-capped flycatcher that's been living in Golden Gate Park all winter.

The largest estuary on the West Coast, the San Francisco Bay Delta provides habitat and refuge to more than 250 species of waterbirds, some (including pelicans, loons, herons, and egrets) year-round residents, others, like the Wilson’s phalarope and Sabine’s gull, on stopovers to feed and rest before resuming their long-distance migrations. As many as 800,000 birds inhabit Bay Area waterways at any given time.

To find out which birds you’re likely to see in your area, go to Cornell’s eBird, click on “View and Explore Data,” then click on “Bar Charts,” select “United States,” “California,” and then “Counties in California.” Choose your county, click “continue,” and you’ll see the occurrence of birds throughout the year.

Last year, participants entered more than 92,000 checklists with 1.4 million birds from 596 species. Their data helped researchers identify changes in abundance (including an increase in evening grosbeaks, which declined 50% between 1988 and 2006) and distribution (winter finches moving south), and spot anomalies (an Asian brown shrike in McKinley, California).

The bird counts give weekend nature lovers an easy way to help scientists gather data on a widely distributed group of animals that serve as valuable indicators of biodiversity. Because birds occupy many different “trophic” levels in food webs, eating everything from insects to fish to mammals (and, for top predators like owls, hawks, and eagles, other birds), they play critical roles in maintaining healthy ecosystems. Among their many “ecosystem services,” all of which benefit humans, birds help regulate prey populations, facilitate plant reproduction through pollination and seed dispersal, and recycle nutrients by scavenging carcasses.

This widespread influence on their environment also makes them extremely sensitive to ecosystem disruptions, including habitat destruction and climate change. An alarming 13% of the world’s birds, 1,253 species, face extinction, according to the 2011 IUCN Red List. The Great Indian bustard, a native of India and Pakistan that barks when alarmed, has been reclassified as critically endangered, a victim of hunting and widespread habitat destruction. Scientists think fewer than 250 mature birds remain.

Closer to home, black-crowned night herons and snowy egrets have been on a downward slide since 2005. And the endangered California clapper rail, once abundant in the tidal marshes of San Francisco Bay, offers a case study in the unintended consequences of development. Extensive filling and diking of the bay has destroyed some 85% of the clapper rail’s salt marsh habitat, making a shy species that seems to prefer scampering over swimming and flying easy pickings for feral cats and invasive red foxes, which now have unfettered access to adults and their ground-nesting offspring.

California clapper rail (Don Roberson)

Roughly 60% of the critically endangered clapper rail population, estimated at between 1,000 and 1,500, lives in San Francisco Bay’s Don Edwards National Wildlife Refuge, in Fremont.

Researchers will use the information collected from the bird count to learn how birds like the clapper rail are coping with these new predation pressures, as well as other stresses from ongoing urbanization, global climate change, and disease.

The decline of suitable habitat for these species affects us as well. Tidal marshes filter contaminants to enhance water quality and serve as natural flood barriers. If the marshes can no longer support species like the clapper rail, chances are they can’t provide these ecosystem services for us either.

Birds are among the most diverse and ubiquitous vertebrates on the planet and often offer humans a first brush with wildlife.

As a little girl, I marveled that my mom always knew when Jenny Wren and her husband, Joe (as she liked to call the resident house wrens), would appear in our backyard, build their nest, and settle into the business of raising, feeding, and protecting their broods.

She couldn’t have known that scientists would one day blame the precipitous declines in Bewick’s wrens in the eastern United States on the expansion of her beloved house wrens, known for ejecting eggs, and even young, from coveted nest sites.

Blue jay (Liza Gross)

As I listened to Mom’s fanciful tales of avian domestic dramas, my young imagination conjured all manner of worrisome scenarios. Would Joe find enough food for the babies? Could Jenny protect them from a torrential summer downpour? How would either of them cope with a curious cat? Some may shudder at such anthropomorphizing, but I wonder: If more people viewed birds the way my mom did, struggling to survive like the rest of us, would they worry about their welfare, too?

Henry David Thoreau first said “In wildness is the preservation of the world” in a lecture some months after Audubon’s death. I like to think, had they discussed the question, Audubon would have objected: “My dear sir, I believe you meant to say, ‘In birds is the preservation of the world.’ ”

Dickcissel - a grassland bird. Photo Credit: Amy Larson

In an effort to improve the sustainability and health of their land, farmers are increasingly interested in taking a systems approach to farmland management. A systems approach acknowledges the key connections between ecological, economic, and social components. Given the ensuing complexity, measuring the health of a farm system requires good diagnostic tools. In addition, these tools need to be clear and straightforward.

Our current effort at the University of Nebraska Lincoln to develop a set of such indicators for farmers, the Healthy Farm Index, focuses on biodiversity and ecosystem services at the farm scale. One indicator in the index is the presences of a given set of birds on the farm. Birds are a popular indicator because they are sensitive to change in farm practices, found broadly in the environment, and are easy to detect by sight and sound.

The ability to detect birds by sound has spurred our research group to develop resources to aid farmers and other people interested in the songs and calls of farmland birds. As researchers, we use auditory detections of birds as one of our primary monitoring tools. With acoustic recorders, we have recorded the songs and calls of our local bird communities. Back in the lab, we use software to identify and isolate the best songs and calls. These vocalizations have been posted to our website, Farmland Birds of Nebraska, and distributed back to farmers and others interested on CDs. With the acoustic recordings, farmers can select a group of indicator species suitable for their area, learn its call, and listen for the bird while working in the field. This information can be used by the farmer in assessing their own farm or can be shared more broadly with researchers.

The recordings also allow farmers to share with consumers (many of whom are birders) an added environmental benefit of their farm. This spring we were able to take these recorded vocalizations back to one of our participating farms. In partnership with Common Good Farm, we hosted a “Birding on the Farm” tour. Local residents and other farmers spent the morning listening for and identifying the community of birds at the farm. New and experienced birders alike were surprised at the diversity found on the single farm.

In the coming months, we are expanding our network of recorders. This winter we will be monitoring winter bird communities on participating farms and testing the influences that road noise may have on bird vocalization and communication.

The earth at night as viewed from a space, in a composite image from NASA.

The world is not as dark as it used to be. Streetlights, parking lot security lights, office building lights, and neon signs shine all through the night. Light pollution can come directly from light bulbs, or it can bounce off of dust and water droplets in the air, creating a bright haze called skyglow. This 24-7 illumination can be seen from space, and it has negative effects on humans and wildlife. But there are ways to dim the lights and reduce their effects—and save energy in the process.

Astronomers have long aware of the problems associated with nighttime illumination—it makes stars disappear. Big telescopes are built away from big cities for this reason, although bright lights have a way of encroaching. QUEST blogger Ben Burress talks about light pollution and astronomy here and here.

Non-astronomers are affected by nighttime lighting, too; exposure to light at night affects our circadian rhythm, the 24-hour cycle deep inside our bodies. Seeing light at night can cause sleep disorders. And long-term exposure to light at night has been linked to breast cancer, because light inhibits the production of melatonin, which slows the growth of cancer cells.

Exposure to light affects animals, too. Anyone who has sat next to a porch light on a summer evening knows that moths are drawn to light—along with a multitude of other insects. Outdoor lights disturb insects’ nighttime navigation, and affect their feeding and mating. Lizards are often found feeding on the tasty insect snacks that gather around lights. Often, these lizards are not normally nocturnal—staying up at night gives them access to a “night-light niche” and an abundant food source. It also creates the opportunity for interactions between animals that would never meet in the dark conditions of previous centuries. Some lizards get a double benefit, basking in the warmth given off by artificial lights (incandescent lights are really inefficient; most of the energy they use goes to producing heat, not light).

Night lights make birds sing at odd hours, and mess with their mating and migration schedules. During migration, birds are drawn to the light from tall buildings and towers, resulting in deadly collisions.

Sea turtles are perhaps the most famous example of animals affected by light. Hatchlings swim towards the light—historically the horizon above the ocean. But now that beaches are backed by well-lit condos and hotels, baby turtles crawl further onshore instead of out to sea. There is evidence that sea turtles are drawn to light with short wavelengths, and using bulbs with longer wavelengths or using filters that cut out short light wavelengths reduces the number of baby turtles crawling in the wrong direction.

Simple fixes, like different bulbs or shades that focus light on the ground, can do a lot to re-darken the night sky, as does turning off unnecessary lighting. Dimmer, more efficient bulbs that provide enough light for human needs—but not too much—are a step in the right direction, and can save on energy costs. Dark sky conservation and stricter lighting ordinances will help.

I was surprised by the negative health effects of exposure to nighttime lighting—something to keep in mind as I work late into the night, basking like a lizard in the glow of my computer screen.

37.879329 -122.2463347

Wildfire ripped through this area of forest, which was infested with Sudden Oak Death. Does infestation with SOD make wildfires burn with more intensity? Photo: Kerri Frangioso.

From Oregon to Big Sur, potentially millions of trees have been killed by Sudden Oak Death, or SOD. In 2006 and 2007, researchers from UC Davis set up a large-scale study in the coastal forests near Big Sur to examine the spread of the disease and its impact on forest dynamics. The area was one of the first to be affected by SOD. Members of the Rizzo Lab at UC Davis had established 280 plots across the region, carefully counting and measuring each tree and checking for SOD infection. Then, in June 2008, the Basin Complex Fire ripped through Big Sur, burning over 95,000 hectares of forest. By the time the fire was contained, over a month after it began, one third of the team’s plots were crisp and blackened.

While the fire burned, news media and firefighters assumed that areas of the forest infested with SOD would burn more intensely—all the dead oak trees would fuel the fire. But the natural experiment created by the overlap of the Basin Complex Fire and the UC Davis study allowed researchers to test whether SOD did in fact make wildfire worse. Their study will soon be published in the journal Ecological Applications; a preprint of their paper is available here. What they found was not what the news media or the firefighters predicted.

Andrew Molera State Park, the same plot as the top photo, before the Basin Complex Fire. Photo: Kerri Frangioso.

Invasion of the water molds
Sudden Oak Death came to California in the 1990s, probably on the leaves of a rhododendron shipped in for the nursery industry. The disease is caused by a water mold, called Phytophthora ramorum. It can spread short distances in splashes of water, and can potentially travel longer distances when water is blown about in storms.

Not all trees that are infected with the pathogen will die. Some species, like California Bay Laurel, do just fine. But California Bay is like Typhoid Mary—it serves as a host to the pathogen and allows it to spread to other, more susceptible species. The pathogen is fatal to tanoak and several species of oak trees. These species develop cankers on their trunks, which bleed out a thick, red liquid. Slowly, the bark around the entire circumference of the tree is affected; all tissue above this girdle dies, leading to the death of the tree.

A natural experiment
In 2008, Margaret Metz had just begun a new post-doc in Dave Rizzo’s lab. She was to work on the Big Sur project and analyze the data from the 280 plots to understand SOD impacts in the region. Her colleagues had spent months setting up the plots for their SOD study. They knew the size and location of every tree, whether it was standing upright and healthy (or newly infested with SOD), or whether it was dead and decomposing on the ground. When Metz found out her study site was burning, she was devastated. All that hard work—and all those trees—was going up in flames.

However, the dismay was short-lived. The team had a perfect pre-fire dataset. They just needed to census the plots after the fire, to get a rare comparison of the severity of fire in areas with and without SOD. This was an experiment they didn’t intend on doing—but drought and a dry lightning strike had made it possible. Dave Rizzo was able to quickly procure funding for the researchers to re-census the plots. “You could never do a controlled burn on that scale,” says Metz.

Where there’s SOD, there’s more intense fire?
News articles about the Basin Complex fire linked SOD to fire intensity, and firefighters reported that fires were burning more fiercely in areas with evidence of SOD. So when Metz and her colleagues analyzed their data, they thought they’d see that fires were more severe in plots infested with SOD. But that is not what they found. Their data showed that plots with and without SOD showed no difference in fire severity. They quantified fire severity using something called the Composite Burn Index. It takes into account the effects of fire on the ground, as well as in the shrubs and trees. Composite Burn Index did not differ between plots infested with SOD and plots without SOD. The popular assumption, that SOD makes wildfires burn more intensely, was wrong.

Dead tanoak along the Big Sur Highway. Photo: Karl Buermeyer, COMTF.

However, Metz and the team could dig deeper into their data. From their pre-fire data, they knew whether SOD had infested the plots recently, or whether SOD had been there for some time. It can take several years for a tree to die from SOD. When trees are first infected with SOD and die, their leaves turn dry and brown, and they remain on the tree for a year or more. Later, the branches fall to the ground, and eventually the whole trunk falls over. The fuel created by newly infected trees and trees that have been infected for several years is quite different. Metz and her colleagues found that in plots that were newly infested, plots with more dead biomass (or fuel) burned more intensely. In plots that were infested some time ago, the amount of biomass was not related to the intensity of the fire. They suspect that crisp brown leaves on newly infected trees allow the fire to burn high in the canopy. In plots infested long ago, the dead trees are on the ground; in this case, the fire damages the soil and the tree roots, which makes slopes vulnerable to erosion from mudslides. The conventional wisdom about SOD and fire was not quite right, but there was some truth to it—it just depends on when the forest was infested with SOD. Newly infested forests burn with more intensity than un-infested forests or forests that were infested some time ago.

Future forests
It has been almost three years since the Basin Complex Fire burned up Metz’s plots. Now, she and her colleagues are looking to see how the forest recovers—from the fire, and from SOD. Maia Beh, a grad student in the Rizzo Lab, found that of the plots that had SOD in the pre-fire surveys, only 20% still have it today. They’re not sure whether it’s because of the fire, or because there have been two years of drought. The pathogen, P. ramorum, is dependent on water, and doesn’t do well in drought conditions. They’re looking at plots that did not burn up in the fire to see whether the decline in the pathogen is due to drought, fire, or some combination of the two.

Though the incidence of the pathogen has declined on land, it is still present in almost all the watersheds in the area. And, last year we had late rains, extending through spring into the early summer. Late rains with warm temperatures create conditions that are ideal for the pathogen, says Metz.

With continued careful sampling of those 280 plots—and maybe a few more unintended natural experiments—Metz and her colleagues will learn how forests recover from both fire and SOD.

Learn more about SOD
To prevent the spread of the pathogen P. ramorum, take steps make sure it isn’t hitchhiking on your boots. Clean your boots into the buckets of diluted bleach that you might find at trailheads, or spray your boots down with Lysol.

Take part in a SOD-blitz, a citizen science project. Learn more about SOD and help figure out where the pathogen has spread, with UC Berkeley plant pathologist Matteo Garbolotto. You can see Garbolotto on the QUEST video Plant Plague: Sudden Oak Death.

37.879329 -122.2463347

Backyard chickens (credit: Meredith Hall)

The recent salmonella outbreak has led to a recall of half a billion eggs, and has sickened thousands of people. (Check this FDA page to see if the eggs in your fridge are safe to eat.) Many of the contaminated eggs have been traced to two giant farms in Iowa. It is not entirely clear what caused the outbreak—and there may have been multiple sources. But at least some of the contaminated eggs were laid by hens that ate contaminated chicken feed. Rodents carrying salmonella had gotten into the feed. In large-scale egg farms, salmonella can spread easily. Backyard chickens can still be subject to salmonella, but at least if you’re in charge of the coop, you can be sure to take precautions to keep your birds healthy.

These precautions include keeping the habitat clean, making sure the food isn’t contaminated by rodents or other animals (reptiles carry salmonella too), and maybe even vaccinating your chickens. Vaccination is common in the UK and other parts of Europe (though in this country, the FDA has deemed it unnecessary). I have no idea if vaccines are available for backyard birds—but it might be a good idea.

Not being a bird owner myself, I wondered how a first-time chicken raiser could learn about keeping birds healthy. I read Oakland urban farmer Novella Carpenter’s book Farm City, and I couldn’t remember if her mail-order poultry had come with instructions. Then, I found out that the USDA recently started a public education campaign on backyard bird health. And, urban homesteaders swap chicken husbandry tips thanks to internet sites like Meetup. There are whole communities out there, dedicated to raising healthy birds.

Still, I am not ready build a coop on my back porch and fill it with chickens. But the salmonella outbreak and the poultry experts at the Eat Real Festival reminded me that farmers, with their great knowledge of how animals and diseases and the environment are all entwined, are the world’s original ecologists.

To learn more about eggs and the differences between supermarket eggs or farm fresh eggs, watch City Egg, Country Egg on QUEST.

37.7941971 -122.2760333

Tamalpais Manzanita, Mount Tamalpais State Park. Photo: randomtruth.

Serpentine, California’s state rock, is feeling some pressure—and not just because it’s a metamorphic rock! The California Legislature is considering a bill that would strip serpentine of its state rock status; geology blogger Brian Romans explained the details in this recent QUEST blog. Basically, proponents of the bill say that because asbestos is made from serpentine rock, and asbestos causes cancer, serpentine should not be the state rock. Never mind that serpentine does not cause cancer. In fact, many organisms thrive on serpentine soils. And that is what today’s post is about—the unique plants and animals that call serpentine soil home.

Serpentine soil is a tough environment: the soil is coarse, so water runs right through it, making it very dry. It is often dark in color, so it heats up in the sun. And its chemical makeup is challenging to plant life, to say the least. The soil has high concentrations of heavy metals, like nickel, iron, and chromium, and low concentrations of nutrients, like nitrogen and phosphorus. It is also really high in magnesium, which makes it hard for plants’ roots to take up those already-scarce nutrients. And it is low in calcium, which causes ion balance problems for plants.

With nutrients scarce, serpentine inhabitants tend to be small in stature—it’s hard to grow big without much food. And, with low water availability, serpentine plants are drought-tolerant. They often have tough little leaves, which don’t lose much water. Some examples are the Tamalpais manzanita (Arctostaphylos montana), and the Leather Oak (Quercus durata).

Plants on serpentine soils also have to deal with those heavy metals, which can interfere with metabolic processes. Some plants, like the Milkwort Jewelflower (Strepthanus polygaloides), have a really high tolerance for heavy metals. Milkwort Jelweflower is a nickel hyperaccumulator—it can take up lots of nickel from the soil, with no ill effects. In fact, some serpentine plants are used in bioremediation; people plant them in contaminated soil, where they pull the heavy metals out of the ground and sequester them in their tissues.

Serpentine soils are home to many endemic species—species that live in a particular habitat type, and nowhere else. Sometimes plants or animals are limited to one habitat because they can’t survive the physical conditions of other habitat types. But in the case of serpentine endemics, many can live in other habitats’ nutrient-rich soils, but are total weaklings when it comes to competition with other plants. They can’t live in other habitats simply because they are out-competed.

Serpentine soils are home to more than just plants—there are butterflies, too, like the beautiful California White (Pontia sisymbrii). Some, like a rare variant of the Edith’s checkerspot butterfly, Euphydryas editha luestherae, are serpentine endemics, because they lay their eggs exclusively on plants living on serpentine soils.

The Geoblogosphere is buzzing with commentary about California’s serpentine bill. If you feel passionate about keeping serpentine as the state rock, by all means write your state representative—but also visit some serpentine habitat! There are lots of places in the Bay Area where you can check out serpentine soils and their inhabitants. There are serpentine outcroppings on Mount Tamalpais, Mount Diablo (be sure to check out QUEST’s Mount Diablo State Park Exploration!), and in the Berkeley and Oakland hills.

37.879329 -122.2463347

Oil on the surface of the San Francisco Bay in November 2007. Photo: NOAA.

We have no idea how much oil gushed out of BP’s Deepwater Horizon well into the Gulf of Mexico—estimates vary from 92 million gallons to over 320 million gallons, according to the NewsHour’s widget. By comparison, a much smaller amount of oil—53,000 gallons—was spilled into San Francisco Bay when the container ship Cosco Busan ripped its hull open on the Bay Bridge in November 2007. The volume of oil spilled in the Gulf is several thousand times what was spilled in San Francisco Bay, and obviously the environmental consequences of the Gulf spill will far exceed what we’ve seen here. But the ecological studies conducted in the wake of the Cosco Busan spill give us an idea of what we can expect in the Gulf.

After the Cosco Busan spill, scientists looked at the effects of oil on different coastal habitats, and on individual species. A year after the spill, the QUEST radio story Oil Spill Anniversary discussed a study that revealed the negative effects of oil on Herring embryo development. Other studies looked at the impact of oil on intertidal areas, eelgrass beds, native oysters, Brown Pelicans, Marbled Murrelets, and more—a full list of studies that assessed damage to natural resources is at this NOAA site (click on “Case Documents” on the right to download the list as a PDF). Not all organisms fared poorly; the snowy plover, a bird that lives on beaches and is already a threatened species, was fine. They build their nests far enough from the water to be buffered from oil contamination.

Research about impacts and restoration in the Gulf is just getting started. The official US government website about the oil spill switched from a mindset of emergency response to one of restoration, reflecting the huge challenge that lies ahead—provided the oil doesn’t start flowing again. Some government agencies, like the EPA, are sharing the data that is being collected as you read this. My hope is that these research efforts will involve extensive long-term monitoring; the effects of oil spills can last for decades, and we need to understand how ecosystems function over time, with and without oil. We have the opportunity to learn a lot from this disaster, and hopefully we’ll have the money to fund it. The company that operated the Cosco Busan was fined $10 million, $2 million of which is slated for environmental efforts. If BP is fined in proportion to the volume of oil spilled, billions could go towards ecological research.

37.804556 -122.3711