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.”

Top 5 big cat moments, BBC video


This 3 September 2019 video says about itself:

Heart Stopping Big Cat Moments | Top 5 | BBC Earth

Here are our Top 5 Big Cat moments! Big Cats are some of the most majestic – and adorable – creatures to grace the natural world. From Jaguars and Panthers to Lions and Tigers, watch as these beautiful animals navigate life both in the wild and in captivity.

Texas pumas saving Florida panthers


This video from the USA says about itself:

Florida Panther Encounter – 7/5/2014

There are only about 160 Florida Panthers in the wild, and we were fortunate to see this young one – on public lands from the front seat of our car. (This is the long, minimally edited version of our adventure.) Please support funding for environmental protection!

From Ohio State University in the USA:

How the Texas puma saved the Florida panther

Uncovering the genetic details of a conservation success story

October 3, 2019

Scientists have pieced together the first complete picture of the Florida panther genome — work that could serve to protect that endangered population and other endangered species going forward.

Florida panthers are the only documented population of pumas (Puma concolor) found east of the Mississippi River.

In the mid-1990s, Florida panthers were facing desperate times. Their small numbers (fewer than 30 in the wild) made inbreeding inevitable and that brought the usual health troubles that emerge when any animals, including humans, mate with partners of a similar genetic background. Heart failure, undescended testicles, pathogenic diseases and parasites were common among the animals. So biologists introduced eight female Texas pumas into South Florida, hoping that genetic variation would help shore up the Florida panthers’ future.

In the new study, researchers used advanced computer techniques to analyze the genomes of Florida panthers, Texas pumas and their offspring to better understand how the mid-1990s introduction program contributed to Florida panthers’ genetic diversity.

Among their findings: Genetic diversity tripled.

“Florida panthers were in trouble because of inbreeding depression. It’s like royalty in human history, where mating with close relatives increases the risk of manifesting harmful DNA mutations and reduces the ability to survive and reproduce,” said lead author Alexander Ochoa, a postdoctoral researcher in the Department of Evolution, Ecology and Organismal Biology at The Ohio State University.

The study appears online in the journal G3: Genes, Genomes, Genetics.

Five of the pumas introduced in the 1990s produced at least 20 offspring. Today, upwards of 230 known individual panthers — many the descendants of this introduction program — roam southern Florida, many in Everglades National Park and Big Cypress National Preserve.

Ochoa and his collaborators examined the DNA of 10 animals — a mixture of Florida panthers and Texas pumas and their immediate offspring. They compared the animals’ genetics, looking for patterns that would tell them what happened during the mixing of the populations.

“This tells us a lot about the genetic underpinnings of this iconic conservation success story. The genetic diversity we found was much greater than some scientists previously thought, and likely contributed to the recovery of Florida panthers after the introduction of the Texas pumas,” Ochoa said.

In the mid-1990s, about 21 percent of Florida panthers had a heart problem called atrial septal defect, and more than 60 percent of the males had undescended testicles, a serious threat to the survival of the population. In recent years, those numbers have dropped to 7 percent and 3 percent respectively.

Ochoa and his colleagues also identified 17 genes that were linked to the refinement of sensory capabilities in pumas, most notably to improved vision. They also found that the number of genes linked to the animals’ sense of smell decreased.

“We believe there’s a tradeoff between the development of genes related to the sense of smell and the development of genes related to vision, because pumas are nocturnal hunters,” Ochoa said.

The researchers hope this work will serve to help conservationists understand how genetic diversity can impact at-risk animal populations, and that the genetic details they discovered could potentially help those working in veterinary and human medicine, he said. For the Florida panther population specifically, the genetic blueprint offered in this research could help in the detection of harmful DNA mutations.

“It’s possible you’d want to intervene in a way to decrease the frequency of these mutations so that there isn’t a resurgence of traits that are harmful to the population,” Ochoa said.

His next study will focus on the specific contributions of the Texas pumas to the Florida panther gene pool, work that should clarify which introduced genes were beneficial and detrimental to the population.

“Introducing Texas pumas made sense as they were geographically the closest living population of pumas and they carried potential for restoring Florida panther genetic variation, but this activity also could have presented some risks due to the mixing of individuals with adaptations to particular environments. We want to better understand what happened to the Florida panthers on a genetic level.”

Other researchers who worked on the study were Melanie Culver of the University of Arizona, Robert Fitak of the University of Central Florida (previously of Ohio State), David Onorato of the Florida Fish and Wildlife Conservation Commission and Melody Roelke-Parker of Leidos Biomedical Research, Inc. and the Frederick National Laboratory of Cancer Research.

Wolves, cougars, elk in Yellowstone, USA


This video says about itself:

Fearless predator – Cougar attack bears, deer and jaguar

Puma (mountain lion, cougar) is a predator of the Puma [genus] of the cat family. It lives in North and South America.

From the S.J. & Jessie E. Quinney College of Natural Resources, Utah State University in the USA:

Fearing cougars more than wolves, Yellowstone elk manage threats from both predators

August 2, 2019

Wolves are charismatic, conspicuous, and easy to single out as the top predator affecting populations of elk, deer, and other prey animals. However, a new study has found that the secretive cougar is actually the main predator influencing the movement of elk across the winter range of northern Yellowstone National Park.

The study highlights that where prey live with more than one predator species, attention to one predator that ignores the role of another may lead to misunderstandings about the impact of predators on prey populations and ecosystems. It also offers new insight into how prey can use differences in hunting behavior among predators to maintain safety from all predators simultaneously.

Utah State University researchers Michel Kohl and Dan MacNulty co-led the study, published in Ecology Letters, with Toni Ruth (Hornocker Wildlife Institute and Wildlife Conservation Society), Matt Metz (University of Montana), Dan Stahler, Doug Smith, and P.J. White (Yellowstone National Park). Their work was supported, in part, by the National Science Foundation, Ford Foundation, and Utah State University as part of Kohl’s doctoral research. The study was based on long-term data from the Park’s wolf and elk monitoring programs and Ruth’s cougar research, which is detailed in a forthcoming book from the University Press of Colorado.

The team revisited global positioning system (GPS) data from 27 radio-collared elk that had been collected in 2001-2004 when numbers of wolves and cougars were highest. Kohl and MacNulty combined the elk GPS data with information on the daily activity patterns of GPS-collared cougars and wolves and the locations of cougar- and wolf-killed elk to test if elk avoided these predators by selecting for ‘vacant hunting domains’, places and times where and when neither predator was likely to kill elk.

“Cougars hunted mainly in forested, rugged areas at night, whereas wolves hunted mainly in grassy, flat areas during morning and at dusk” said Kohl, lead author of the paper and now an assistant professor at the Warnell School of Forestry and Natural Resources at the University of Georgia in Athens. “Elk sidestepped both cougars and wolves by selecting for areas outside these high-risk domains, namely forested, rugged areas during daylight when cougars were resting, and grassy, flat areas at night when wolves were snoozing.”

Recognizing that cougars and wolves hunted in different places and at different times allowed the researchers to see how elk could simultaneously minimize threats from both predators. “Had we ignored the fact that these predators were on different schedules, we would have concluded, incorrectly, that avoiding one predator necessarily increased exposure to the other,” said MacNulty, who is an associate professor in USU’s Department of Wildland Resources and Ecology Center. “Movement out of the grassy, flat areas and into the forested, rugged areas to avoid wolves did not result in greater risk from cougars and vice versa because these predators were active at different times of the day.”

Despite the compatibility of elk spatial responses to cougars and wolves, Ruth, who is now executive director of the Salmon Valley Stewardship in Salmon, Idaho, cautioned that “some adult elk still end up on the cougar and wolf menu, with those in poor condition during winter being most at risk.”

Nevertheless, “the findings help explain why we observe wolves, cougars, and elk all coexisting and thriving on the Yellowstone landscape” said Stahler, who leads the current study of cougars in the Park. He notes that the ability of elk to coexist with wolves and cougars is consistent with their “long, shared evolutionary history”.

More surprising, however, was that cougars, not wolves, exerted the most pressure on elk habitat selection. “Wolves are often the presumed or blamed predator for any change in a prey population, numerical or behavioral,” said Smith, who leads the Park’s wolf program. “Our research shows that this is not necessarily true, and that other large predators in addition to wolves need to be considered.”

“Despite the fact that most prey species live in habitats with multiple predators, the majority of research on predator-prey interactions focuses on a single predator species,” added Betsy von Holle, program director for the National Science Foundation’s Division of Environmental Biology. “The novelty of this research is the simultaneous study of multiple predator species, revealing the complexity of predator avoidance behavior by the prey.”

Lynx in Turkey, new study


This 2015 video is about a lynx in Turkey.

From Forschungsverbund Berlin in Germany:

Lynx in Turkey: Noninvasive sample collection provides insights into genetic diversity

June 17, 2019

Summary: A team of scientists collected data and samples (feces, hair) from the Caucasian Lynx (Lynx lynx dinniki), in a region of Anatolian Turkey over several years. The results of the genetic analyses indicated an unexpectedly high genetic diversity and lack of inbreeding despite the recent isolation of the study population.

Little is known about the biology and the genetic status of the Caucasian Lynx (Lynx lynx dinniki), a subspecies of the Eurasian lynx distributed across portions of Turkey, the Caucasus region and Iran. To collect baseline genetic, ecological, and behavioural data and assist future conservation efforts, a team of scientists from the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) collected data and samples in a region of Anatolian Turkey over several years. They were particularly interested in the question whether non-invasive samples (faeces, hair) were helpful to discern genetic diversity of the study population. The results of the genetic analyses indicated an unexpectedly high genetic diversity and lack of inbreeding despite the recent isolation of the study population, a result that would not have been obtained with the use of conventional samples. The data also revealed that females stay near home ranges in which they were born whereas males disperse after separation from their mothers. These insights into the genetics and behaviour of the Caucasian Lynx are published in the scientific journal PLOS ONE.

Among lynx species, the Eurasian Lynx has the widest geographical distribution. Previous research has largely focused on European populations, with the result that there is little known about the subspecies in Asia, such as the Caucasian and Himalayan subspecies. “Scientists still know surprisingly little about their ecological requirements, spatial structure and genetic diversity,” says Leibniz-IZW researcher Deniz Mengulluoglu (Department for Evolutionary Ecology). “Our study aimed at collecting baseline genetic, ecological and behavioural data of the lynx population in a mountainous region in north-west Anatolia.” Making use of box trapping and non-invasive faecal sampling allowed Mengulluoglu to extract DNA and conduct genetic analyses on a population scale. The lynx population had also been monitored via camera traps at 54 different stations for nearly a decade.

Looking into family relationships of individual lynx, the data revealed that females stay near the territories in which they were born whereas males disperse after separation from their mothers. Such behaviour is known from many mammals, most likely to avoid inbreeding. “We can conclude from our analyses that territoriality in lynx and philopatry in female lynx can result in low genetic diversity estimates if sampling is done in small study areas via box trapping alone,” says Mengulluoglu. This behaviour — females remaining in close proximity to their mothers’ territory — is called female philopatry, and Mengulluoglu and his team confirmed it for this subspecies. “Using faecal samples that were non-invasively collected, we were able to sample more non-territorial individuals, gaining information about an additional component of this lynx population.” Unless individuals become used to the presence of box traps within their own range (habituation), and thus are ready to enter them, sampling them by conventional means is unlikely. Hence habituation will bias conventional sample collection in favour of resident territorial individuals and their kittens.

A second important finding is that genetic diversity is unexpectedly high in this population. Lynx in north-west Anatolia are isolated from southern and north-eastern populations by a series of natural and human constructed barriers. “Population isolation can be harmful and, for example, lead to a loss of genetic variation. But it appears that genetic diversity is in fact substantial at the moment and matches the diversity found in European endogenous populations,” states senior author Daniel Foerster from the Leibniz-IZW, Department of Evolutionary Genetics. “Management should therefore focus on maintaining the current level of diversity.” As a first step, Mengulluoglu and Foerster recommend identification and conservation of primary lynx habitats and corridors in the region.

“We also need to address threats that can lead to future loss of genetic variation” adds Mengulluoglu. Since this study has set a baseline for comparison with future findings, similar work is needed for the other two Turkish populations in order to determine whether the three big populations are currently connected by gene flow at all, Mengulluoglu and Foerster say. Mengulluoglu is currently working on a long-term lynx monitoring project and the development of a “Turkish Lynx Conservation Action Plan” in collaboration with the Wildlife Department of Turkey.

Asiatic golden cats’ colours, new research


This 2017 video is called Rarest cats in the world: Asian Golden Cat.

From the Zoological Society of London in England:

The benefits of being different

Six different ‘color morphs’ of the Asiatic golden cat discovered in India’s Arunachal Pradesh

June 12, 2019

Six different colour morphs of the elusive Asiatic golden cat have been discovered in Northeast India — with the findings being hailed as “an evolutionary puzzle” — as the world’s greatest number of different coloured wild cat species in one area are reported.

The Indian scientists from international conservation charity ZSL (Zoological Society of London) and UCL discovered the colour morphs, during a wide-scale camera trapping study covering both community forests and protected areas across Dibang Valley, Northeast India.

The study, published on 7 June 2019 in the Ecological Society of America’s journal Ecology, aimed to uncover a greater understanding of human-wildlife interactions in the region but discovered a group of entirely different-looking animals on their camera traps — with an inkling they were all the exact same species.

The finding is said to spark more questions than it answers. However, understanding how this remarkable phenomenon takes hold in a population, may help scientists grasp how quickly species can adapt and evolve to changing environments. This would advise scientists of the resilience of the species to climate change or habitat degradation and destruction.

Colour morphs are not classed as different subspecies as they may live in the same area and even interbreed. However, if differences in their behaviour prevented them from interbreeding — this could represent the beginning of the evolutionary process into separate subspecies. A more well-known example of a colour morph is the melanistic (dark coloured) morph (aka black panther) of the common leopard (Panthera pardus).

Within the six colour morphs recorded, an entirely new colour morph was also found in one of the community-owned forests. The now named “tightly-rosetted” morph after the leopard-like rosettes tightly spaced on their gray coat, now sits alongside the already known: cinnamon, melanistic, gray, golden, and ocelot (due to its ocelot-like markings) types.

ZSL scientists believe that the wide variation displayed in the cat’s coats provides them with several ecological benefits. It enables them to occupy different habitats at different elevations — from wet tropical lowland forests to alpine scrubs — and provides camouflage while hunting different prey such as tropical pheasants or Himalayan pika (a small mountain-dwelling rabbit-like mammal).

Colour morphs are thought to arise from random genetic mutations and take hold in the population through natural selection. In this region, scientists suspect that the phenomenon is driven by competition with other big cats such as tigers (Panthera tigris) and clouded leopards (Neofelis nebulosa). Being melanistic in the misty mountains during nocturnal hunts, for example, may mean they are better concealed from their prey; making them more efficient predators.

Dr Sahil Nijhawan, the India-based lead author and British Academy Fellow at ZSL’s Institute of Zoology and UCL said: “According to evolutionary theory, if a colour morph is not beneficial for a species survival — over time, it should die out in the population. The fact that we have so many different colour morphs persisting in Dibang Valley shows there must be some ecological advantages to the variety of colours.

“We now know Dibang Valley hosts the world’s most diverse range of colour morphs of a wild cat species ever reported in one site, but we are only just starting to understand this rare ecological phenomenon. We need more studies that shed light on such unique adaptations and the benefits they provide to species, especially in a world where they must adapt quickly.”

Big cat evolution, videos


This 16 May 2019 video says about itself:

The Ghostly Origins of the Big Cats

All of today’s big cat species evolved less than 11 million years ago and yet their evolutionary history remains an almost total mystery.

But scientists have recently discovered a major clue about the origins of the big cats, one that could provide a whole new starting place for solving this puzzle. Thanks to Ceri Thomas for the excellent Panthera blytheae and Panthera atrox!