Endangered lizard conservation in California, USA

This 2014 video from the USA is called Blunt-nosed leopard lizard, endangered species project.

From the University of California – Davis in the USA:

Detection dogs and DNA on the trail of endangered lizards

Noninvasive scat sampling could strengthen reptile conservation

October 30, 2019

Detection dogs trained to sniff out the scat of an endangered lizard in California’s San Joaquin Valley, combined with genetic species identification, could represent a new noninvasive sampling technique for lizard conservation worldwide. That is according to a study published today from the University of California, Davis, in partnership with the nonprofit Working Dogs for Conservation, U.S. Geological Survey and the U.S. Bureau of Land Management.

Scientists have used trained conservation dogs to locate scat and collect DNA samples for everything from bears and foxes to gorillas and whales. But the technique had not been used for reptiles until this study, for which scientists developed a novel approach to identify the presence of the blunt-nosed leopard lizard in the Panoche Hills Recreation Area and Carrizo Plain National Monument, both managed by BLM.

They developed new methods to recover DNA from feces and genetically identify lizard species in the same area. The study, published in the Journal of Wildlife Management, is a proof of concept for a host of reptiles.

“So many reptilian species have been hit so hard,” said lead author Mark Statham, an associate researcher with the Mammalian Ecology and Conservation Unit of the UC Davis School of Veterinary Medicine. “A large proportion of them are endangered or threatened. This is a really valuable way for people to be able to survey them.”


Current methods for surveying lizard species typically rely on live capture or visual surveys. Scat sampling allows biologists to study elusive, rare or dangerous animals without the need for direct contact. In addition to informing about the presence, habitat and genetics of an animal, scat can also be analyzed to inform researchers about diet, hormones, parasites and other health factors.

Using the new method, the authors genetically identified specific species for 78 percent of the 327 samples collected by dog-handler teams across four years. Most (82 percent) of those identified were confirmed as being from blunt-nosed leopard lizards.

To meet regulatory monitoring requirements, more research is needed to assess the viability of using detection dogs to recover usable DNA at larger scales. But the research highlights the broad potential this method holds for surveying and monitoring reptiles.

Study co-authors include Deborah A. Woollett, Alice Whitelaw and Ngaio L. Richards of Working Dogs for Conservation; Susan Fresquez, Jerene Pfeiffer and Benjamin Sacks from UC Davis School of Veterinary Medicine; Jonathan Richmond from the U.S. Geological Survey; and Michael F. Westphal of the U.S. Bureau of Land Management.

Funding was provided by the Bureau of Land Management.

United States police killed Isiah Murrietta-Golding, RIP

This 23 October 2019 video from California in the USA says about itself:

Fresno Police Fatally Shoot Unarmed Teenager in the Back

By Tom Carter in the USA:

The police murder of Isiah Murrietta-Golding

26 October 2019

Shock and outrage continue to reverberate around the world following the release Wednesday of a video showing the police murder of Isiah Murrietta-Golding in Fresno, California in April 2017.

It was a sunny Saturday, and the video shows the 16-year-old boy scrambling over a low fence and taking a few steps onto an empty preschool lawn. Then, in a moment that jars horribly with the bright green and pristine surroundings, the boy suddenly collapses to the ground and curls into a fetal position—his brain pierced by a single bullet fired by police officer Ray Villalvazo, who was crouched on the other side of the fence.

An audio recording of the shooting indicates that immediately after the boy’s body drops to the ground, another officer shouts, “Good shot!” The expression and tone of voice suggest that the officers are on a hunting safari, and someone has just bagged a prize animal.

Something truly awful is suggested about the state of American society by the footage of another officer jogging up to the boy’s limp body, hoisting it up by one arm, kicking it over, and then handcuffing the wrists together—a rote action simultaneously brutal and absurd.

The video explodes the official account of the shooting, according to which the boy had “reached into his waistband several times,” prompting the officer to shoot him in self-defense because he was afraid for his life.

According to the available accounts, Isiah was a good student at his school, where he was in the 10th grade. He has been described as a “small boy”, standing 5 foot 4 inches tall and weighing 109 pounds. He died several days later at the hospital, his grief-stricken mother at his side.

His alleged involvement in an incident that led to a fatal car crash with his older brother the previous day remains murky. He may just have been in the wrong place at the wrong time. But even if he was in some way culpable, as a minor he would have been subject to confidential juvenile proceedings and efforts at rehabilitation, not summary assassination by a police officer acting as judge, jury and executioner.

When he was stopped by the police, Isiah initially complied with instructions. He was unarmed, never threatened anyone, and never attempted to hurt anyone. He simply tried to run away. One cannot help imagining the boy’s final, terrified moments.

According to a lawsuit filed by the boy’s parents, the officers delayed calling for medical assistance following the shooting. When the ambulance arrived, the police refused a paramedic’s request to take the handcuffs off the body, even though the boy was in a coma.

The American military refuses to do “body counts” overseas, and the US government similarly avoids gathering statistics on the use of deadly force by the police within the country’s borders. Nevertheless, a Washington Post database indicates that around a thousand people are killed by police each year, with 717 killed as of this writing in 2019. This figure likely understates the true number, omitting those killings that are covered up by the police as drug overdoses, suicides, or deaths from “natural causes” or “excited delirium.”

The number of deaths from industrial accidents in the US every year, which is in the thousands, is dwarfed by the number of nonfatal accidents and illnesses, which is in the millions. Similarly, while hundreds of people are killed by the police each year, the number of nonfatal injuries caused by the police each year must be orders of magnitude higher, in the tens or hundreds of thousands: broken jaws and teeth, lost eyes, flesh shredded by police dogs, concussions, permanent nerve damage, traumatic brain injuries, broken legs, backs, shoulders and necks.

In the wake of each episode of police brutality, victims and their families watch as the entire state closes ranks behind the perpetrator.

An “internal investigation”, conducted in secret by the police, almost invariably results in a determination that the officers were acting “within policy”, a determination bolstered in turn by vague policies designed to permit the broadest range of violence.

Meanwhile, in order to help shield officers from accountability, the local prosecutor will often bring charges against the victim, including for such vague crimes as “resisting, delaying, or obstructing” a police officer. In other cases, someone bitten by a police dog will be charged with “battery to a police dog”.

In Fresno, the results of the internal investigation into the shooting of Isiah Murrietta-Golding were announced in March of last year: “Sgt. Villalvazo’s actions were within department policy.”

As late as 1985, in the case of Tennessee v. Garner, the US Supreme Court wrote: “Where the suspect poses no immediate threat to the officer and no threat to others, the harm resulting from failing to apprehend him does not justify the use of deadly force to do so. It is no doubt unfortunate when a suspect who is in sight escapes, but the fact that the police arrive a little late or are a little slower afoot does not always justify killing the suspect. A police officer may not seize an unarmed, nondangerous suspect by shooting him dead.”

However, even after the release of the video, The Fresno Bee reports that the Fresno Police Officers Association “is in full support of the sergeant and says its members believe the shooting to be justified.”

As part of his fascistic appeal to law enforcement, President Trump has gone out of his way to incite the police against the population, famously telling a crowd of police officers in New York in 2017 that he likes watching footage of “rough” treatment of “thugs”. “Please don’t be too nice”, Trump intones, drawing cheers from the assembled cops.

At a recent rally in Minnesota, Trump appeared flanked by police officers wearing “Cops for Trump” shirts featuring an American flag and the shapes of police badges. Trump had evidently wanted the officers to appear in uniform, a prohibited form of political endorsement.

Meanwhile, the Democrats, for all their posturing and expressions of concern, preside over cities infamous for police brutality like Chicago, New York, and Los Angeles. The Obama administration, for its part, repeatedly intervened on the side of the police in civil rights cases before the Supreme Court, invoking the authoritarian doctrine of “qualified immunity”.

In schools and neighborhoods across the US, the population is seething with anger over the mounting number of victims and the belligerent intransigence of the authorities. Certain political conclusions must be drawn from this state of affairs.

Vladimir Lenin, in his treatise State and Revolution, describes how Friedrich Engels draws “the attention of the class-conscious workers to what prevailing philistinism regards as least worthy of attention, as the most habitual thing, hallowed by prejudices that are not only deep-rooted but, one might say, petrified.”

“The state,” Engels writes, “has not existed from all eternity. There have been societies that did without it, that had no idea of the state and state power. At a certain stage of economic development, which was necessarily bound up with the split of society into classes, the state became a necessity owing to this split.”

The state, therefore, “is a product of society at a certain stage of development; it is the admission that this society has become entangled in an insoluble contradiction with itself, that it has split into irreconcilable antagonisms which it is powerless to dispel. But in order that these antagonisms, these classes with conflicting economic interests, might not consume themselves and society in fruitless struggle, it became necessary to have a power, seemingly standing above society, that would alleviate the conflict and keep it within the bounds of ‘order’; and this power, arisen out of society but placing itself above it, and alienating itself more and more from it, is the state.”

Lenin asks, “What does this power mainly consist of?” It consists mainly of “special bodies of armed men”, together with prisons and other forms of repression. Quoting Engels, Lenin explains that this power becomes more forceful in proportion as class antagonisms become more acute.

In the United States, the institution of the police did not exist on a significant scale until the middle of the 19th century. The development of many of the municipal police departments into their present centralized form in the late 19th century coincided with a massive wave of labor unrest. Modern police departments emerged onto the scene as “special bodies of armed men” that could be deployed against demonstrations of workers, often with extreme violence, and also to make mass arrests of workers for violations of “public order”.

With this social and historical framework in mind, the phenomenon of escalating police violence in the 21st century must be understood in the first instance as a function of the acute crisis of the whole social order. The decades-long social counterrevolution, skyrocketing social inequality, the endless wars for plunder abroad, the paralysis and collapse of democratic institutions, and the resurgence of open struggles by the working class around the world all constitute aggravating factors in the equation.

The reign of arbitrary police terror also functions to condition the population and the police themselves to extreme violence, in preparation for future campaigns of mass repression.

Racism does play a role in many individual episodes of police brutality, and anger over the persistence of such prejudices is legitimate. …

In the final analysis, the epidemic of police brutality in the US, which enjoys the full backing of the state, is a product of a social and economic system in deep crisis.

California condor chick fledges, video

This video from the USA says about itself:

California Condor Chick #980 Fledges! – Oct. 14, 2019

Big news! At just over 6 months of age, the young condor nestling #980 has fledged after 187 days. Watch the young condor confidently take wing on October 14. After making a sustained flight out of view, the fledgling returns to perch on its favorite rock in the nesting cave. Way to fly #980!

Watch live at www.allaboutbirds.org/condors

This condor nest, known as the Pole Canyon nest, is located in a remote canyon near the Hopper Mountain National Wildlife Refuge. The parents of the chick in the Pole Canyon nest are mom #563 and dad #262. Dad #262 was laid in 2001 and was the first viable egg laid in the wild since the reintroduction program began. He was actually one of two eggs laid to a trio (male #100 and females #111 and #108) but was brought into captivity to ensure proper incubation. He hatched at the Los Angeles Zoo and was released back to the wild a year later in 2002. Mom #563 hatched at the Oregon Zoo in 2010. This is their first nesting attempt together but both have nested previously with mates who are now deceased. A single egg was laid in this nesting cavity, and the chick hatched on April 10, 2019.

American mountain lions, research and conservation

This September 2014 video from the USA is called Mountain lion encounter in Montana.

From the Howard Hughes Medical Institute in the USA:

Whole genome sequencing could help save pumas from inbreeding

October 18, 2019

Summary: The first complete genetic sequences of individual mountain lions point the way to better conservation strategies for saving threatened populations of the wild animals.

When students at the University of California, Santa Cruz (UCSC) found a dead mule deer on campus, they figured it had been killed by coyotes. Wildlife biologist Chris Wilmers rigged up a video camera to spy on the carcass at night. But the animal that crept out of the shadows to dine on the deer was no coyote — it was a mountain lion.

Mountain lions, or pumas, stay close to their prey, “so it must have been hiding in a nearby gorge all day,” says Howard Hughes Medical Institute Investigator Beth Shapiro, an evolutionary biologist at UCSC.

The persistent puma was already well-known by Wilmers, who had radio-collared and tagged him as part of a long-term study of California mountain lions. But now the animal, dubbed 36m, is becoming even more famous: he’s the first puma to have his complete genome deciphered by scientists.

The information in 36m’s genes may lead to better conservation strategies, Shapiro, Wilmers, and their colleagues report October 18, 2019, in the journal Nature Communications. Many puma populations across North America are becoming increasingly isolated, Wilmers says. That ups their chances of succumbing to inbreeding and its consequences — serious abnormalities such as damaged hearts and malformed sperm. But with whole genomic information, scientists can pinpoint populations that need an influx of new genes or identify the best pumas to move between populations.

Such work could stop inbreeding in its tracks and help keep local populations from going extinct, Shapiro says. “This is the first time that whole genomes have been used in this way.”

Pumas in peril

The team’s new sequencing work is not the first effort to unlock pumas’ genetic secrets. Years of painstaking research by geneticist Stephen O’Brien, molecular ecologist Warren Johnson, and others had previously shown that Florida’s tiny population of pumas (also known as cougars or panthers) had become dangerously inbred, resulting in health defects like holes in their hearts and missing testicles. These abnormalities threatened the animals’ ability to reproduce.

The research team also proved that the introduction of eight female cougars from west Texas in 1995 had added enough new genes to boost health and help the population grow from about 30 individuals to more than 120. But the team’s effort was limited by the genetic technology available at the time, which relied on analyzing just small snapshots of DNA, or markers, scattered throughout the genome. So the scientists didn’t have a complete picture of the pumas’ genes.

Animals get two versions of every gene — one from mom and, usually, a different one from dad. This means that offspring have the genetic diversity needed to keep populations healthy. But when populations become small and isolated, relatives breed with each other. As a result, genetic diversity plunges, and many genome locations end up with two identical versions of a gene. That’s when weird things happen to animals, like the kinked tails, damaged hearts, and malformed sperm found in the inbred Florida panthers before the infusion of Texas cougar genes.

Using DNA markers alone, scientists can estimate the average amount of genetic variation within a population and get a rough picture of the level of inbreeding. But this approach can’t say whether major stretches of DNA between those markers contain copies of genes that are the same. These runs of identical gene copies are crucial, says Johnson, who is at the Walter Reed Biosystematics Unit and affiliated with the Smithsonian Conservation Biology Institute’s Center for Species Survival.

The number and length of these stretches provide a precise measure of both the extent of inbreeding and how recent it is — and, therefore, how close a population is to falling off a genetic cliff. Inbreeding is not a slow and progressive process, Shapiro explains. Instead, once enough long runs of DNA with identical copies accumulate, the effects of inbreeding kick in suddenly, like turning off a light switch, she says.

From mammoths to mountain lions

Shapiro is best known for recovering and sequencing tiny bits of DNA from ancient bones, charting the genetic changes in mammoths and other now-extinct animals as their numbers shrank. But she also has a keen interest in applying the same techniques to existing creatures, like the North American mountain lion. She wants to learn more about the genetic roads to extinction — and possibly prevent those creatures from suffering the same fate. While talking with Wilmers one day about the Santa Cruz lion population, the two scientists realized that a crucial piece of information was missing: the puma’s complete genetic sequence.

Using blood that Wilmers had already collected from puma 36m, Shapiro and her team, including graduate student Nedda Saremi and postdoc Megan Supple, read the lion’s entire genome to serve as a reference for the species. Then, for comparison, they sequenced the genomes of nine other mountain lions using stored samples — another from the Santa Cruz area, two from the Santa Monica mountains, one from Yellowstone, three from Florida, and one from Brazil.

The work let Shapiro see what had taken years to figure out in Florida — that the translocation of Texas cougars had boosted genetic diversity and health of the Florida panthers. The sequences also brought new insights: even after mixing in the Texas DNA, the Florida population remains closer to the genetic brink than previously thought. “The big takeaway is that translocation worked, but the lights are going to go off because they continue to inbreed,” Shapiro explains.

Similarly, the population in the Santa Cruz Mountains “is not doing as well as we expected,” she says. The 10 genomes also held controversial hints that mountain lions may have existed in North America far longer than previously thought — as many as 300,000 years, instead of fewer than 20,000 years. “What Beth and her students are able to learn from just 10 individuals greatly extends what could be inferred with traditionally used DNA markers,” Johnson says.

More insights will come as scientists ramp up whole genome sequencing. Sequencing the full genomes of many individuals across a species’ range is “tremendously valuable,” explains Brad Shaffer, director of the UCLA La Kretz Center for California Conservation Science. “That can tell us a lot about the potential for climate adaptation and other critical conservation goals.” And with costs rapidly declining — Shapiro says reading 36m’s genome cost about $10,000, down from $30,000 a couple of years ago, with subsequent lions sequenced for just $400 each — O’Brien and others are pushing for a much larger effort. “Whole genome sequencing should be done for every critter we can catch,” says O’Brien, of Nova Southeastern University.

Already, Shapiro’s work is shining a powerful new spotlight on the genetic health of individual mountain lions and populations, pointing the way to more effective conservation strategies. Isolated populations, for example, may benefit from wildlife bridges across major highways, to allow animals to wander more widely. In other cases, scientists may need to move animals from one region to another. Overall, a more complete picture of the genome makes it possible to spot populations at greatest risk for inbreeding ¬- and the best candidates for translocation.

“Now we can make more informed decisions,” says Johnson. “In the past, we made decisions based on limited genetic information.” The new approach takes out much of the uncertainty about a population’s genetic heritage, he says. It also offers clues about how to preserve genetic variation and may help populations adapt to change.

Though puma 36m didn’t live to see any of these advances, his genetic legacy will remain. “While 36m was a badass puma by any measure, he might one day come to be the most recognized puma anywhere,” Wilmers wrote in a tribute.”[His] will be the puma genome against which other puma genomes can be compared and used to test all sorts of evolutionary and ecological questions.”

Marine fog brings more than cooler temperatures to coastal areas. Researchers at UC Santa Cruz have discovered elevated levels of mercury in mountain lions, the latest indication that the neurotoxin is being carried in fog, deposited on the land, and making its way up the food chain: here.