Extinct Caribbean bird yields DNA after 2,500 years in watery grave

Date: August 15, 2019

Source: Florida Museum of Natural History

Scientists have recovered the first genetic data from an extinct bird in the Caribbean, thanks to the remarkably preserved bones of a Creighton's caracara from a flooded sinkhole on Great Abaco Island.

Studies of ancient DNA from tropical birds have faced two formidable obstacles. Organic material quickly degrades when exposed to heat, light and oxygen. And birds' lightweight, hollow bones break easily, accelerating the decay of the DNA within.

But the dark, oxygen-free depths of a 100-foot blue hole known as Sawmill Sink provided ideal preservation conditions for the bones of Caracara creightoni, a species of large carrion-eating falcon that disappeared soon after humans arrived in the Bahamas about 1,000 years ago.

Florida Museum of Natural History postdoctoral researcher Jessica Oswald extracted and sequenced genetic material from a 2,500-year-old C. creightoni femur from the blue hole. Because ancient DNA is often fragmented or missing, Oswald had modest expectations for what she would find -- maybe one or two genes. But instead, the bone yielded 98.7% of the bird's mitochondrial genome, the set of DNA that most living things inherit only from their mothers.

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Scarlet macaw DNA points to ancient breeding operation in Southwest

August 13, 2018, Pennsylvania State University

Somewhere in the American Southwest or northern Mexico, there are probably the ruins of a scarlet macaw breeding operation dating to between 900 and 1200 C.E., according to a team of archaeologists who sequenced the mitochondrial DNA of bird remains found in the Chaco Canyon and Mimbres areas of New Mexico.

Remains of a thriving prehistoric avian culture and breeding colony of scarlet macaws exist at the northern Mexican site of Paquimé, or Casas Grande. However, this community existed from 1250 to 1450, well after the abandonment of Chaco Canyon, and could not have supplied these birds to Southwest communities prior to the 13th century, said Richard George, graduate student in anthropology, Penn State.

Historically, scarlet macaws lived from South America to eastern coastal Mexico and Guatemala, thousands of miles from the American Southwest. Previously, researchers thought that ancestral Puebloan people might have traveled to these natural breeding areas and brought birds back, but the logistics of transporting adolescent birds are difficult. None of the sites where these early macaw remains were found contained evidence of breeding—eggshells, pens or perches.

"We were interested in the prehistoric scarlet macaw population history and the impacts of human direct management," said George. "Especially any evidence for directed breeding or changes in the genetic diversity that could co-occur with different trade networks."

The researchers sequenced the mitochondrial DNA of 20 scarlet macaw specimens, but were only able to obtain full sequences from 14. They then directly radiocarbon-dated all 14 birds with complete or near complete genomes and found they fell between 900 and 1200 CE.

"We looked at the full mitochondrial genome of over 16,000 base pairs to understand the maternal relationships represented in the Chaco Canyon and Mimbres regions," said George.

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DNA to help find suspects in bird of prey offences

A BREAKTHROUGH in the recovery of human DNA could help police crack wildlife crimes, including the illegal persecution of Scotland’s iconic birds of prey. Investigations could be supported by new research into retrieving human DNA found at crime scenes.

By DAVID SCOTT

PUBLISHED: 18:49, Fri, Apr 20, 2018 | UPDATED: 19:04, Fri, Apr 20, 2018

GETTY / SALTIRE EDINBURGH

DNA testing could help catch wildlife criminals who harm birds of prey

The research was initiated by the Partnership for Action Against Wildlife Crime (PAW) Scotland and carried out by the Scottish Police Authority’s (SPA) Forensic Services, the Scottish Government and the University of Strathclyde.

It found DNA can be traced on traps that have been outside for at least 10 days, and from rabbit baits and bird carcasses at crime scenes after at least 24 hours. Until now, efforts to prosecute have been hampered by a lack of evidence.

The RSPB’s most recent Birdcrime report revealed there were nine confirmed incidents of raptor persecution in Scotland in 2016, but not a single prosecution.

It was claimed the number was likely to be “the tip of the iceberg”, as many illegal killings go undetected or unreported.

Continued 

Ancient moas may have furthered the spread of beech forests by eating mushrooms.

Jamie Wood

Fossil poop reveals critical role of giant birds in New Zealand’s ecosystem

By Elizabeth PennisiFeb. 12, 2018 , 3:00 PM

When the first humans landed on what is now known as New Zealand 700 years ago, they didn’t find mammals. Instead, they discovered giant birds called moas, as well as a host of other indigenous bird species. Soon, they had eaten many of them into extinction.

Now, by deciphering ancient DNA found in fossilized bird droppings, researchers have a better idea of the toll those extinctions took on New Zealand’s forests and shrublands. The study shows that mushrooms and other fungi were important to the extinct birds’ diets, and suggests moas had a strong hand in shaping New Zealand’s native landscape by helping fungi spread, says co-author Alan Cooper, an ancient DNA specialist at The University of Adelaide in Australia. Now that the moas are gone, “The forest has potentially lost a potentially major way to spread.”

“This paper is a clear example of the great potential of ancient DNA-based techniques,” says Melania Cristescu, an ecological geneticist at McGill University in Montreal, Canada, who was not involved in the work. Cristescu says she was surprised by how much information the DNA contained. “The authors were able to identify a wide variety of species and to reconstruct the ecology of an extinct species.”

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What DNA Says About the Extinction of America’s Most Common Bird ... and its possible resurrection

 NOV 16, 2017

On September 1, 1914, an old, trembling passenger pigeon named Martha died at Cincinnati Zoo. With her demise, her entire species slid into extinction. But in many ways, the species was already gone, for a solitary passenger pigeon is almost not a passenger pigeon at all. This is an animal that existed in gestalt. Its essence was in the flock.

Passenger pigeons were once the most abundant bird in North America, and quite possibly the world. At their peak, there were a few billion of them, traversing the continent in gargantuan, nomadic flocks that would blacken the sky for hours as they passed overhead. Simon Pokagon, a Potawatomi author and leader, described them as “the grandest waterfall of America” and their sound as that of “distant thunder” or “an army of horses laden with sleigh bells.”

And then, people started shooting them. They poisoned them, netted them, gassed them, hit them with sticks. In a matter of decades, the continent’s most common bird has been completely wiped out, down to the last individual. “It’s always astounded me how something could have that large a population and entirely disappear,” says Beth Shapiro from the University of California, Santa Cruz. “Why didn’t tiny populations survive somewhere in refugia? I mean, we are pretty good at murdering things, but how did we kill every one of them?”

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DNA tests on albatross excrement reveal secret diet of top predator

Date:  October 18, 2017

Source:  University of Tasmania - Institute for Marine and Antarctic Studies

Summary:

A study that used DNA tests to analyse the scats of one of the world's most numerous albatrosses has revealed surprising results about the top predator's diet. DNA analysis of 1460 scats from breeding sites around the Southern Ocean has shown that the diet of black-browed albatrosses contains a much higher proportion of jellyfish than previously thought.

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DNA from faeces identifies a rare warbler that visited the Isle of Man from central Asia

Wednesday, 12 April 2017

Birdwatchers have extracted DNA from faeces to establish the identity of a rare bird seen in the Isle of Man.

They have concluded that a rare warbler spotted in Ballasalla in January is from the central Asian population found in Kazakhstan.

Ballasalla resident Paul Bromley first spied the diminutive warbler on January 30 when it was feeding on fat balls put out by his neighbours in their back garden.

Paul alerted local birdwatcher Peter Christian, who in turn contacted Neil Morris at Manx BirdLife.

From its appearance, it was presumed that the bird was most probably a form of Lesser Whitethroat of an unknown eastern origin.

To solve the identity, Neil Morris collected a sample of the bird’s faeces - conveniently deposited on the garden fence by the bird - and sent it for analysis to Professor J. Martin Collinson at the University of Aberdeen. Professor Collinson is the world’s leading authority on the DNA profiling of wild birds from around the world.

After detailed DNA analysis, Professor Collinson confirmed to Manx BirdLife that the bird was a Lesser Whitethroat of the sub-species blythi.

The population of this form of Lesser Whitethroat breeds in central Asia in and around Kazakhstan.

It is likely that the bird got its migratory instincts wrong, heading north and west last autumn instead of south to its usual wintering grounds in southern Asia and east Africa.

The journey from Kazakhstan to the Isle of Man (as the ’Whitethroat’ flies) is about 3,200 miles.

The bird was last seen in mid-February.

Birdwatchers hope that it will find its way back to its nesting grounds in Asia this spring.

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Bird DNA shows inbreeding linked to shorter lifespan

Date: May 16, 2016

Source: University of East Anglia

Pieces of DNA that predict lifespan are shorter in birds that are inbred, according to new research from the University of East Anglia (UEA).

The findings mean that inbreeding could be linked to a shorter lifespan.

The team also found effects that spanned generations -- with the young of inbred mothers also being negatively affected.

The DNA pieces in question, known as telomeres, are found in almost all animals -- including humans.

They act as protective caps at each end of a chromosome -- providing protection from damaging substances.

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DNA that only females have

Date:

June 4, 2015

Source:

Uppsala Universitet

Summary:

In many animal species, the chromosomes differ between the sexes. The male has a Y chromosome. In some animals, however, for example birds, it is the other way round. In birds, the females have their own sex chromosome, the W chromosome. For the first, researchers have mapped the genetic structure and evolution of the W chromosome.

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Hidden bird migrations revealed by DNA

By 

Erik Stokstad

12 August 2014 6:30 pm 2 Comments

Every fall, countless songbirds migrate from their breeding grounds in the United States and Canada. Often flying at night to avoid hawks, the animals head south to spend the winter in Mexico and Central America. But exactly where many of them go, and how they get there, has been something of a mystery. Now, a team has shown that analyzing DNA in feathers can provide new details about bird migrations. Although the technique is still in the proof-of-principle stage, it “could be an immensely powerful tool in implementing conservation measures for the most at-risk bird populations with fine-scale precision,” says Jeff Wells of the Boreal Songbird Initiative in Seattle, Washington.

Ornithologists have many ways to track migratory birds. The most common is to put small identification bands on their legs. The trouble is that netters recapture only a tiny fraction of the banded birds. Electronic tracking devices can work well for individual birds, but may not yield insights for an entire population. More recently, researchers have shown that the ratio of isotopes in feathers can provide a rough guide to where a bird has been feeding, because the feather ratios mirror those of food sources. Analysis of mitochondrial and nuclear genes has also offered clues, for example confirming that some birds have geographically distinct breeding populations. But even those techniques couldn’t tease out fine-grained differences in where birds summer and winter. “This is a really big issue,” because conservation groups need to know where to spend their resources to best effect, says Robert Fleischer, a geneticist at the Smithsonian Conservation Biology Institute in Washington D.C.

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Liverpool pigeon found to be related to iconic dodo

After 200 years of being somewhat of an enigma, and having unknown provenance, the extinct spotted green pigeon has been found to be related to the iconic but extinct, flightless dodo.

Scientists in Australia analysed tiny DNA fragments extracted from feathers of the only remaining specimen (which is on show in the World Museum in Liverpool) and found it to be related to the nicobar pigeon of Indonesia and distantly related to the dodo of Mauritius.

Clem Fisher from the World Museum said: "We are very pleased that the extinct Spotted Green Pigeon has its correct place in the world of birds finally, after more than 230 years.”

The bird is often referred to as the 'Liverpool Pigeon' after the city in which the specimen is kept, but it would have come from either the Indian subcontinent, southeast Asia or Oceania.

Leading scientist Dr Tim Heupink, from Griffith University in Australia said: "This study improves our ability to identify novel (new) species from historic remains, and also those that are not novel after all. Ultimately this will help us to measure and understand the extinction of local populations and entire species."

http://www.wildlifeextra.com/go/news/Liverpool-pigeon.html

Elachuridae: Ornithologists Describe New Family of Passerine Birds

Jun 16, 2014 by Sergio Prostak

A group of ornithologists led by Dr Trevor Price of the University of Chicago has described a new family of birds that is represented by just one species, the Spotted wren-babbler.

The Spotted wren-babbler (Elachura formosa),
a painting by John Gerrard Keulemans, 1892.

The Spotted wren-babbler is a small perching bird found in China, India, Nepal, Bangladesh, Bhutan, Laos, Myanmar and Vietnam.

This bird measures about 10 cm in length and has a short tail. It is brown above, white below, with rufous wings. It also has white speckles all over its body.

Previously, the spotted wren-babbler was included in the genus Spelaeornis as Spelaeornis formosus along with eight other species of wren-babblers.

But a new study of bird DNA has uncovered a big surprise.

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Ancient DNA ends Australia's claim to kiwi origins

Date:

May 22, 2014

Source:

University of Adelaide

Summary:

Australia can no longer lay claim to the origins of the iconic New Zealand kiwi following new research showing the kiwi’s closest relative is not the emu as was previously thought. Instead, the diminutive kiwi is most closely related to the extinct Madagascan elephant bird -- a 2-3 meter tall, 275 kg giant. And surprisingly, the study concluded, both of these flightless birds once flew.

Continued

Ancient DNA: Barnyard chickens living just a few hundred years ago looked far different from today's chickens

Date:

April 18, 2014

Source:

National Evolutionary Synthesis Center (NESCent)

Summary:

Ancient DNA adds a twist to the story of how barnyard chickens came to be. Analyzing DNA from the bones of chickens that lived 200-2,300 years ago in Europe, researchers report that some of the traits we associate with modern domestic chickens -- such as their yellowish skin -- only became widespread in the last 500 years, much more recently than previously thought.

Read on

Chicken bones tell true story of pacific migration

Date:

March 17, 2014

Source:

University of Adelaide

Summary:

Did the Polynesians beat Columbus to South America? Not according to the tale of migration uncovered by analysis of ancient DNA from chicken bones recovered in archaeological digs across the Pacific. The ancient DNA has been used to study the origins and dispersal of ancestral Polynesian chickens, reconstructing the early migrations of people and the animals they carried with them.

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Songbirds May Have 'Borrowed' DNA to Fuel Migration

Sep. 20, 2013 — A common songbird may have acquired genes from fellow migrating birds in order to travel greater distances, according to a University of British Columbia study published this week in the journal Evolution.

While most birds either migrate or remain resident in one region, the Audubon's warbler, with habitat ranging from the Pacific Northwest to Mexico, exhibits different behaviours in different locations. The northern populations breed and migrate south for the winter, while southern populations have a tendency to stay put all year long.

Evolutionary biologists have long been puzzled by research that indicates some Audubon's warblers share the same mitochondrial DNA (mtDNA) with myrtle warblers -- a different species of songbird that migrates annually to the southeastern U.S., Central America and the Caribbean -- even though they look dramatically different.

"Mitochondria are only passed down from mothers to their offspring," says David Toews, a PhD candidate in UBC's Department of Zoology. "So it's a very useful marker for differentiating species. In this case, finding two species of songbirds sharing the same mtDNA is very surprising, so we set out to find out why."

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Moa bird bones reveal DNA half-life but Jurassic Park remains fiction

Moa birds disappeared from New Zealand following the arrival of human settlers in the 13th century, but their fossils now provide us with a valuable clues about long-term DNA survival and how DNA decays over thousands of years.

In a paper published today in Proceedings of the Royal Society B, we show that fragments of DNA from these extinct, flightless birds can be used to estimate how DNA decays over time. The findings have implications in choosing where to look for DNA-containing fossils and in forensic casework involving bones.

Sadly, the findings won’t satisfy those people wanting us to talk about dinosaur DNA. When telling someone our day-job involves working with ancient DNA (aDNA), more often than not, the response is: “Ahhhh, you mean like Jurassic Park?”.

Then we explain how resurrecting the dinosaurs is not possible and that the early papers describing isolation of dinosaur DNA were likely based on a combination of contaminating human and chicken DNA.

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Ancient origin of hepatitis B viruses revealed by DNA fossils in bird genomes

As the old adage goes; "One man's trash is another man's treasure": what has often been described as "junk DNA" has revealed a hidden gem. Not only can we find the ancient ancestor of the human hepatitis B virus nestled in songbird genomes, but according to research published recently by a team of scientists at theUniversity of Münster, this virus is 63 million years older than originally thought, a finding that may help improve human health outcomes.

Hepatitis B virus (HBV) is one of the most common human viral infections in the world. This virus specifically infects the liver cells of many primates (including humans), causing severe flu-like symptoms. Although most people fully recover, roughly 5 percent remain infected throughout their lives; acting as carriers who can infect others whilst also suffering a variety of serious liver diseases, including cancer. In fact, HBV is second only to tobacco amongst known human carcinogens, causing up to eighty percent of all hepatocellular carcinomas worldwide.

Where did HBV come from? Were other animals once infected by this virus before evolving defences against it? If so, how did these animals protect themselves from HBV?

Read on

Pigeon DNA gives up fancy secrets

By Jonathan Amos
They may not be everybody's favourite, but pigeons have now joined that elite club of animals to have had their DNA laid bare by researchers.

A team from the US, Denmark and China reports the sequencing of the genome of the rock pigeon (Columba livia) in this week's Science magazine.

It has allowed the origins of some of the roughly 350 breeds to be traced.

The researchers have even managed to pinpoint the gene responsible for the head-crests seen in many fancy birds.

This gene, known as EphB2, controls whether the head and neck feathers on a bird turn upwards to create the ostentatious displays or downwards to maintain a line of smooth plumage.

It is a single mutation, or error, in EphB2 that turns the crest on.

By analysing the DNA around the gene, the scientists have been able to show this feather feature, much prized by pigeon "fanciers", to have evolved just the once. It was then spread through the various bird populations by breeders who wanted to see it in their own animals.

Continued: http://www.bbc.co.uk/news/science-environment-21279422