Koala epidemic provides lesson in how DNA protects itself from viruses

Date: October 10, 2019

Source: Cell Press

In animals, infections are fought by the immune system. Studies on an unusual virus infecting wild koalas, by a team of researchers from the University of Massachusetts Medical School and the University of Queensland, reveal a new form of "genome immunity." The study appears October 10 in the journal Cell.

earRetroviruses, including pathogens like HIV, incorporate into the chromosomes of host cells as part of their infectious lifecycle. Retroviruses don't usually infect the germ cells that produce sperm and eggs and are therefore usually not passed from generation to generation, but this has happened several times during evolution. Out of the entire 3 billion nucleotides of the human genome, only 1.5% of the sequence forms the 20,000 genes that code for proteins -- and 8% of the human genome comes from fragments of viruses. These pathogen invasions of the genome have sometimes been beneficial. For example, a gene "co-opted" from a virus is required for formation of the placenta in all mammals, including humans.

Read on

Collecting polar bear footprints to map family trees

By Anne-Marie Bullock Producer, Costing The Earth

Scientists from Sweden are using DNA in the environment to track Alaskan polar bears.

The technique which uses DNA from traces of cells left behind by the bears has been described as game changing for polar bear research.

It's less intrusive than other techniques and could help give a clearer picture of population sizes.

Environmental DNA (eDNA) comes from traces of biological tissue such as skin and mucus in the surroundings.

Scientists and now conservationists are increasingly using such samples to sequence genetic information and identify which species are present in a particular habitat.

It's often used to test for invasive species or as evidence of which animals might need more protection.

In another application of the technique, geneticist Dr Micaela Hellström from the Aquabiota laboratory in Sweden worked with WWF Alaska and the Department of Wildlife Management in Utqiagvik (formerly Barrow) to collect snow from the pawprints of polar bears.

They tested the technique on polar bears in parks in Sweden and Finland.

Continued

Prehistoric puma feces reveals oldest parasite DNA ever recorded

The oldest parasite DNA ever recorded has been found in the ancient, desiccated feces of a puma

Date: August 27, 2019

Source: Cambridge University Press

A team of Argentinian scientists from the National Council of Scientific and Technical Research (CONICET) made the discovery after studying a coprolite taken from a rock-shelter in the country's mountainous Catamarca Province, where the remains of now extinct megafauna have previously been recovered in stratigraphic excavations.

Radiocarbon dating revealed that the coprolite and thus the parasitic roundworm eggs preserved inside dated back to between 16,570 and 17,000 years ago, towards the end of the last Ice Age.

At that time, the area around the shelter at Peñas de las Trampas in the southern Andean Puna was thought to have been wetter than today, making it a suitable habitat for megafauna like giant ground sloths, and also smaller herbivores like American horses and South American camelids which the pumas may have preyed on.

Ancient mitochondrial DNA analysis was used to confirm the coprolite came from a Puma (Puma concolor) and that the eggs belonged to Toxascaris leonina, a species of roundworm still commonly found in the digestive systems of modern day cats, dogs and foxes.

The study, published in the journal Parasitology, explains that the extremely dry, cold and salty conditions which took hold at the Peñas de las Trampas site since the onset of the Holocene would have helped to reduce the breakdown of the DNA, allowing it to be preserved.

Read on 

DNA of wolf declared extinct in wild lives on in Texas pack

January 13, 2019 by David Warren

In this June 13, 2017, file photo, the parents of this 7-week old red wolf pup keep an eye on their offspring at the Museum of Life and Science in Durham, N.C. A pack of wild canines found frolicking near the beaches of the Texas Gulf Coast …more

Researchers say a pack of wild canines found frolicking near the beaches of the Texas Gulf Coast carries a substantial amount of red wolf genes, a surprising discovery because the animal was declared extinct in the wild nearly 40 years ago.

The finding has led wildlife biologists and others to develop a new understanding that the red wolf DNA is remarkably resilient after decades of human hunting, loss of habitat and other factors had led the animal to near decimation.

"Overall, it's incredibly rare to rediscover animals in a region where they were thought to be extinct and it's even more exciting to show that a piece of an endangered genome has been preserved in the wild," said Elizabeth Heppenheimer, a Princeton University biologist involved in the research on the pack found on Galveston Island in Texas. The work of the Princeton team was published in the scientific journal Genes.

The genetic analysis found that the Galveston canines appear to be a hybrid of red wolf and coyote, but Heppenheimer cautions that without additional testing, it's difficult to label the animal.

Ron Sutherland, a North Carolina-based conservation scientist with the Wildlands Network, said it's exciting to have found "this unique and fascinating medium-sized wolf." The survival of the red wolf genes "without much help from us for the last 40 years is wonderful news," said Sutherland, who was not involved in the Princeton study.

The discovery coincides with similar DNA findings in wild canines in southwestern Louisiana and bolsters the hopes of conservationists dismayed by the dwindling number of red wolves in North Carolina that comprised the only known pack in the wild.

The red wolf, which tops out at about 80 pounds (49 kilograms), was once common across a vast region extending from Texas to the south, into the Southeast and up into the Northeast. It was federally classified as endangered in 1967 and declared extinct in the wild in 1980. The U.S. Fish and Wildlife Service in the 1970s captured a remnant population in Texas and Louisiana that eventually led to a successful captive breeding program. Those canines in 1986 became part of the experimental wild population in North Carolina. That group has been declining since peaking at an estimated 120 to 130 wolves in 2006. A federal report in April said only about 40 remained.

An additional 200 red wolves live in zoos and wildlife facilities as part of captive breeding programs.

Read more at: 

Mammoth DNA found in Cambodia market items

January 4, 2019

Scientists tackling the illegal trade in elephant ivory got more than they bargained for when they found woolly mammoth DNA in trinkets on sale in Cambodia, they revealed Friday.

"It was a surprise for us to find trinkets made from woolly mammoth ivory in circulation, especially so early into our testing and in a tropical country like Cambodia," said Alex Ball, manager at the WildGenes laboratory, a wildlife conservation charity based at Edinburgh Zoo.

"It is very hard to say what the implications of this finding are for existing elephant populations, however we plan to continue our research and will use genetics to work out where it has come from."

The giant mammals have been extinct for around 10,000 years and are not covered by international agreements on endangered species.

WildGenes has been using genetic data to tackle wildlife crime by determining the origin of ivory finding its way to the marketplace.

Read more at: 

Primates of the Caribbean: Ancient DNA reveals history of mystery monkey

Weird evolution revealed in now-extinct monkey which inhabited Jamaica until a few hundred years ago

Date:  November 12, 2018

Source:  Zoological Society of London

Analysis of ancient DNA of a mysterious extinct monkey named Xenothrix -- which displays bizarre body characteristics very different to any living monkey -- has revealed that it was in fact most closely related to South America's titi monkeys (Callicebinae). Having made their way overwater to Jamaica, probably on floating vegetation, their bones reveal they subsequently underwent remarkable evolutionary change.

The research published today in Proceedings of the National Academy of Sciences (12 November 2018) and carried out by a team of experts from international conservation charity ZSL (Zoological Society of London), London's Natural History Museum (NHM), and the American Museum of Natural History in New York, also reveals that monkeys must have colonised the Caribbean islands more than once. The study reports an incredible discovery of how the unusual ecology of islands can dramatically influence animal evolution.

Xenothrix, unlike any other monkey in the world, was a slow-moving tree-dweller with relatively few teeth, and leg bones somewhat like a rodent's. Its unusual appearance has made it difficult for scientists to work out what it was related to and how it evolved. However, the scientific team have successfully extracted the first ever ancient DNA from an extinct Caribbean primate -- uncovered from bones excavated in a Jamaican cave and providing important new evolutionary insights.

Continued 

DNA project to decode 'all complex life' on Earth

By Victoria GillScience correspondent, BBC News

1 November 2018 

A mission to sequence the genome of every known animal, plant, fungus and protozoan - a group of single-celled organisms - is underway.

The Earth BioGenome Project (EBP) has been described as a "moonshot for biology".

A key aim is to use the information in efforts to conserve threatened species.

Scientists say clues about how species adapt to environmental change could be hidden in their DNA code.

As part of the project, the Wellcome Sanger Institute, which played a major part in the human genome project, has committed to sequencing the genomes of all 66,000 UK species.

Dr Jim Smith, director of science at the Wellcome Trust described the mission as timely, adding that it was "incumbent upon human beings to raise awareness of biodiversity".

Continued

Bale monkeys living in different areas have very different DNA

Date:  July 9, 2018

Source:  BioMed Central

Summary:

Bale monkey's that live in continuous bamboo forests have different mitochondrial DNA to Bale monkeys living in fragmented forests, according to a study published in the open access journal, BMC Evolutionary Biology.

Dr Addisu Mekonnen and colleagues at The University of Oslo, Norway, looked at the genetic diversity of the two populations of Bale monkeys. Analysis of mitochondrial DNA suggested strong genetic differences between the Bale monkeys who lived in continuous forests or fragmented forests. The researchers found that the populations of Bale monkeys were so different from each other that the Bale monkeys from fragmented forests were more similar to vervets and grivets than Bale monkeys from continuous forests.

Dr Addisu Mekonnen, corresponding author of the study, explains: "Remarkably, our phylogenetic analysis showed that Bale monkeys in fragmented forests are more closely related to their sister species, vervets and grivets, than Bale Monkeys from continuous forests. This suggests that hybridization had taken place between Bale monkeys from fragmented forests and vervet and grivet monkeys, but not with bale monkeys in continuous forests. This hybridization could be due to habitat fragmentation and close proximity to similar monkeys."

Read more  

The Oldest DNA from Giant Pandas Was Just Discovered in a Cave in China

By Rafi Letzter, Staff Writer | June 18, 2018 05:28pm ET

Scientists in China found a fossil from a giant panda that lived 22,000 years ago. Until they excavated the fossil, reassembled it and analyzed its mitochondrial DNA, biologists had no idea this panda lineage even existed.

It's now considered the oldest DNA from giant pandas to date, the researchers said.

The panda fossil turned up in Cizhutuo Cave in the Guangxi region of China. No pandas live there today, the researchers from the Chinese Academy of Sciences wrote in a paper published today (June 18) in the journal Current Biology. An unexpected giant-panda fossil find was exciting, they wrote, because researchers don't have a good sense of the history of the 2,500 giant pandas alive in the world today. Researchers know that 20 million years ago, the current batch of living giant pandas split from all other bears. They don't know much about their lineage since.

Continued  

Cockroaches' DNA reveals why they thrive in filthy places

By identifying which genes are key to the bugs’ survival, scientists hope to find ways to better control them

Ian SampleScience editor

Tue 20 Mar 2018 16.00 GMTLast modified on Tue 20 Mar 2018 16.01 GMT

The secrets of the cockroach’s ability to thrive in some of the most disgusting places on Earth have been discovered in its DNA.

The American cockroach spread around the world after it was introduced to the US from Africa in the early 16th century. Its population exploded as the insects made themselves at home in the dark and moist corners of houses, restaurants and offices, where toilets and kitchens became their favourite haunts.

To understand how the species, which can grow to 5cm long, came to succeed in such filthy and unsanitary nooks and crannies, Chinese scientists deciphered the entire genetic makeup of the American cockroach, Periplaneta americana. They found that the species has more than 20,000 genes, making its genetic code as large as a human’s.

Amid the sequenced DNA, Shuai Zhan, who worked on the project at the Institute of Plant Physiology and Ecology in Shanghai, spotted unusually large groups of genes that appear to help the American cockroach survive in the unenviable niches it has adapted to.

Continued  

DNA secrets of how vampire bats became bloodthirsty

By Helen Briggs BBC News

19 February 2018

DNA analysis is giving clues to how the vampire bat can survive on blood alone.

The bat can drink up to half its weight in blood a day unlike other relatives, which dine on fruit, nectar or insects.

Blood is low in nutrients and can harbour deadly viruses.

Vampire bats have key differences in genes involved in immunity and food metabolism compared with other bats.

The researchers say the bat's gut microbes are also distinct.

They found evidence of more than 280 types of bacteria in the bat's droppings that would have made most other mammals unwell.

"The data suggests that there is a close evolutionary relationship between the gut microbiome and the genome of the vampire bat for adaptation to sanguivory (feeding exclusively on blood)," said study author, Dr Marie Zepeda Mendoza of the University of Copenhagen in Denmark.

The common vampire bat harbours many genes that have been selected to cope with blood feeding, she added.

Continued  

Clues from an endangered blue whale population

January 31, 2018, Flinders University

Clues in the DNA of endangered blue whales – the largest living animal – has shown that Australia is home to one population that likely travels widely and is adapted to a range of environmental conditions.

Blue whales are at this moment in Australian waters taking advantage of the abundance of krill that occurs during the summer.

They feed typically in waters off Cape Jaffa (east of Adelaide) to Cape Otway (west of Melbourne) and also in waters west of Rottnest Island in Western Australia.

However, these giants will not stay long: they will soon be migrating north to spend the winter in warmer waters around Indonesia, and will return again next summer.

"The question remains whether the blue whales using Australian waters are one, interbreeding population, or are multiple populations that may have different adaptations to different environmental conditions," says Dr. Catherine Attard, a member of a team of scientists from Flinders University who set out to answer this question with their collaborators the Centre for Whale Research in Western Australia and the Blue Whale Study in Victoria.

Read more at: 

DNA evidence used to protect the rhinoceros from extinction

Genetic evidence helping match confiscated rhinoceros horns to crime scenes -- Already used in scores of successful prosecutions

Date:  January 8, 2018

Source:  Nova Southeastern University

Summary:

A new study shows that genetic database now being used in the fight against poaching the rhinoceros.

Continued  

Abominable Snowman? Nope: Study ties DNA samples from purported Yetis to Asian bears

New paper shows how science can explore the roots of folklore

Date:  November 28, 2017

Source:  University at Buffalo

The Yeti or Abominable Snowman -- a mysterious, ape-like creature said to inhabit the high mountains of Asia -- looms large in the mythology of Nepal and Tibet.

Sightings have been reported for centuries. Footprints have been spotted. Stories have been passed down from generation to generation.

Now, a new DNA study of purported Yeti samples from museums and private collections is providing insight into the origins of this Himalayan legend.

The research, which will be published in Proceedings of the Royal Society B, analyzed nine "Yeti" specimens, including bone, tooth, skin, hair and fecal samples collected in the Himalayas and Tibetan Plateau. Of those, one turned out to be from a dog. The other eight were from Asian black bears, Himalayan brown bears or Tibetan brown bears.

Read on  

Genetic study uncovers evolutionary history of dingoes

October 31, 2017 by Deborah Smith

A major study of dingo DNA has revealed dingoes most likely migrated to Australia in two separate waves via a former land bridge with Papua New Guinea.

The find has significant implications for conservation, with researchers recommending the two genetically distinct populations of dingoes – in the south-east and north-west of the country – be treated as different groups for management and conservation purposes.

"Care should be taken not to move dingoes between the different wild populations," says study first author and UNSW Sydney scientist Dr Kylie Cairns. "And captive breeding programs should ensure the two dingo populations are maintained separately, with genetic testing used to identify ancestry."

Dr Cairns says there is also an urgent need to prevent further inter-breeding between domestic dogs and the south-eastern population of dingoes, which is threatened by genetic dilution, habitat loss and lethal control measures such as baiting and the recently reintroduced wild dog bounty in Victoria.

"Effective containment or neutering of male dogs in rural areas may help achieve this reduction in inter-breeding," says Dr Cairns, of the School of Biological, Earth and Environmental Sciences.

"Additionally, baiting and culling practices break apart dingo packs, leading to increased incidences of hybridisation. Alternative livestock protection measures need to be explored, such as livestock guardians, predator deterrents and improved dingo-proof fencing," she says.

Read more at: 

10,000 year-old DNA proves when fish colonized lakes

September 20, 2017

DNA molecules in lake sediment are few and hard bound to particles. This resulted in challenging analyses and required development of new methods, both for extracting sufficiently clean DNA and for the statistical analysis of data. For this work, doctoral student Fredrik Olajos and researcher Folmer Bokma's efforts were of particular importance.

"It's fantastic news that DNA can be stored for so long in lake sediment. Normally, free DNA molecules break down within days, but certain DNA fragments are preserved because they bind to clay particles," says Professor Göran Englund, one of the researchers behind the study.

"Being able to map the prevalence of DNA in lake sediments is now opening up a new window into history, which lets us see how nature has developed over a long period of time," says Göran Englund. We have already started a project aiming to study how lake ecosystems are affected by historical climate changes. That can provide important clues to a better understanding of how the current global warming will affect ecosystems."

Read more at: 

DNA Analysis Reveals Why 'Water Bears' Are the World's Toughest Animals

By Jen Viegas, Seeker | July 29, 2017 08:10am ET

Tardigrades, also known as water bears, are less than a fraction of an inch in length, yet they are believed to be Earth's toughest, hardiest animals. They are virtually indestructible. Tardigrades have the ability to withstand complete dehydration. Once desiccated, they have been frozen in blocks of ice, exposed to radiation, and sent into the vacuum of space, and yet they still usually spring back to life when water becomes available again.

New genetic research, published in the journal PLOS Biology, reveals how tardigrades achieve such resurrections after drying to a crisp. The authors now even believe that alien life forms could possess this remarkable ability.

"If life exists on other planets, and it is water-based, then those organisms that live out of water will evolve to resist extreme events, including the threat of drying out," said co-author Mark Blaxter of the University of Edinburgh's Institute of Evolutionary Biology.

Read on 

DNA links male, female butterfly thought to be distinct species

Date: July 27, 2017

Source: Florida Museum of Natural History

Summary: Researchers recently discovered what was thought to be a distinct species of butterfly is actually the female of a species known to science for more than a century.An international team of nine butterfly researchers from the U.S., Brazil, the U.K., Peru and Germany used DNA sequence data to associate the female sunburst cerulean-satyr, or Caeruleuptychia helios, an Amazonian brush-footed butterfly, with its male counterpart.

Males and females of this group look dramatically different from each other, a phenomenon known as sexual dimorphism, and the species was named and described in 1911 based on the brilliantly iridescent blue males. Rarer than the male, the brown female was considered another species and was recently named and placed in a different genus, Magneuptychia keltoumae.

Continued

DNA Solves 200-Year-Old Mystery of Weird Ice Age Creature

By Mindy Weisberger, Senior Writer | June 27, 2017 01:05pm ET

An odd extinct mammal that lived in South America during the last ice age had a long neck like a llama's, three-toed feet like a rhino's and what may have been a tapir-like trunk. This peculiar combination of traits fueled a mystery lasting nearly two centuries about how to classify the bizarre beast.

The Macrauchenia genus has puzzled scientists since Charles Darwin discovered limb bones and vertebrae fossils "of some very large animal" in Patagonia and fancied it to be a mastodon, as he wrote in a letter to his mentor, the naturalist John Stevens Henslow, in March 1834. Upon analyzing Darwin's finds, the scientist Sir Richard Owen declared in a species description published in 1838 that the creature resembled a camel, but uncertainty remained about where Macrauchenia fit on the mammal family tree.

The recent discovery of a rare DNA sample from the unusual species provided a crucial missing piece: genetic evidence confirming Macrauchenia lineage and its closest relatives, scientists reported in a new study. 

Continued  

Dog DNA influences face shape

May 26, 2017 

A study of dog DNA has revealed a genetic mutation linked to flat face shapes such as those seen in pugs and bulldogs. 

The research reveals new insights into the genes that underpin skull formation in people and animals.

Skull development

Scientists say their findings also shed light on the causes of birth defects that affect babies' head development in the womb.

Researchers at the University of Edinburgh's Roslin Institute analysed DNA samples from 374 pet dogs of various pedigree and mixed breeds. The dogs were being treated at the Royal (Dick) School of Veterinary Studies.

Animal scans

All of the animals underwent body scans as part of their care, producing detailed 3-dimensional images of the dogs' heads.

These high-resolution images – called CT scans – enabled the researchers to take precise measurements of the shape of the dog's skull.

"Our results shed light on the molecular nature of this type of skull form that is so common and popular among dogs," says Dr Jeffrey Schoenebeck.

By comparing the dogs' genetic information with measurements of their skulls, the team were able to pinpoint DNA variations that are associated with different head shapes.

Read more at: