A horse is a horse, of course, of course -- except when it isn't

Analysis of ancient DNA reveals a previously unrecognized genus of extinct horses that once roamed North America

Date:  November 28, 2017

Source:  University of California - Santa Cruz

Summary:

Scientists have discovered a previously unrecognized genus of extinct horses that roamed North America during the last ice age. The new findings are based on an analysis of ancient DNA from fossils of the enigmatic 'New World stilt-legged horse' excavated from sites such as Natural Trap Cave in Wyoming, Gypsum Cave in Nevada, and the Klondike goldfields of Canada's Yukon Territory.

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New species of beaked whale confirmed by DNA

DNA analysis identifies eight known specimens of elusive North Pacific species

Date: July 26, 2016

Source: NOAA Fisheries West Coast Region

An international team of scientists who searched out specimens from museums and remote Arctic islands has identified a rare new species of beaked whale that ranges from northern Japan across the Pacific Ocean to Alaska's Aleutian Islands.

Japanese whalers call the enigmatic black whales "karasu," the Japanese word for raven. The new species is darker in color and about two-thirds the size of the more common Baird's beaked whale, but so scarce that even whalers rarely see them.

A DNA analysis of 178 beaked whales from around the Pacific Rim found eight known examples of the new species, the scientists reported today in the journal Marine Mammal Science. The eight included specimens from the Smithsonian Institution and Los Angeles County Museum of Natural History, a skeleton on display in an Alaska high school, and another that puzzled researchers trying to identify it when it washed up on an island in the Bering Sea.

"The challenge in documenting the species was simply locating enough specimens to provide convincing evidence," said Phillip Morin, a research molecular biologist at NOAA Fisheries' Southwest Fisheries Science Center, and lead author of the new study. "Clearly this species is very rare, and reminds us how much we have to learn about the ocean and even some of its largest inhabitants."

An earlier Japanese study had suggested that the black whales, sometimes considered a dwarf form of Baird's beaked whale, might represent a new species. That sent Morin in search of additional genetic samples to definitively answer the question and better understand the range of the elusive species.

He turned first to the Southwest Fisheries Science Center's marine mammal tissue collection, the largest in the world, and found two samples that appeared to represent a new species. One came from a whale found in Alaska's Aleutian Islands in 2004, whose skeleton now hangs on display at Unalaska High School. Then he and his colleagues pursued additional DNA samples from museums, research institutions and Japanese markets where whale meat is sold.

In 2014 scientists found a dead beaked whale on St. George Island, one of the Pribilof Islands in the Bering Sea. When it did not match any known species, they sent samples to Morin. Genetic tests later showed it to be the new species.

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DNA analysis is latest weapon in combating illegal ivory trade

DNA proves conclusively whether ivory comes from African or Asian elephants

A collaborative project between Thailand’s Department of National Parks, the Wildlife and Plant Conservation (DNP) and TRAFFIC, the wildlife trade monitoring network, has trialled forensic DNA examination of ivory products commonly available in local markets to assess their origins.

One hundred and sixty items of small ivory products legally acquired by TRAFFIC researchers, primarily from retail outlets in Bangkok, were subjected to DNA analysis at the DNP’s Wildlife Forensics Crime Unit (WIFOS Laboratory).

The aim of the exercise was to determine whether the ivory products were made from African Elephant or Asian Elephant tusks. 

The forensic results showed that African Elephant ivory accounted for a majority of the items tested. 

Continued ...

Extinct relative helps to reclassify the world's remaining two species of monk seal

Date:

May 14, 2014

Source:

Pensoft Publishers

Summary:

The recently extinct Caribbean monk seal was one of three species of monk seal in the world. Its relationship to the Mediterranean and Hawaiian monk seals, both living but endangered, has never been fully understood. Through DNA analysis and skull comparisons scientists have now clarified the Caribbean species' place on the seal family tree and created a completely new genus.

Continued

Tuna Closely Related to Some of the Strangest Fish in the Sea

Sep. 13, 2013 — Some of the strangest fish in the sea are closely related to dinner table favourites the tunas and mackerels, an international team including Oxford University scientists has found.

Deep sea fish such as the black swallower, with an extendable stomach that enables it to eat fish larger than itself, and manefishes, some sporting spiky fins like a Mohican haircut, are close cousins to mackerels and tuna despite having completely different body shapes and lifestyles.

The team, led by Dr Masaki Miya at Chiba Natural History Museum in Japan, suggests that this extended family of fishes might owe its success today to the devastating extinction that marked the demise of dinosaurs and many other creatures 66 million years ago.

The researchers report in the journal PLOS ONE this week how they combined DNA analysis of over 5,000 modern fish species with fossil evidence to solve the mystery of which species were closest to tunas and mackerels in the fish family tree.

'What was immediately clear from our result is that the extended family of tunas and mackerels is made up of fishes that all look very different from one another, with different ways of life, but which share one key trait: they all dwell in the open ocean,' said Dr Miya of Chiba Natural History Museum. 'This had been suggested before, but we were able to show that many additional groups of fishes inhabiting the open ocean -- called the pelagic realm -- were closely related to one another and to tunas.'

Continued

Cornwall’s chough came from Ireland

Chough ID

July 2012. The red-billed chough stands proud on the Cornish coat of arms but the species became extinct in the Duchy in 1947, denuding Cornwall of one of its most charismatic birds and cultural symbols.

That was until three choughs of unknown origin appeared in Cornwall in 2001 and founded a new breeding population, restoring the ‘Cornish chough' to its historic home and causing great excitement among birdwatchers and conservationists alike.

But where did the three pioneer choughs come from?

Brittany or Wales? - Neither
Until now, they were speculated to have travelled from chough populations in south Wales or Brittany. 

But now some clever genetic detective work has suggested that the Cornish pioneers came from even further afield - Ireland.

Researchers collected moulted feathers that were naturally dropped by the Cornish choughs, and by choughs in other populations across Europe.

DNA analysis
Scientists from the University of Aberdeen then extracted DNA from the feather tips, and compared the DNA sequences of the new Cornish choughs with those of choughs living elsewhere. By far the best match to the Cornish choughs was the Irish choughs, suggesting an unexpected Celtic origin for the new Cornish birds.

Continued:  http://www.wildlifeextra.com/go/news/cornwall-chough.html

Jockeying for Genetic Advantage: DNA Analysis to Evaluate Thoroughbreds

ScienceDaily (May 2, 2012) — When you buy a racehorse, you pays your money and you takes your chances. Top yearlings at Keeneland's 2011 Thoroughbred auction, for instance, averaged nearly $350,000 and hadn't yet raced a step. Odds are that some of them never will. Now, thanks to a Binghamton University biologist, it's possible to boost the odds of getting a winner with a simple genetic test.

ThoroughGen, founded by Steven Tammariello, associate professor of biological sciences, performs genetic testing on horses. The company offers a basic three-gene test for Thoroughbreds at a cost of $175. It screens for one gene that is vital to energy production and two tied to muscle function. Energy production is linked to stamina, muscle twitch to speed. But according to Tammariello, this is just the tip of the iceberg, adding that the horse has some 27,000 genes.

Tammariello carts a portable testing device to sales. All he needs is one strand of hair from the horse's mane and if he receives a sample by 4 p.m., he can give clients results the next morning. But the field is so new that it's still fighting pockets of resistance. Still, for many breeders in the Thoroughbred industry, genetic testing is the future. And it's the future for other breeds of horses as well, not just the racers.

Continued:  http://www.sciencedaily.com/releases/2012/05/120502162520.htm

Snow Leopard Poop Reveals Endangered Cats' Meals

Scientists have gotten their hands dirty in the name of closer study of snow leopards, one of the planet's most endangered big cats.

Because it's notoriously difficult to get their hands on the elusive cats to learn about their movements and habits, the researchers had to settle for the next best thing: their poop. Studying their feces not only allows for DNA analysis, but also offers a glimpse of what the animals like to eat.

Researchers recently analyzed 81 fecal samples found in Mongolia, which revealed that the local snow leopards were eating mostly Siberian ibex, followed by domestic goats and wild sheep.

They also found that nearly 80 percent of the leopards' diet consisted of wild animals, meaning that only about a fifth of the big cats' prey are domestic animals — relatively good news for local farmers.

Snow leopards have been spotted in many places in Central Asia in recent months, thanks to a network of camera traps set up in isolated spots around the region.

In Tajikistan, young snow leopards stole one of the cameras set up to spy on them.

The IUCN, an independent international body that assesses the status of species around the globe, has listed snow leopards as endangered since at least 1986. The big cats, known for their cloudy gray fur and dark spots, are native to Central Asia's high mountains, and their numbers have been decreasing.

Hard numbers are difficult to establish, but it is estimated that between 4,000 and 6,500 snow leopards are left in the wild. 

The study on snow leopard feces is published in the Feb. 29 edition of the open access journal PLoS ONE.

http://news.yahoo.com/snow-leopard-poop-reveals-endangered-cats-meals-174608566.html;_ylt=AkdD8E5Rj2zMAg929FZyCmh4hMgF;_ylu=X3oDMTRhcDZsMDIxBG1pdANUb3BTdG9yeSBTY2llbmNlU0YgQW5pbWFsUGV0c1NTRgRwa2cDM2E5MzI4YzgtNDFmYS0zMzZhLWExMTQtMzRjOWVhZTA2ZWI4BHBvcwMxBHNlYwN0b3Bfc3RvcnkEdmVyA2NmZWU2YzFhLTY0OTEtMTFlMS1hNzVlLWUwZWViMDljOWFkMA--;_ylg=X3oDMTI5ZXFsbjJlBGludGwDdXMEbGFuZwNlbi11cwRwc3RhaWQDBHBzdGNhdANzY2llbmNlfGFuaW1hbCAtIHBldHMEcHQDc2VjdGlvbnMEdGVzdAM-;_ylv=3

Oetzi the Iceman's nuclear genome gives new insights

By Jason PalmerScience and technology reporter, BBC News

New clues have emerged in what could be described as the world's oldest murder case: that of Oetzi the "Iceman", whose 5,300-year-old body was discovered frozen in the Italian Alps in 1991.

Oetzi's full genome has now been reported in Nature Communications.

It reveals that he had brown eyes, "O" blood type, was lactose intolerant, and was predisposed to heart disease.

They also show him to be the first documented case of infection by a Lyme disease bacterium.

Analysis of series of anomalies in the Iceman's DNA also revealed him to be more closely related to modern inhabitants of Corsica and Sardinia than to populations in the Alps, where he was unearthed.

'Really exciting'

The study reveals the fuller genetic picture as laid out in the nuclei of Oetzi's cells.

This nuclear DNA is both rarer and typically less well-preserved than the DNA within mitochondria, the cell's "power plants", which also contain DNA.

Continued:  http://www.bbc.co.uk/news/science-environment-17191398

Stroud deer carcass tested for 'big cat activity'

DNA tests for "big cat activity" are being carried out on a roe deer carcass found near Stroud in Gloucestershire.

Swabs were taken from the wounds of the deer by experts who visited Woodchester Park to examine the evidence.

The carcass was seen and photographed by a local walker at the National Trust-owned countryside estate.

A National Trust spokesman said the deer's injuries and way the carcass had been consumed were "thought to be highly indicative of big cat activity".

The DNA samples were taken by a professor from the School of Life Sciences at the University of Warwick and the results are expected later this month.

'Occasional sightings'

David Armstrong, the National Trust's head ranger for the Gloucestershire countryside, said the deer carcass was found near an area of beech woodland sloping down to pastures.

"There are some very occasional sightings of big cats in the Cotswolds but they have wide territories, so are rarely present in one particular spot for long," he added.

"We'd be interested to hear of any more sightings at Woodchester."

Gloucestershire big cat expert, Rick Minter, said it was very helpful to have a forensic study of the deer carcass done "so we can learn about the subject".

"Although people occasionally report a possible big cat from a distance, close up encounters with such cats are rare," he said.

"Their hearing and movement are exceptional, which helps them avoid close contact with people."

Read more at: http://www.bbc.co.uk/news/uk-england-gloucestershire-16516500

DNA in a Cup of Water Reveals Lake Denizens

To monitor the biodiversity of a freshwater habitat, you could camp out by the water and count the rare wildlife. Or you could just scoop up a cup of water. A new Dutch study has found that the DNA traces in a small sample of a body of water can reveal the species that live in it. The work is in the journal Molecular Ecology. [Philip Francis Thomsen et al., "Monitoring endangered freshwater biodiversity using environmental DNA"]


As animals swim through a lake, they leave behind traces of DNA. The more individuals of a particular species, the more DNA of that species will be shed. And be available to be measured.

The researchers tested about 100 European lakes and streams, comparing the DNA evidence to traditional fauna observations. And the small-sample technique enabled them to correctly identify the species and the sizes of their populations.

Measuring biodiversity is an important part of protecting endangered species. This quick and easy method of snagging a water sample, which can be tested at a lab miles away from the site, could refresh the process of species monitoring.

—Sophie Bushwick

http://www.scientificamerican.com/podcast/episode.cfm?id=dna-in-a-cup-of-water-reveals-lake-11-12-19

Okla. Officials Find Doughnuts Help Trap Bears

COOKSON, Okla. — Oklahoma wildlife officials say nothing traps a black bear quite like a doughnut.


Wildlife officers are studying the growing black bear population in the eastern part of the state, and they say they've had the best success in trapping the animals when they use pastries as bait.

Craig Endicott of the Wildlife Department told Tulsa television station KOTV the agency usually finds 300-pound male bears and 200-pound females in its traps. But on a recent day, a 50-pound cub got to the doughnut first.

The bears are tagged and researchers take fur and tissue samples for DNA analysis. Some adult bears get tracking collars.

Researchers also are setting up about 200 bait stations equipped with hair snares. DNA from the hair will help map bears' movement.
http://www.huffingtonpost.com/2011/07/23/doughnuts-trap-bears_n_907767.html

Unknown Animals Nearly Invisible Yet There

Individuals of the bryozoan Alcyonidium diaphanum
stretch out their tentacles to filter food particles
out of the water. (Credit: Judith Fuchs.)

ScienceDaily (Mar. 22, 2011) — Bryozoans (moss animals) are a group of aquatic invertebrates that are found in great variety throughout the world, with well over 100 species in Sweden alone. Yet little is known about them. Researchers at the University of Gothenburg have now studied Swedish bryozoan species using DNA techniques.

"There are currently over 6 000 known species of Bryozoa. Earlier studies were based on visible characteristics of these animals, which is not sufficient to decide how the species are related to each other. To understand the evolution of bryozoans and how they are related to other animals, it is necessary to use molecular data, that's to say DNA," says Judith Fuchs of the Department of Zoology at the University of Gothenburg.

When Bryozoa were discovered in the 16th century, they were regarded as plants. Later on they were found to have a nervous system, muscles and an intestinal system and were classified as animals. On their own, bryozoans are barely visible to the naked eye, but like coral animals all bryozoans build colonies that reach several centimetres in size and some species build colonies of over 30cm.

In her thesis, Fuchs has studied the evolution and relationships of Bryozoa using molecular data (DNA) from more than 30 bryozoan species, most collected in Sweden. The results show that this animal group developed from a common ancestor that probably lived in the sea. Two groups of Bryozoa evolved from this common ancestor: a group that stayed in the marine environment and another that evolved in freshwater. The DNA studies of the larval stage of Bryozoa can also contribute to a better understanding of the evolution of life cycles and larval stages of other multicellular animals.

Together with her supervisor, Matthias Obst, over a period of four years she has also taken part in the marine inventory of the Swedish Species Project along the west coast of Sweden. The collection of all marine bottom-living animals is based on more than 500 samples from 400 locations.

"We found as many as 120 marine bryozoan species in our waters, and many of them had not been previously known in Sweden. We also found a completely new species of Bryozoa. This is a very small bryozoan with characteristic spikes on its surface, which I have described in my thesis."

To date, 45 per cent of the bryozoans collected in the inventory have been determined.

"Sweden has a very rich bryozoan fauna. On your next trip to the beach you might perhaps take a closer look at seaweed or pebbles. If you see a white covering with small holes in it, you have found a bryozoan colony for yourself."

There are currently over 6 000 known species of Bryozoa. Earlier studies were based on visible characteristics of these animals, which is not sufficient to decide how the species are related to each other. To understand the evolution of bryozoans and how they are related to other animals, it is necessary to use molecular data, that's to say DNA," says Judith Fuchs of the Department of Zoology at the University of Gothenburg.

http://www.sciencedaily.com/releases/2011/03/110322105740.htm

Experts DNA test England's adders to help halt decline

28 March 2011

Ecologists are running DNA tests on adders to check their genetic diversity amid fears the UK's only venomous snake is vanishing from the wild.

A recent study found that numbers of the reptile had declined since 2007.

Conservationists believe inbreeding in small, isolated populations could lead to a further decrease in numbers.

Experts from Natural England, the Zoological Society of London and Oxford University are taking swabs from the reptiles at 16 sites across England.

Ecologist Nigel Hand has already carried out health checks and collected DNA samples from five snakes at a Surrey Wildlife Trust site and 27 adders from an area in Norfolk.

Once captured, the reptiles are placed in a plastic tube to measure their length and protect the handler from their bite.

A swab is taken and they are marked before they are released back into the wild.

The DNA is then analysed to see whether larger or smaller populations have different levels of genetic variety.

Jim Foster, of Natural England, said: "With around a third of adder populations now restricted to isolated pockets of habitat, and with only a handful of snakes per sites, they could be especially vulnerable."

It is estimated that there are 1,000 populations of adder in the country with some groups made up of fewer than 10 adults.

Mr Foster said the tests would also help them understand why some adders had been found with abnormalities including malformed scales and missing eyes.

He added: "In the longer term, the last resort option is whether we should move animals between populations, artificially encouraging them to mix."

http://www.bbc.co.uk/news/uk-england-12878563

Species ID challenged by DNA analysis

Identifying species: looks are no longer enough. Increasingly common problem for 21st century biologists

November 2010: What happens when a species isn't the one it looks like? It is a problem being faced increasingly by biologists. Although Linnaean taxonomy is still a cornerstone of biology, modern DNA techniques have erased many of the established boundaries between species, making it far more difficult, in practice, to know exactly what you are looking at.

A researcher from Sweden's University of Gothenburg is now highlighting the potential pitfalls this can cause. ‘If you can't recognise a species by looking at it, this can have serious consequences,' says Emma Vodoti from university's Department of Zoology. ‘For example, there is a species of leech that is widely used in medical studies, and it was discovered recently that sometimes a leech was being used that looks the same but has a different genetic make-up. This naturally has an effect on the results of the studies conducted. All work based on having to be able to identify species may have to change.'


Three hundred and fifty years after Linnaeus created his system for organising and categorising species of plants and animals, the system is being pulled apart. Newly discovered organisms are still categorised and named in line with his system, but there is a big difference between species described before and after the discovery of DNA. Until the 1980s, scientists had to rely entirely on appearance, anatomy and other characteristics, such as a bird's song. Since then, genetic patterns have also been taken into account when identifying new species.

Genetic studies have erased many established boundaries between species
'Ironically, these genetic studies have erased many of the established boundaries between species and even disproved the existence of previously described species that have turned out not to be related. Attempts have been made to establish universal boundaries between species by quantifying how much DNA needs to be different between two organisms in order for them to be viewed as separate species, but this doesn't always work.'

In her thesis, Vodoti looks at the practical problems with species identification today, after having studied the relationship between the genetic relatedness and the appearance and geographical distribution of various sea creatures. The common horse mussel Modiolus modiolus found in the Atlantic and on the west coast of Sweden turns out to be totally different genetically from the one found on the Pacific coast of the USA, despite looking identical. Nemertean worms may have similarities in appearance but turn out to consist of a hotchpotch of different species, more or less independent of looks. Nemerteans include worms just a few millimetres in length to one of the world's longest creatures, Lineus longissimus, which can grow up to 15 metres.

‘It's probably impossible to find a universal way of defining, identifying and delimiting species,' says Vodoti. ‘My thesis shows that there is a need for individual assessment on a case-by-case basis when identifying species, taking account of both appearance and genes.'

http://www.wildlifeextra.com/go/news/species-identification.html