A previously undescribed, cold-loving fungus has been linked to white-nose syndrome, a condition associated with the deaths of over 100,000 hibernating bats in the northeastern United States.  The findings are published in this week’s issue of Science.

The probable cause of these bat deaths has puzzled researchers and resource managers urgently trying to understand why the bats were dying in such unprecedented numbers.  Since the winter of 2006-07, bat declines at many surveyed hibernation caves exceeded 75 percent.

The fungus – a white, powdery-looking organism – is commonly found on the muzzles, ears and wings of afflicted dead and dying bats, though researchers have not yet determined that it is the only factor causing bats to die.  Most of the bats are also emaciated, and some of them leave their hibernacula – winter caves where they hibernate – to seek food that they will not find in winter.

USGS microbiologist and lead author David Blehert isolated the fungus in April 2008, and identified it as a member of the group Geomyces.  The research was conducted by U.S. Geological Survey scientists in collaboration with the New York State Department of Environmental Conservation, the New York State Department of Health, and others.

Geomyces are a group of fungi that live in soil, water and air and are capable of growing and reproducing at refrigerator-level temperatures.  Although the new fungus is a close genetic relative of known Geomyces, it does not look like a typical member of this group under the microscope.  “We found that this fungus had colonized the skin of 90 percent of the bats we analyzed from all the states affected by white-nose syndrome,” Blehert said.

Researchers don’t know yet if white-nose syndrome emerged because this newly identified fungus was introduced into caves or whether the fungus already existed in caves and began infecting bats after they were already weakened from some other cause.  “This fungus may have been recently introduced to bat hibernation caves and, if so, human and animal movements among these caves are causes that need to be considered,”says Blehert.  “Data show the occurrence of white-nose syndrome radiating outward from the site of its first appearance, and genetic identity among fungal isolates from distant caves argues for a recent introduction of this microbe.  Before the identification of white-nose syndrome, mass mortality events in bats as a result of disease were very rare.”

WNS was first seen in New York during the winter of 2006.  Since then, populations of cave-hibernating bats have been drastically declining in Connecticut, Maine, New York and Vermont.  Affected species include little brown bats, northern bats, tricolored bats, Indiana bats, small-footed myotis and big brown bats.

Worldwide, bats play critical ecological roles in insect control, plant pollination and seed dissemination, and the decline of North American bat populations would likely have far-reaching ecological consequences, the researchers wrote.  They noted that parallels can be drawn between the threat posed by WNS and chytridiomycosis, a lethal fungal skin infection that has recently caused precipitous global amphibian population declines.

“Right now,” said Blehert, “we are uncertain about the long-term effects of white-nose syndrome on North American bats, but we are quite concerned about future effects on bat populations wherever environmental conditions are conducive to growth of the fungus.  To manage and perhaps halt this disease, we have to first better understand it.”

Putting together the Who’s Who of bats, bears, beaked whales and all of Earth’s other known mammals was a gigantic task ably assisted by a Field Museum scientific team with access to one of the planet’s most extensive and diverse mammal collections.

A team headed by the IUCN (International Union for Conservation of Nature) is releasing its comprehensive status on the world’s mammals, including assessments of diversity, threat and knowledge of the creatures.  The Oct. 10 issue of Science will feature the results of the study.

A major reason for doing the assessment is to get a picture of how mammals on our planet are doing.  The news isn’t good.  One in four appears to be threatened with extinction and half the known species appear to be losing rather than gaining population.  For land mammals, destruction or degradation of their habitats is the biggest threat, while marine mammals suffer more from accident deaths stemming from fishing practices and pollution.

Field Museum Provides “Gold Standard” for Study

The comprehensive assessment, which covers 5,487 wild mammal species, represents five years of work by more than 1,700 scientists from 130 countries and is the first update on mammals since 1996.

Among those scientists were seven affiliated with Chicago’s Field Museum who helped colleagues from around the world by accessing the museum’s data base of 200,000 records that document the existence and relationships of thousands of species.  Field Museum zoologists have active survey programs and expertise in Asia, Africa, and the Americas; their recent collections inform and authenticate the status report.  Just this summer, Field zoologists Bill Stanley, Steve Goodman, and Julian Kerbis Peterhans returned to Chicago with important new collections from Tanzania, Madagascar, and the Congo Basin.

“The Field Museum provides the gold standard for biodiversity studies,” said Lawrence Heaney, a Field mammal curator and co-author of the study.  “Our records are based on research collections that are permanent and are constantly updated.”

Scientists Discover and Describe New Species

Besides information about mammals gathered over the 115 years that the Field Museum’s collection has existed, scientists have access to specimens that can provide genetic material and anatomic information to help clarify whether animals are members of different species, are part of a subspecies, or fall into some other category.

In the current mammal update from the IUCN, such questions loomed often as scientists raised the number of recognized species by nearly 20 percent over what it had been just 14 years ago.  This included 349 newly described species and 512 others that saw their status elevated to full-fledged species from some lesser category.

An example is the clouded leopard in Southeastern Asia, which was recently split into two separate species, with one living on the Southeast Asian continent and another native to the island of Borneo.

“Scientists are discovering 25 new mammal species a year,” said Bruce Patterson, a Field mammal curator and also a study co-author.  “We’re still describing them.  These aren’t beetles or flies.  They are our fellow vertebrates living on this planet.  And we don’t know them all.”

Storing thousands of samples in its collection, the Field can provide scientists access to specimen that may be difficult to find or even extinct for analysis with the latest technology.  Analysis of DNA is now possible for animals that lived and died before scientists even knew that DNA existed.

“We also can do isotopic analysis and study anatomy using a scanning electron microscope,” said Heaney, again applying techniques that were unknown at the time when the collection samples were taken.

Although many mammal species are endangered, the Field Museum’s Patterson found at least one upbeat message in the assessment project.  “It was possible to marshal this much expertise and information and focus it on critical environmental issues,” he said, “and it was all privately funded.  That is impressive.”

One of the smallest seals – the Caspian has joined a growing list of mammal species in danger of extinction.

Scientists from the University of Leeds together with international partners have documented the disastrous decline of the seal a species found only in the land-locked waters of the Caspian Sea – in a series of surveys which reveal a 90 per cent drop in numbers in the last 100 years.

The research findings have prompted the International Union for Conservation of Nature (IUCN) to move the Caspian seal from the Vulnerable category to Endangered on its official IUCN Red List of Threatened Species, announced today in Barcelona [06 October 2008].

Dr Simon Goodman of Leeds’ Faculty of Biological Sciences says: “Each female has just one pup a year, so with numbers at such a low levels, every fertile female that dies is a nail in the coffin of the species.  We’re hoping that the seal’s change in Red List status will help raise awareness about their plight, and the many important conservation issues facing the whole Caspian ecosystem.”

Commercial hunting, habitat degradation, disease, pollution and drowning in fishing nets have caused the population of the seal collapse from more than 1 million at the start of the 20th century to around 100,000 today.

Results from surveys conducted in 2005 and 2006, published recently in the scientific journal Ambio, show that in 2006 there were only 17,000 breeding females, barely enough to keep the population viable, given the low survival rate of pups.

Moreover, new results from surveys conducted by the team in 2007 and 2008, show that since 2005 the number of pups being born has plummeted by a catastrophic further 60 per cent to just 6,000-7,000, and the number of adults seen on the breeding grounds of the winter ice-field is down by a third on 2005.

With commercial hunters from Dagestan in the Russian Federation killing more than 8,000 pups in recent years, the team is urging the governments of the Caspian countries to instate a ban on hunting as the first step in avoiding further declines.  “Without a suite of conservation measures there is a very high risk the species will become extinct, and possibly within our lifetime,” says Dr Goodman.

The team is using its latest figures and ongoing research to develop a conservation action plan, which will prioritise a ban on hunting the seal and establish protected areas with the countries bordering the Caspian Sea.  The basic plan has been completed, but the main recommendations are yet to be fully implemented by the countries of the region.

Dr Susan Wilson, a consultant in seal conservation biology and one of the authors of the Ambio paper says: “Although there are no easy fixes to the problems facing Caspian seals, we hope to get some concrete measures in place over the next year, particularly in Kazakhstan where the government has been quick to recognise the need for urgent action.”

From majestic African elephants to tiny and often unappreciated rodents, mammals on Earth are in a state of crisis.  One in four mammal species on Earth is being pushed to extinction, according to the Global Mammal Assessment, the most comprehensive assessment of the world’s mammals.

Writing in the October 10 issue of Science, (”The Status of the World’s Land and Marine Mammals: Diversity, Threat, and Knowledge”) and unveiling a “Red List” of endangered mammal species (at the International Union for Conservation of Nature World Conservation Congress in Barcelona, Spain), the researchers who worked on the exhaustive study say that from 25 percent to 36 percent of species may be in danger of extinction.

“It is frightening that after millions and millions of years of evolution that have given rise to the biodiversity of mammals we are perched on a crisis where 25 percent of species are threatened with being lost forever,” said Andrew Smith, an Arizona State University professor who played a key role in the mammalian assessment.  Smith and his research assistant, Charlotte Johnson, are two of the 103 authors of the Science paper.

The Global Mammal Assessment was conducted by more than 1,800 scientists from more than 130 countries working under the auspices of the International Union for Conservation of Nature.  It was made possible by the volunteer help of IUCN Species Survival Commission’s specialist groups and collaborations between top institutions and universities, including Arizona State University, Texas A&M University, University of Virginia, Conservation International, Sapienza Università di Roma and the Zoological Society of London.

The mammal assessment is the first comprehensive look at the health of terrestrial and marine mammals across the globe.  It is a companion assessment to similar documentation of the world’s amphibians, released four years ago by IUCN.

“Mammals are important because they play key roles in ecosystems and provide important benefits to humans,” Smith explained.  “If you lose a mammal, you often are in danger of losing many other species.”

The assessment shows that at least 1,141 of the 5,487 mammals on Earth are known to be threatened with extinction.  At least 76 mammals have become extinct since 1500.  The real situation could be much worse as 836 mammals are listed as “data deficient.”

The culprits driving this precarious position include habitat loss and over exploitation for terrestrial mammals, and pollution, global warming and over exploitation for marine mammals, Smith said.

“Within our lifetime hundreds of species could be lost as a result of our own actions, a frightening sign of what is happening to the ecosystems where they live,” said Julia Marton-Lefevre, IUCN director general in announcing the Red List.  “We must now set clear targets for the future to reverse this trend to ensure that our enduring legacy is not to wipe out many of our closest relatives.”

In the Science article, which includes the contributions of more than 1,700 scientists, the researchers state that 188 mammals are in the highest threat category of “critically endangered,” including the Iberian Lynx (Lynx pardinus), which has a population of just 84 to 143 adults and has continued to decline due to a shortage of its primary prey, the European Rabbit (Oryctolagus cuniculus).

China’s Père David’s Deer (Elaphurus davidianus), is listed as “extinct in the wild.”  However, the captive and semi-captive populations have increased in recent years and it is possible that truly wild populations could be re-established soon.  It may be too late, however, to save the additional 29 species that have been flagged as “critically endangered, possibly extinct” including Cuba’s Little Earth Hutia (Mesocapromys sanfelipensis), which has not been seen in nearly 40 years.

Nearly 450 mammals have been listed as “endangered,” including the Tasmanian Devil (Sarcophilus harrisii), after its global population declined by more than 60 percent in the last 10 years due to a fatal infectious facial cancer.  The Fishing Cat (Prionailurus viverrinus), found in Southeast Asia, was listed as endangered due to habitat loss in wetlands.  Similarly, status of the Caspian Seal (Pusa caspica) was moved to endangered.  Its population has declined by 90 percent in the last 100 years due to unsustainable hunting and habitat degradation.

Habitat loss and degradation affect 40 percent of the world’s mammals.  It is most extreme in Central and South America, west, east and central Africa, Madagascar, and in south and Southeast Asia.  Over harvesting is wiping out larger mammals, especially in Southeast Asia, but also in parts of Africa and South America.

The Grey-faced Sengi or Elephant-shrew (Rhynchocyon udzungwensis) is only known from two forests in the Udzungwa Mountains of Tanzania, both of which are protected but vulnerable to fires.  The species was first described this year and has been placed in the vulnerable category.

In order to improve the current state of these mammals, Smith suggests a few actions that could help immediately.

“Curtail the trade of endangered species,” he said.  “It would do an amazing amount of good for stabilizing the situation in Southeast Asia, which is a biodiversity hot spot.  There also is so much needless habitat loss.  Trees from too many lush tropical forests end up as coffee tables or in high-end furniture.”

Conservation’s role

“Our results paint a bleak picture of the global status of mammals worldwide,” the authors of the Science article state.  “Yet, more than simply reporting on the depressing status of the world’s mammals, these Red List data can and should be used to inform strategies for addressing this crisis, for example, to identify priority species and areas for conservation.

“Further, these data can be used to indicate trends in conservation status over time,” they added.  “Despite the general deterioration in the status of mammals, our data also show that species recoveries are possible through targeted conservation efforts.”

For example, the Black-footed Ferret (Mustela nigripes) moved from extinct in the wild to endangered after a successful reintroduction by the U.S. Fish and Wildlife Service into eight western states and Mexico from 1991-2008.  Similarly, the Wild Horse (Equus ferus) moved from extinct in the wild in 1996 to critically endangered this year after successful reintroductions started in Mongolia in the early 1990s.

The African Elephant (Loxodonta africana) moved from vulnerable to near threatened, although its status varies considerably across its range.  The move reflects the recent and ongoing population increases in major populations in southern and eastern Africa.  These increases are big enough to outweigh any decreases that may be taking place elsewhere.

“This work sets a benchmark for us to understand what is happening with biodiversity of mammals worldwide and provides a platform from which all future conservation efforts can be measured,” said Smith, who initiated the database that was used to inventory the world’s mammals.  “This effort hopefully will spur greater attention on the conservation of mammals and the habitats they occupy, for the benefit of all biodiversity.”

In the wild, mammalian coat color is essential for camouflage and plays a role in social behavior.  Coat color also strongly influences the animals we choose to breed both as livestock and as pets.  Understanding the genetic determinants of coat color in livestock species such as sheep, specifically bred for their coat color, is critical for improving efficient selection of the desired trait.

Classical genetics has associated alternative forms, or alleles, of the agouti signaling protein gene (ASIP) with coat color variation in a number of mammals including mice, rats, dogs, cats, pigs, and sheep.  However, most research has been focused on the mouse, with little understood about the genetic basis for coat color in economically important livestock species such as sheep.

The wild-type coat color of sheep is typically dark-bodied with a pale belly, however sheep raisers have strongly selected for a uniformly white coat domestic sheep.  A problem for the sheep industry is a recessive black “non-agouti” allele of the ASIP gene carried by white sheep that cannot be distinguished within the flock, resulting in black coat color at a low, but persistent frequency.  Determining the exact genetic differences at the ASIP locus could assist in efficient selection for white coat color.

Scientists at the CSIRO Queensland Bioscience Precinct in Australia have now taken this step and identified the molecular mechanisms underlying white and black coat color in domestic sheep.  The researchers investigated the genetic architecture of the ASIP gene in several sheep breeds by sequencing the ASIP locus and measuring gene expression.  “Surprisingly what we found was in fact that the genetic cause of domestic white and black sheep involves a novel tandem duplication affecting the ovine agouti gene and two other neighboring genes, AHCY and ITCH,” explains Dr. Belinda Norris, lead author of the study.  “We discovered a novel mechanism in which the dominant white sheep is caused by the ubiquitous expression of a duplicated agouti coding sequence located immediately downstream of a duplicated ITCH gene promoter region.”  It was found that recessive black sheep harbor only poorly expressed non-duplicated agouti alleles, likely a result of a defective single-copy ancestral agouti gene promoter.  The researchers also studied the ASIP locus in Barbary sheep, an ancient species exhibiting a tan body and pale belly.  They confirmed in this ancient sheep that expression of a single-copy agouti gene determines coat color patterning, similarly to findings previously described in mice and pigs.

Norris notes that this work will aid in the development of gene copy number detection and analysis methods in the mapping and association of heritable traits in livestock animals.  For sheep raisers, this could ultimately mean a genetic test that would identify carriers of the black non-agouti allele.  Furthermore, these findings will help to unravel the events leading to the domestication of sheep, and future work may be able to pinpoint when the dominant Agouti mutation occurred, and whether it occurred as single or multiple events.