Sunday, April 26, 2015

1.5m volunteers discover #penguins need to use the faeces in order to breed


Images looked at by 1.5 million online volunteers flagged up images to aid scientists in the discovery.

A citizen science project has found that penguins use their faeces to melt rocky breeding sites in order to lay their eggs.

The project of 1.5 million online volunteers, organised by the University of Oxford, clicked through 175,000 images of penguins and flagged up images showing strange or surprising behaviour in order to aid scientific discovery.

It suggests penguins form large groups before they start to breed with the dark colour of their faeces attracting heat faster than the lighter colours of the surrounding snow, causing the area to melt faster.
The video below shows one year of the Cuverville Island Gentoo penguin colony on the Antarctic Peninsula.



Researchers hope that over the coming year, with 500,000 new images for volunteers to look at, and cameras that will take photos every minute during the breeding season, that they will learn more about the animals through Penguin Watch.

source

Friday, April 17, 2015

Repeated marine predator evolution tracks changes in ancient and Anthropocene oceans

Date:
April 16, 2015
Source:
Smithsonian
Summary:
Scientists synthesized decades of scientific discoveries to illuminate the common and unique patterns driving the extraordinary transitions that whales, dolphins, seals and other species underwent as they moved from land to sea. Drawing on recent breakthroughs in diverse fields such as paleontology, molecular biology and conservation ecology, their findings offer a comprehensive look at how life in the ocean has responded to 
environmental change from the Triassic to the Anthropocene.
___________________________________________________










Modern dolphins (pictured) and extinct marine reptiles called ichthyosaurs descended from distinct terrestrial species, but independently converged on an extremely similar fish-like body plan although they were separated in time by more than 50 million years. In April 2015, a team of Smithsonian scientists synthesized decades of scientific discoveries to illuminate the common and unique patterns driving the extraordinary transitions that whales, dolphins, seals and other species underwent as they moved from land to sea, offering a comprehensive look at how life in the ocean has responded to environmental change from the Triassic to the Anthropocene. Credit: Courtesy of NOAA


For more than 250 million years, four-limbed land animals known as tetrapods have repeatedly conquered the Earth's oceans. These creatures--such as plesiosaurs, penguins and sea turtles--descended from separate groups of terrestrial vertebrates that convergently evolved to thrive in aquatic environments.

In a new scientific review, a team of Smithsonian scientists synthesized decades of scientific discoveries to illuminate the common and unique patterns driving the extraordinary transitions that whales, dolphins, seals and other species underwent as they moved from land to sea. Drawing on recent breakthroughs in diverse fields such as paleontology, molecular biology and conservation ecology, their findings offer a comprehensive look at how life in the ocean has responded to environmental change over time. The paper also highlights how evolutionary history informs an understanding of the impact of human activities on marine species today. More information is available in the April 17 issue of Science.

Marine tetrapods represent a diverse group of living and extinct species of mammals, reptiles, amphibians and birds that all play--or played--a critical role as large ocean predators in marine ecosystems. The repeated transitions between land and sea have driven innovation, convergence and diversification against a backdrop of changing marine ecosystems and mass extinctions dating back to the Triassic period. In this way, they provide ideal models for testing hypotheses about the evolution of species over long periods of time. Modern species of marine tetrapods now face a suite of human-driven impacts to their environment, including climate change, habitat degradation, ship collisions and underwater noise.

"We know from the fossil record that previous times of profound change in the oceans were important turning points in the evolutionary history of marine species," said Neil Kelley, a Peter Buck post-doctoral researcher in the National Museum of Natural History's department of paleobiology and lead author in the study. "Today's oceans continue to change, largely from human activities. This paper provides the evolutionary context for understanding how living species of marine predators will evolve and adapt to life in the Anthropocene."

Recent investigations in the fossil record have provided new insight into the evolution of traits that allowed marine tetrapods to thrive in the sea. In some cases, similar anatomy evolved among lineages that adapted to marine lifestyles. For example, modern dolphins and extinct marine reptiles called ichthyosaurs descended from distinct terrestrial species, but independently converged on an extremely similar fish-like body plan although they were separated in time by more than 50 million years. 

The repeated transformation of legs adapted for walking on land into fins is another classic example of convergent evolution. Species ranging from seals to mosasaurs independently developed streamlined forelimbs as they transitioned from living on land to the ocean, allowing them to move quickly and efficiently in the water. This transformation may have been achieved by parallel changes at the genome level.

"Land to sea transitions have happened dozens of times among reptiles, mammals and birds, across major mass extinctions," said Nicholas Pyenson, the museum's curator of fossil marine mammals. "You often get similar looking results but convergence is more than skin deep. It can be seen on a broad range of scales, from molecules to food webs, over hundreds of millions of years."

In the case of deep divers such as beaked whales and seals, these species have independently evolved to have positively charged oxygen-binding proteins called myoglobin in their muscles, allowing them to survive underwater for long periods of time. Scientists also have found identical genetic sequences in different marine species, such as whales, seals and sea cows. Whether these invisible molecular similarities account for larger-scale visible patterns of convergent evolution, or whether convergent anatomy follows different genetic pathways in different groups, remains an important open question to be tackled as genomic sequences become available for more species.

Not all adaptations observed in marine tetrapods can be attributed to convergent evolution. For instance, as baleen whales evolved to live underwater, they developed a unique filter-feeding system that depends on hair-like plates instead of teeth. In contrast, toothed whales evolved to catch and feed on prey by emitting calls and using echolocation, a kind of sonar, to process the echoes from these noises and detect objects in the sea.

Kelley and Pyenson synthesized research from existing studies and referenced the Smithsonian's paleobiology collections during the course of their research. They intend that this comprehensive review will encourage future collaboration between researchers across scientific fields and lead to new insights about evolutionary biology, paleontology and marine conservation.

Story Source:
The above story is based on materials provided by Smithsonian. Note: Materials may be edited for content and length.

Journal Reference:
  1. Neil P. Kelley, Nicholas D. Pyenson. Evolutionary innovation and ecology in marine tetrapods from the Triassic to the Anthropocene. Science, 2015 DOI: 10.1126/science.aaa3716


Smithsonian. "Repeated marine predator evolution tracks changes in ancient and Anthropocene oceans." ScienceDaily. ScienceDaily, 16 April 2015. <www.sciencedaily.com/releases/2015/04/150416145547.htm>.

Saturday, March 21, 2015

From sea lions to #penguin chicks, adorable animals are dying in droves





We know and love sea lions for their soulful eyes and playful antics — they’re basically the golden retrievers of the ocean. But recently, sea lions have been making headlines for much sadder reasons: Droves of malnourished sea lion pups have been washing up all over the Southern Californian coast. More than 1,450 pups have stranded without their mothers since January, reported the Washington Post.

The cause? Starvation.

Warmer waters off the coast of California are likely driving away sea lions’ prey such as squid, anchovies, and sardines, said Justin Viezbicke, stranding services coordinator for the National Oceanic and Atmospheric Administration (NOAA). As a result, mother sea lions are having to go further from birthing grounds — usually around the Channel Islands — to forage for food, meaning that pups probably don’t get enough nutrients from their mothers when they return. The pups then wean off their mothers earlier and are underweight when they leave the island, likely to find food of their own.

“They’re leaving with a low tank of gas and there’s really not much out there to help them out,” said Viezbicke. “They’re jumping into … a challenging environment and then they’re ending up washing ashore on the mainland, starving.”

Organizations like NOAA and other animal rescue programs have been taking in pups and feeding them — but that’s only a stopgap measure.

“This is something that’s naturally occurring out there, so there’s really not much we can do other than watch and learn from the situation,” Viezbicke said. “We can’t really prevent or stop it, unfortunately.”

Left to their own devices, these stranded sea lion pups probably wouldn’t make it. (No judgement if you need a tissue here. I’ll wait.)
auklet
Fred Hochstaedter
As sad as it sounds, starvation events and mass mortality events (in which vast numbers of animals die), are becoming more and more common in this wacky, warming world. Thanks to a number of large-scale, systemic alterations (lookin’ at you, El Niño and warming ocean temps), the world’s ecosystems hang in a delicate balance.

Meet the Cassin auklet — a pudgy, fist-sized seabird with crescent-shaped eye markings and pale blue feet. They’re pretty dang cute. And thousands of them are washing up dead along the West Coast — all the way from Northern California to British Columbia.

“My volunteers alone … have found 7,000 carcasses [over the last four months],” said Julia Parrish, executive director of the Coastal Observation and Seabird Survey Team (COASST) at the University of Washington. “It’s a scary big number.”

Like the sea lions, auklets are literally dying for a meal. The birds primarily feed on zooplankton or krill. However, in the last year, a mass of warm water — very scientifically named “the blob” — drove the usual Pacific krill into deeper waters and brought in a host of zooplankton that the auklets don’t eat, reported Audubon Magazine.

When a high number of birds wash ashore dead, the events are called “wrecks.” Generally speaking, smaller wrecks are fairly normal, Parrish explained. If there’s a storm out at sea, it’s not unusual for seabirds caught in its path to die, whether from starvation or storm conditions, and later wash up on beaches. That’s just how it goes.

But this time, something is different. “This is the biggest wreck we’ve ever seen in the 16 years we’ve been doing this work,” Parrish said. “I think it’s probably the largest wreck we’ve seen on West Coast … That makes me sit up and take notice.”

This winter’s wreck could be especially bad if enough of the dead auklets turn out to be adults, because an entire reproductive group may have been wiped out. They won’t know for sure until the birds return to their breeding grounds. Until then, it’s a lot of waiting and counting dead birds.
beachedaucklets
D. Derickson/COASST
So is this climate change at play? Scientists are hesitant to say.

Dee Boersma, a conservation scientist and founder of the Penguin Sentinels Project at UW, compares the vulnerability of seabirds to weather and climate to the vulnerability of a human crossing a busy street: You could get hit by a truck, but it doesn’t happen every time. And just as it’s hard to predict exactly how likely you are to survive a street-crossing as a human, the same goes for storms and their effects on Magellanic penguins, she said.

In 2014, Boersma and other penguin researchers published a study in PLOS ONE which found that climate change was directly responsible for the deaths of more than 200 Magellanic penguin chicks from 1983 to 2010 in Punta Tombo, Argentina. There, climate change is increasing the intensity and frequency of storms, while lowering the reproductive success of Magellanic penguins, the study reported.

During the 27-year-long study, young penguins perished at a high rate due to a combination of starvation and overexposure during exceptionally rainy and hot seasons. The chicks’ feather coats keep them cozy when they are dry, but that changes when they get wet: The fluffy down isn’t waterproof, like adult penguin feathers. So if a penguin chick gets caught in the rain during a storm, it’s like a human “being stuck outside and naked in a wet sleeping bag … the penguins basically die of hypothermia like you or I would,” said Boersma.

Plus, a lack of food leaves the chicks unprepared to cool themselves down when things heat up, since they rely on the food their parents bring them for all of their water. Without adequate hydration, the chicks can’t depend on evaporation to keep cool and become vulnerable to heat stress.

It’s a lethal combination: Over the course of the study, an average of 65 percent of the Punta Tombo chicks died every year, with about 40 percent dying of starvation.
Chicks that died of hypothermia after a rainstorm.
Chicks that died of hypothermia after a rainstorm.
Dee Boersma / University of Washington
So what was that about climate change again? Mass animal die-offs and starvation epidemics are shocking no matter what, even to hardened scientists. Climate change is just exacerbating these kinds of things.

“The fact is that we have populations responding to warming events, whether the warming is temporary or inexorable,” said Parrish, the researcher studying the dying auks.

The world’s ecosystems are hanging on as best they can, but small things can throw them out of balance. It’s unfair to compare the temperatures that a wild ecosystem can withstand to the temperatures humans can, because we have tools and technology on our side. “Wildlife needs habitat,” Parrish said. “In today’s crowded world, habitat only exists in certain places — places that we protect. And when the climate warms, those places change.”

“[Even one degree] is a huge deal,” Parrish points out. To understand and support conservation efforts, humans need to “think like a fish, a clam, or an oyster, and not like a person.”

Guess it’s time to get in touch with your inner oyster or auklet — getting hungry yet?

source

Tuesday, March 17, 2015

Penguin waddle put to the test




Thinkstock  
A penguin's waddle is one of nature's weirdest walks
"Come on Puddle… You can do it!" yells Prof John Hutchinson.
Puddle - a Humboldt penguin - seems more than a little bemused.
And with good reason.

***
 
A team of scientists have come to Penguin Beach at London Zoo, installed a hi-tech track and are now trying to lure Puddle and his penguin pals across it.
"Go Puddle, go!" encourages Prof Hutchinson, from the Royal Veterinary College (RVC).
And at last - with a fishy treat to help him along the way - the little bird waddles along the runway.
It is this distinctive walk that scientists from RVC and University of Texas at Austin are here to study.
Beneath the track lie force plates loaded with sensors, which allow the researchers to analyse how these birds get around.

"Penguins move in a really weird way," explains Prof Hutchinson.
"They have a very upright posture like a human, but they also have very short, crouched legs - it is very comical."Prof John Hutchinson on the eccentricity of the penguin's walk
He adds: "But when I see an animal do something weird, as an evolutionary biologist, I want to know how that evolved, how it got that way.
"And with these experiments, we're trying to tie what we know about penguin evolution with penguin physics."

Foot swing

Previous studies of the penguin's ungainly gait have revealed that the waddle is in fact the most energy efficient way for them to get about on land.
But these experiments will reveal exactly how they are doing this.
"They are applying forces left and right as they swing their bodies from side to side," says Prof Hutchinson.
"But what is not known about penguins is how the legs do that, how big are the sideways forces on penguin legs and how that compares to other waddling birds.
"And that's why we need these force platforms to measure the forces in the legs individually."
Waimanu  
 
The Waimanu is one of the oldest penguins discovered - and most likely had a more horizontal posture
But it turns out that penguins didn't always waddle. Fossils reveal that their ancient ancestors moved in a different way.
"We have all kinds of fossils as far back as 60 million years ago from the Southern Hemisphere," says palaeobiologist James Proffitt, who has come from Texas to study the birds.

"That gives us a chance to understand how these unusual anatomies and behaviours have evolved in deep time and how we have all these bizarre things we see today."
The bird bones show that the first penguins were a varied bunch: some were tiny, but others grew as tall as humans, hunting large fish with their spear-like beaks.
James Proffitt is particularly interested in a genus of penguins known as Waimanu.
These birds, unearthed in New Zealand, are the oldest-known penguins, living between 58-60 million years ago.

Mr Proffitt explains: "We know that penguins such as Waimanu were also flightless, wing-propelled divers based on things like their wing proportions and their relative size.
"But in many ways they were different, and they probably moved about differently on land based on the anatomy of their legs and hip bones."
The team believes that these proto-penguins had a more horizontal posture, and their walk would have looked similar to that of a modern-day albatross.

Today's penguins most likely evolved their unusual anatomy and resulting waddle as they became better and better adapted to swimming.
As their body shape changed to help them fly through the water with ease, they became more and more clumsy on land.

Penguin Penguins use their wings to fly through the water

Back at the running track, and the penguins seem to be enjoying not quite doing what they are told.
But Zuzana Matyasova, London Zoo's deputy team leader for the bird department, has found a way to attract their attention.

A combination of some dangling string, a tennis ball on a stick - or some fish - is proving hard for some penguins to resist.
"Some of the youngsters are really inquisitive: anything new in their enclosure is almost like a challenge and they want to be the first ones to try it out," she explains.
She's hoping all this hard work will shed light on these birds.
"I work with them every day, and I wonder about their way of moving - their distinctive waddle is just amazing."

While not every bird fancies taking a waddle down the runway, after several days, the scientists manage to collect enough data to begin their analysis.
And by comparing this with their studies of ancient penguins, they hope to establish how and when one of nature's most distinctive walks evolved.

 source

Thursday, March 5, 2015

#Penguins Rapidly Conquered New Zealand After Humans Ate Rivals

by Becky Oskin, Senior Writer   |   March 03, 2015

Sunday, March 1, 2015

Genetics reveal Antarctica was once too cold for #penguins

 
 
Emperor penguins are adapted to the bitter cold of Antarctica, but a new study reveals that during the last ice age it got too cold even for them.
Not too hot, not too cold, but just right. Gary Miller/Australian Antarctic Division, Author provided
Emperor penguins are truly remarkable birds – they thrive in the coldest environment on Earth and live year-round on the ice. Breeding colonies congregate on sea ice during the Antarctic winter and must withstand temperatures that regularly drop below -30C.

In fact, emperor penguins are so adapted to cold conditions that they become heat stressed when temperatures climb above 0C. Emperor penguins are therefore particularly threatened by climate change, and their numbers are expected to decline in the coming decades.

However a new study, published today in Global Change Biology, shows that it was once too cold even for emperor penguins.

Penguins past and present

In our study of how changing climate has affected emperor penguins over the past 30,000 years we found that, during the last ice age, emperor penguins were roughly seven times less common than today. What’s more, it appears that only three populations survived the last ice age. The Ross Sea was a refuge for one of these populations.

In the first continental-scale genetic study of emperor penguins, we examined genetic diversity of penguins modern and ancient to find out how they’re related. We collected genetic samples from eight breeding colonies – no easy feat given that emperor penguins live in some of the remotest places on Earth in conditions that would send most people running for a roaring fire and a hot cup of tea.
A rookery near Mawson station. Chris Wilson/Australian Antarctic Division, Author provided
Reaching the colonies involved weeks on the notoriously wild Southern Ocean (and considerable seasickness), helicopter journeys over pristine expanses of sea ice, and long snow shoe and ski traverses. The “A” (for Antarctic) factor was a constant presence, with delays caused by heavy sea ice that trapped ships for days at a time and blizzards that grounded helicopters.

Nevertheless, the effort paid off. Analyses of genetic data allowed us to reconstruct the population history of penguins, and correlate it with environmental conditions inferred from ice core data. The findings indicate that approximately 12,000 years ago, after the ice age ended and temperatures began to rise and sea ice around Antarctica decreased, emperor penguin numbers began to climb.

Goldilocks penguins

The emperor penguin’s relationship with sea ice can be described as a Goldilocks phenomenon.
The penguins need stable sea ice to stand on during their breeding season. If the sea ice extent is too great then the journey between the colony and their feeding grounds in the ocean may prove too costly in terms of energy reserves.

If there is too little sea ice or if the sea ice is not stable enough, then the penguins cannot establish successful breeding colonies. The duration of the sea ice season is also important – if the season is too short for the chicks to adequately mature, then they may not have time to grow their adult, waterproof feathers and will not survive at sea.
Some like it hot… but not emperor penguins. Frederique Olivier/Australian Antarctic Division, Author provided
During the last ice age there was about twice as much ice as there is today. Emperor penguins were probably unable to breed in more than a few locations around Antarctica. The distances from the open ocean, where the penguins feed, to the stable sea ice where they breed was probably too great in most of their modern breeding locations.

The three populations that did manage to survive the ice age may have done so by breeding near polynyas – areas of ocean that are kept free of sea ice by wind and currents. One of the most important of these polynyas was located in the Ross Sea.

Uncertain future

Because of this Goldilocks relationship emperor penguins are facing an uncertain future. Antarctic sea ice extent has been measured using satellites for the past 35 years. In this time, large changes with very different trends in different regions have been observed.

For the past three years in a row winter sea ice has broken records for total maximum extent. This overall increasing trend masks major regional changes in the extent of the sea ice field and the duration of the sea ice season.
Emperor penguin colonies are found right around the Antarctic continent. Jane Younger, Author provided

In some areas, such as the Bellingshausen Sea, there has been a large decline in sea ice while in others, including the Ross Sea, sea ice is increasing. These fluctuations in sea ice are likely placing a huge strain on emperor penguin populations, which is set to continue into the future. As areas suitable for emperor penguin breeding become scarcer it is becoming increasingly important to conserve areas known to support penguin populations.

It’s clear that the Ross Sea was a critical area for emperor penguins in the past and this suggests it will provide an important refuge for breeding colonies in the future. This emphasises the need for careful protection of this vital part of the Antarctic ecosystem.

A marine protected area, to protect roughly 1.34 million square kilometres of the Ross Sea from commercial fishing, was proposed by New Zealand and the United States at the last meeting of the Commission for the Conservation of Antarctic Marine Living Resources in October 2014. The proposal was rejected, but a Ross Sea marine park is likely to be on the agenda again at the 2015 meeting.

Emperor penguins are remarkably hardy birds, surviving in one of the harshest environments on earth. However their reliance on a narrow range of suitable habitat highlights their fragility, and raises concern over their future in a world undergoing its most rapid environmental change in history.

What does the future hold for Emperor penguins? Gary Dowse/Australian Antarctic Division, Author provided
 
source 

Monday, February 16, 2015

Sweet? Bitter? #Penguins Can't Tell, Research Suggests

Feb 16, 2015
                                               Wikimedia Commons/Tekken50

NEW YORK (GenomeWeb) – Penguins appear to lack taste receptor genes governing three of the five tastes, according to a genomic analysis conducted by a trio of researchers from the US and China.

The trio, led by Jianzhi Zhang at the University of Michigan, searched through the genomes of the Adélie penguin (Pygoscelis adeliae) and emperor penguin (Aptenodytes forsteri) and other birds for taste receptor genes. Penguins, they found, lacked receptors involved in perceiving sweet, bitter, and umami taste, but have retained salty and sour taste receptors, as they reported in Current Biology.

"Penguins eat fish, so you would guess that they need the umami receptor genes, but for some reason they don't have them," Michigan's Zhang said in a statement. "These findings are surprising and puzzling, and we do not have a good explanation for them. But we have a few ideas."

Zhang and his team searched for genes that encode taste receptors — sour's PKD2L1, salty's ENaC, umami's Tas1r1–Tas1r3 heterodimer, sweet's Tas1r2–Tas1r3 heterodimer, and bitter's Tas2r genes — in Adélie and emperor penguins, as well as in the little egret and a dozen or so other birds whose genomes were publicly available.

None of the birds had the Tas1r2 gene, which encodes part of the sweet taste receptor, though the researchers did find the gene in mammalian and reptile outgroups.

Tas1r3, which makes up the other part of the sweet taste receptor heterodimer as well as part of the umami taste receptor heterodimer, was also lacking in penguins. It was, the researchers noted, present in other birds.

The other half of the umami taste-specific receptor, Tas1r1, is actually a pseudogene in penguins, the researchers found, as it contains a two basepair deletion that leads to a premature stop codon.
Other penguin species shared this pseudogene, but other birds have working copies, Zhang and his team reported.

Similarly, the researchers identified three Tas2r pseudogenes in penguins while most other birds had working copies of the gene behind bitter taste. They noted, though, those three penguin pseudogenes were orthologous to the two working copies and one pseudogene version of Tas2r found in the little egret.

This, Zhang and his colleagues said, indicates that the common ancestor of all penguins lost the umami and bitter tastes, while the sweet taste was lost even earlier in the avian lineage.
The receptor gene for sour taste was present in all birds, including penguins, as were the genes encoding the subunits of the salty taste receptor, ENaC.

Zhang and his colleagues said they suspect that the penguin's ancestral stomping grounds of Antarctica might have had a role in this gene loss.

Trpm5, which is involved in transducing the sweet, umami, and bitter tastes, doesn't work well at lower temperatures. At freezing temperatures, the researchers suggested that it might not work at all, leading to the inability to taste sweet, umami, and bitter, and then to the loss of the genes linked to those tastes.



Journal Reference:
  1. Huabin Zhao, Jianwen Li, Jianzhi Zhang. Molecular evidence for the loss of three basic tastes in penguins. Current Biology, 2015; 25 (4): R141 DOI:10.1016/j.cub.2015.01.026

Tuesday, February 10, 2015

#Penguin change stuns scientists


Yellow-eyed penguin. Adult standing showing wing 'flippers'. Otago Peninsula, January 2006. Image © Craig McKenzie

Dunedin
When yellow-eyed penguins arrived in New Zealand just decades after the country's native waitaha penguin became extinct, it became one of the most rapid prehistoric animal turnovers ever found, University of Otago researchers say.

The team of researchers used carbon dating and DNA analysis of penguin remains from coastal New Zealand to establish the timing of the waitaha's extinction and the colonisation by yellow-eyed penguins from the subantarctic.

University of Otago postdoctoral research fellow Dr Nic Rawlence, who carried out the study, said the combination of ecology, archaeology and DNA in this way was new and was also being used to investigate if similar patterns exist with New Zealand sea lions, Stewart Island shags, elephant seals and fur seals.

Previous research had shown at the time of human arrival, New Zealand was inhabited by the waitaha penguin. ''Hunting and habitat change apparently caused the extinction of this unique mainland penguin, before the yellow-eyed penguin later arrived here from the subantarctic,'' Dr Rawlence said.

The new dating study showed waitaha went extinct around the same time as the giant flightless moa, within 200 years of Polynesian settlement of New Zealand - before 1500 AD. The yellow-eyed penguin then replaced the extinct penguin within about 20 to 30 years, in the early 1500s. ''It's one of the most rapid biological turnovers ever documented.''

Associate Prof Ian Smith, who was also involved in the study, said the very rapid biological shift implied a substantial change in human pressure around that time. ''Interestingly, recent archaeological studies similarly suggest that the Maori population in southern New Zealand declined around 1500 AD, and coincided with a major dietary shift.''

Dr Rawlence said if there had not been the dietary shift from large animals to fish and shellfish, yellow-eyed penguins would not have been able to fill the niche left by the waitaha. ''Yellow-eyeds would have arrived and then become extinct if there hadn't been that change.''

The near absence of the yellow-eyed penguin from the mainland before the extinction of the waitaha was similar to what happened to New Zealand's sea lions.

A University of Otago study published last year found today's sea lions replaced an extinct prehistoric New Zealand sea lion. The Marsden and Allan Wilson Centre-funded research on penguins included team members from the Universities of Auckland, Otago, Adelaide and Oslo, as well as Canterbury Museum and Te Papa.

The team's findings were published this week in the leading international journal Quaternary Science Reviews.

source

Tuesday, January 20, 2015

Climate Change Puts Picky #Penguin Eaters At Risk

By Jenna Iacurci
Jan 20, 2015 
 
penguins
Climate change is putting picky penguin eaters at risk, according to a new study. (Photo : Rachael Herman, LSU) 
 
Climate change is putting picky penguin eaters at risk, according to a new study.

Chinstrap and Gentoo penguins live in close proximity to one another in the Antarctic Peninsula, especially during the summer breeding season. So in order to peacefully co-exist and avoid competition for food resources, they evolved different feeding strategies over time. Now, however, this seems to be backfiring on one of the two species.

Named for the black stripe under their chins, Chinstrap penguin populations are decreasing while Gentoo penguins, recognized by their bright orange beaks, are actually increasing in number.

"Our data shows Gentoo penguins have a more diverse and flexible diet than Chinstrap penguins, which forage farther offshore and preferentially feed on Antarctic krill during the breeding season," lead author Michael Polito, from Louisiana State University, said in a press release.

Thanks to climate change, the Antarctic Peninsula is the fastest warming region in the Southern Hemisphere, according to the British Antarctic Survey. Over the past 50 years, the annual air temperature has risen by about 5 degrees Fahrenheit (2.8 degrees Celsius).

"For a region that for most of the year hovers around the point of freezing, a few degrees plus or minus is the difference between freezing and melting, particularly of sea ice," Polito explained.
This isn't just bad for penguins, but for the Antarctic krill that they mainly feed on, which use sea ice for protection from predators. Krill also feed on algae that grow beneath these slabs of ice, so as temperatures warm the lack of sea ice means fewer krill are around for penguin species to eat.

Based on the laws of supply and demand, there isn't enough krill to go around - especially during breeding season when penguins have to worry about feeding their chicks. So Chinstrap penguins whose diet relies on Antarctic krill find themselves in a tough spot.

On the other hand, adaptable Gentoo penguins are doing just fine, even amongst rapidly changing environmental conditions. They are flexible in their diet and breeding location, and also likely ease the transition of their chicks into adulthood by feeding them for a longer period of time.

Researchers determined the species' feeding habits by examining their stomach contents, studying the ear bones of fishes to determine if the penguins were feeding nearshore or offshore, and analyzing breast feathers from fully grown chicks to see how much krill versus fish they were fed. The results showed two very different strategies.

"These may be the reasons why Gentoo penguins in the Antarctic Peninsula are benefiting from changes in climate and their populations are increasing, but Chinstrap penguins are decreasing," Polito said.

The results are described further in the journal Marine Ecology Progress Series.

source

Friday, December 19, 2014

Antarctic tourism may pose disease threat to #penguins

  • 19 December 2014 by Penny Sarchet
A take-off in tourism could open the door to new bird diseases <i>(Image: Frans Lanting/National Geographic Creative)</i>
A take-off in tourism could open the door to new bird diseases (Image: Frans Lanting/National Geographic Creative)

For those who go, it's the trip of a lifetime – and it wouldn't be complete without a selfie with penguins. But growing tourism to the Antarctic, in combination with its warming climate, could be placing penguins at a risk of infectious diseases.

Antarctic species are believed to have weaker immune systems due to their long isolation from the world's common pathogens. Humans only started visiting Antartica roughly 200 years ago.
Antarctica is no longer a stranger to human contact: more than 37,000 people visited the continent in the 2013-14 season as part of a growing tourist industry, compared with an estimated 8000 just twenty years earlier. An additional 4400 researchers can be accommodated simultaneously in Antarctica during peak months.

"The effects of both a growing tourism industry and research presence will not be without consequences," says Wray Grimaldi of the University of Otago in Dunedin, New Zealand. "Penguins are highly susceptible to infectious diseases." She bases that on a survey by her team of penguin diseases in captivity, reaching as far back as 1947. It found reports of Salmonella, E. coli, West Nile virus and Avian pox virus infections, among others.

Widespread deaths

The team also found evidence of a number of mass penguin mortality events across the Antarctic since 1969. A number of infectious agents are implicated, including Avian pox, which killed more than 400 gentoo penguins in 2006, and caused 60 per cent mortality rates throughout another outbreak in 2008.

Grimaldi says disease agents may have arrived in Antarctica via migrating birds like skuas or giant petrels, although some pathogenic bacteria could have been introduced by humans. There isn't enough evidence to test either possibility, she says.

Yet, as the climate warms, more birds are expected to visit Antarctic regions, bringing their pathogens with them, while diseases borne by other animals could expand their ranges southwards.

But Norman Ratcliffe of the British Antarctic Survey in Cambridge, UK, says there is not a lot of evidence that wild penguin populations have been significantly affected by disease, adding that the Antarctic's tourism industry has been very active for 20 years and takes appropriate precautions.
"The tour companies are quite careful to make sure everyone cleans their boots before they go ashore," he says. "They don't allow any animal products to be taken ashore."

Warming warning

Grimaldi warns that climate change could help drive the emergence of new penguin diseases in Antarctica. Claire Christian of the Antarctic and Southern Ocean Coalition, a group of environmental NGOs, agrees.

"Climate change may result in a number of stressors that make it more difficult for penguin populations to deal with disease," she says. In addition to prompting the arrival of new pathogens or species carrying pathogens, warming temperatures could have a negative impact on food sources like krill, which might leave the penguins less able to fight off illness, she adds.

"A coordinated monitoring system needs to be in place," argues Grimaldi. "That way, responses can be directed by science." Christian agrees, but she says research alone is not enough – the countries that are signatories to the Antarctic Treaty also need to cooperate in implementing protective and precautionary measures.


Friday, December 12, 2014

Tooth loss in birds occurred about 116 million years ago

Date:
December 11, 2014
Source:
University of California - Riverside
Summary:
A question that has intrigued biologists is: Were teeth lost in the common ancestor of all living birds or convergently in two or more independent lineages of birds? A research team used the degraded remnants of tooth genes in birds to determine that teeth were lost in the common ancestor of all living birds more than 100 million years ago.











Birds are evolutionarily derived from theropod dinosaurs.
Credit: Image courtesy of University of California - Riverside




The absence of teeth or "edentulism" has evolved on multiple occasions within vertebrates including birds, turtles, and a few groups of mammals such as anteaters, baleen whales and pangolins. Where early birds are concerned, the fossil record is fragmentary. A question that has intrigued biologists is: Based on this fossil record, were teeth lost in the common ancestor of all living birds or convergently in two or more independent lineages of birds?

A research team led by biologists at the University of California, Riverside and Montclair State University, NJ, has found an answer. Using the degraded remnants of tooth genes in birds to determine when birds lost their teeth, the team reports in the Dec. 12 issue of Science that teeth were lost in the common ancestor of all living birds more than 100 million years ago.

"One of the larger lessons of our finding is that 'dead genes,' like the remnants of dead organisms that are preserved in the fossil record, have a story to tell," said Mark Springer, a professor of biology and one of the lead authors of the study along with Robert Meredith at Montclair State University who was previously a graduate student and postdoctoral researcher in Springer's laboratory. "DNA from the crypt is a powerful tool for unlocking secrets of evolutionary history."

Springer explained that edentulism and the presence of a horny beak are hallmark features of modern birds. "Ever since the discovery of the fossil bird Archaeopteryx in 1861, it has been clear that living birds are descended from toothed ancestors," he said. "However, the history of tooth loss in the ancestry of modern birds has remained elusive for more than 150 years."

All toothless/enamelless vertebrates are descended from an ancestor with enamel-capped teeth. In the case of birds, it is theropod dinosaurs. Modern birds use a horny beak instead of teeth, and part of their digestive tract to grind up and process food.

Tooth formation in vertebrates is a complicated process that involves many different genes. Of these genes, six are essential for the proper formation of dentin (DSPP) and enamel (AMTN, AMBN, ENAM, AMELX, MMP20).

The researchers examined these six genes in the genomes of 48 bird species, which represent nearly all living bird orders, for the presence of inactivating mutations that are shared by all 48 birds. The presence of such shared mutations in dentin and enamel-related genes would suggest a single loss of mineralized teeth in the common ancestor of all living birds.

Springer, Meredith, and other members of their team found that the 48 bird species share inactivating mutations in both dentin-related (DSPP) and enamel-related genes (ENAM, AMELX, AMTN, MMP20), indicating that the genetic machinery necessary for tooth formation was lost in the common ancestor of all modern birds. "The presence of several inactivating mutations that are shared by all 48 bird species suggests that the outer enamel covering of teeth was lost around ~116 million years ago," Springer said.

On the basis of fossil and molecular evidence, the researchers propose a two-step scenario whereby tooth loss and beak development evolved together in the common ancestor of all modern birds. In the first stage, tooth loss and partial beak development began on the anterior portion of both the upper and lower jaws. The second stage involved concurrent progression of tooth loss and beak development from the anterior portion of both jaws to the back of the rostrum. "We propose that this progression ultimately resulted in a complete horny beak that effectively replaced the teeth and may have contributed to the diversification of living birds," Springer said.

The research team also examined the genomes of additional toothless/enamelless vertebrates including three turtles and four mammals (pangolin, aardvark, sloth, and armadillo) for inactivating mutations in the dentin- and enamel-related genes. For comparison, the researchers looked at the genomes of mammalian taxa with enamel-capped teeth. "All edentulous vertebrate genomes that we examined are characterized by inactivating mutations in DSPP, AMBN, AMELX, AMTN, ENAM, and MMP20, rendering these genes non-functional," Springer said. "The dentin-related gene DSPP is functional in vertebrates with enamelless teeth -- sloth, aardvark, armadillo. All six genes are functional in the American alligator, a representative of Crocodylia, the closest living relatives of birds, and mammalian taxa with enamel capped teeth."

The research was supported, in part, by a grant to Springer from the National Science Foundation.
Springer and Meredith were joined in the research by Guojie Zhang at China National GeneBank, China; M. Thomas P. Gilbert at the University of Copenhagen Oster Voldgade, Denmark; and Erich D. Jarvis at Duke University Medical Center, NC.

All the scientists are coauthors with several others, including UC Riverside biologist John Gatesy, on a second paper in the same issue of Science. This paper employs the same 48 bird genomes to ask the question: "What makes a bird a bird?"

"The new bird genomes represent a major advance given that only a handful of bird genomes -- zebra finch, turkey, chicken and duck -- were previously available," Springer said.

Story Source:
The above story is based on materials provided by University of California - Riverside. The original article was written by Iqbal Pittalwala. Note: Materials may be edited for content and length.

Journal Reference:
  1. R. W. Meredith, G. Zhang, M. T. P. Gilbert, E. D. Jarvis, M. S. Springer. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science, 2014; 346 (6215): 1254390 DOI: 10.1126/science.1254390


University of California - Riverside. "Tooth loss in birds occurred about 116 million years ago." ScienceDaily. ScienceDaily, 11 December 2014. <www.sciencedaily.com/releases/2014/12/141211142148.htm>.

'Big Bang' of bird evolution mapped: Genes reveal deep histories of bird origins, feathers, flight and song

 


Crocodiles are the closest living relatives of birds, sharing a common ancestor that lived around 240 million years ago and also gave rise to the dinosaurs.
Credit: Stephen J. O'Brien, Avian Phylogenomics Group

Date:
December 11, 2014
Source:
Duke University
Summary:
The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 29 papers -- eight papers in a Dec. 12 special issue of Science and 21 more in Genome Biology, GigaScience and other journals. The analyses suggest some remarkable new ideas about bird evolution, including insights into vocal learning and the brain, colored plumage, sex chromosomes and the birds' relationship to dinosaurs and crocodiles.
 ______________________________________________________________________________
The genomes of modern birds tell a story of how they emerged and evolved after the mass extinction that wiped out dinosaurs and almost everything else 66 million years ago. That story is now coming to light, thanks to an ambitious international collaboration that has been underway for four years.
The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 29 papers -- eight papers in a Dec. 12 special issue of Science and 21 more in Genome Biology, GigaScience and other journals.

Scientists already knew that the birds who survived the mass extinction experienced a rapid burst of evolution. But the family tree of modern birds has confused biologists for centuries and the molecular details of how birds arrived at the spectacular biodiversity of more than 10,000 species is barely known.

To resolve these fundamental questions, a consortium led by Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, Erich D. Jarvis of Duke University and the Howard Hughes Medical Institute and M. Thomas P. Gilbert of the Natural History Museum of Denmark, has sequenced, assembled and compared full genomes of 48 bird species. The species include the crow, duck, falcon, parakeet, crane, ibis, woodpecker, eagle and others, representing all major branches of modern birds.

"BGI's strong support and four years of hard work by the entire community have enabled us to answer numerous fundamental questions to an unprecedented scale," said Guojie Zhang. "This is the largest whole genomic study across a single vertebrate class to date. The success of this project can only be achieved with the excellent collaboration of all the consortium members."

"Although an increasing number of vertebrate genomes are being released, to date no single study has deliberately targeted the full diversity of any major vertebrate group," added Tom Gilbert. "This is precisely what our consortium set out to do. Only with this scale of sampling can scientists truly begin to fully explore the genomic diversity within a full vertebrate class."

"This is an exciting moment," said neuroscientist Erich Jarvis. "Lots of fundamental questions now can be resolved with more genomic data from a broader sampling. I got into this project because of my interest in birds as a model for vocal learning and speech production in humans, and it has opened up some amazing new vistas on brain evolution."

This first round of analyses suggests some remarkable new ideas about bird evolution. The first flagship paper published in Science presents a well-resolved new family tree for birds, based on whole-genome data. The second flagship paper describes the big picture of genome evolution in birds. Six other papers in the special issue of Science describe how vocal learning may have independently evolved in a few bird groups and in the human brain's speech regions; how the sex chromosomes of birds came to be; how birds lost their teeth; how crocodile genomes evolved; ways in which singing behavior regulates genes in the brain; and a new method for phylogenic analysis with large-scale genomic data.

The Avian Phylogenomics Consortium has so far involved more than 200 scientists hailing from 80 institutions in 20 countries, including the BGI in China, the University of Copenhagen, Duke University, the University of Texas at Austin, the Smithsonian Museum, the Chinese Academy of Sciences, Louisiana State University and many others.

A Clearer Picture of the Bird Family Tree

Previous attempts to reconstruct the avian family tree using partial DNA sequencing or anatomical and behavioral traits have met with contradiction and confusion. Because modern birds split into species early and in such quick succession, they did not evolve enough distinct genetic differences at the genomic level to clearly determine their early branching order, the researchers said. To resolve the timing and relationships of modern birds, the consortium authors used whole-genome DNA sequences to infer the bird species tree.

"In the past, people have been using 10 to 20 genes to try to infer the species relationships," Jarvis said. "What we've learned from doing this whole-genome approach is that we can infer a somewhat different phylogeny [family tree] than what has been proposed in the past. We've figured out that protein-coding genes tell the wrong story for inferring the species tree. You need non-coding sequences, including the intergenic regions. The protein coding sequences, however, tell an interesting story of proteome-wide convergence among species with similar life histories."

This new tree resolves the early branches of Neoaves (new birds) and supports conclusions about some relationships that have been long-debated. For example, the findings support three independent origins of waterbirds. They also indicate that the common ancestor of core landbirds, which include songbirds, parrots, woodpeckers, owls, eagles and falcons, was an apex predator, which also gave rise to the giant terror birds that once roamed the Americas.

The whole-genome analysis dates the evolutionary expansion of Neoaves to the time of the mass extinction event 66 million years ago that killed off all dinosaurs except some birds. This contradicts the idea that Neoaves blossomed 10 to 80 million years earlier, as some recent studies suggested.

Based on this new genomic data, only a few bird lineages survived the mass extinction. They gave rise to the more than 10,000 Neoaves species that comprise 95 percent of all bird species living with us today. The freed-up ecological niches caused by the extinction event likely allowed rapid species radiation of birds in less than 15 million years, which explains much of modern bird biodiversity.

Increasingly sophisticated and more affordable genomic sequencing technologies and the advent of computational tools for reconstructing and comparing whole genomes have allowed the consortium to resolve these controversies with better clarity than ever before, the researchers say.

With about 14,000 genes per species, the size of the datasets and the complexity of analyzing them required several new approaches to computing evolutionary family trees. These were developed by computer scientists Tandy Warnow at the University of Illinois at Urbana-Champaign, Siavash Mirarab, a student at the University of Texas at Austin and Alexis Stamatakis at the Heidelburg Institute for Theoretical Studies. Their algorithms required the use of parallel processing supercomputers at the Munich Supercomputing Center (LRZ), the Texas Advanced Computing Center (TACC) and the San Diego Supercomputing center (SDSC).

"The computational challenges in estimating the avian species tree used around 300 years of CPU time, and some analyses required supercomputers with a terabyte of memory," Warnow said.

The bird project also had support from the Genome 10K Consortium of Scientists (G10K), an international science community working toward rapidly assessing genome sequences for 10,000 vertebrate species.

"The Avian Genomics Consortium has accomplished the most ambitious and successful project that the G10K Project has joined or endorsed," said G10K co-leader Stephen O'Brien, who co-authored a commentary on the bird sequencing project appearing in GigaScience.

A Genomic Perspective of Avian Evolution and Biodiversity

For all their biological intricacies, birds are surprisingly light on DNA. A study led by Zhang, Cai Li and the consortium authors found that compared to other reptile genomes, avian genomes contain fewer of the repeating sequences of DNA and lost hundreds of genes in their early evolution after birds split from other reptiles.

"Many of these genes have essential functions in humans, such as in reproduction, skeleton formation and lung systems," Zhang said. "The loss of these key genes may have a significant effect on the evolution of many distinct phenotypes of birds. This is an exciting finding, because it is quite different from what people normally think, which is that innovation is normally created by new genetic material, not the loss of it. Sometimes, less is more."

From the whole chromosome level to the order of genes, this group found that the genomic structure of birds has stayed remarkably the same among species for more than 100 million years. The rate of gene evolution across all bird species is also slower compared to mammals.

Yet some genomic regions display relatively faster evolution in species with similar lifestyles or phenotypes, such as involving vocal learning. This pattern of what is called convergent evolution may be the underlying mechanism that explains how distant bird species evolved similar phenotypes independently. Zhang said these analyses on particular gene families begin to explain how birds evolved a lighter skeleton, a distinct lung system, dietary specialties, color vision, as well as colorful feathers and other sex-related traits.

Important Lessons

The new studies have shed light on several other questions about birds, including:

How did vocal learning evolve?  Eight studies in the package examined the subject of vocal learning. According to new evidence in the two flagship papers, vocal learning evolved independently at least twice, and was associated with convergent evolution in many proteins. A Science study led by Andreas Pfenning, Alexander Hartemink, Jarvis and others at Duke, in collaboration with researchers at the Allen Institute for Brain Science in Seattle and the RIKEN Institute in Japan, found that the specialized song-learning brain circuitry of vocal learning birds (songbirds, parrots and hummingbirds) and human brain speech regions have convergent changes in the activity of more than 50 genes. Most of these genes are involved in forming neural connections. 

Osceola Whitney, Pfenning and Anne West, also of Duke, found in another Science study that singing is associated with the activation of 10 percent of the expressed genome, with diverse activation patterns in different song-learning regions of the brain, controlled by epigenetic regulation of the genome. Duke's Mukta Chakraborty and others found in a PLoS ONE study that parrots have a song system within a song system, with the surrounding song system unique to them. This might explain their greater ability to imitate human speech. In a BMC Genomics study, Morgan Wirthlin, Peter Lovell and Claudio Mello from Oregon Health & Science University found unique genes in the song-control brain regions of songbirds.

The XYZW of sex chromosomes. Just as the sex of humans is determined by the X and Y chromosomes, the sex of birds is controlled by the Z and W chromosomes. The W makes birds female, just as the Y makes humans male. Most mammals share a similar evolutionary history of the Y chromosome, which now contains many degenerated genes that no longer function and only a few active genes related to "maleness." A Science study led by Qi Zhou and Doris Bachtrog from the University of California, Berkeley, and Zhang found that half of bird species still contain substantial numbers of active genes in their W chromosomes. This challenges the classic view that the W chromosome is a "graveyard of genes" like the human Y.

This group also found that bird species are at drastically different states of sex chromosome evolution. For example, the ostrich and emu, which belong to one of the older branches of the bird family tree, have sex chromosomes resembling their ancestors. Yet some modern birds such as the chicken and zebra finch have sex chromosomes that contain few active genes. This opens a new set of questions on how the diversity of sex chromosomes may drive the diversity of sex differences in the outward appearance of various bird species. Peacocks and peahens are dramatically different; male and female crows are indistinguishable.

How did birds lose their teeth? In a Science study led by Robert Meredith from Montclair State University and Mark Springer from the University of California, Riverside, a comparison between the genomes of living bird species and those of vertebrate species that have teeth identified key mutations in the parts of the genome that code for enamel and dentin, the building blocks of teeth. The evidence suggests that five tooth-related genes were disabled within a short time period in the common ancestor of modern birds more than 100 million years ago.

What's the connection between birds and dinosaurs? Unlike mammals, birds (along with reptiles, fish and amphibians) have a large number of tiny microchromosomes. These smaller packages of gene-rich material are thought to have been present in their dinosaur ancestors. A study of genome karyotype structure in BMC Genomics analyzed whole genomes of the chicken, turkey, Peking duck, zebra finch and budgerigar. It found the chicken has the most similar overall chromosome pattern to an avian ancestor, which was thought to be a feathered dinosaur. This work was led by Darren Griffin and Michael Romanov from the University of Kent, and by Dennis Larkin and Marta Farré from the Royal Veterinary College, University of London.

Another study in Science examined birds' closest living relatives, the crocodiles. This team, led by Ed Green and Benedict Paton from the University of California, Santa Cruz, David Ray from Texas Tech University and Ed Braun from the University of Florida, found that crocodiles have one of the slowest-evolving genomes. The researchers were able to infer the genome sequence of the common ancestor of birds and crocodilians (archosaurs) and therefore all dinosaurs, including those that went extinct 66 million years ago.

Do differences in gene trees versus species trees matter? In the phylogenomics flagship study by Jarvis and others, the consortium found that no gene tree has a history exactly the same as the species tree, partly due to a process called incomplete lineage sorting. Another Science study, led by Tandy Warnow at the University of Texas and the University of Illinois, and her student Siavash Mirarab, developed a new computational approach called "statistical binning." They used this approach to show it does not matter much that the gene trees differ from the species tree because they were able to infer the first coalescent-based, genome-scale species tree, combining gene trees with similar histories to accurately infer a species tree.

Do bird genomes carry fewer virus sequences than other species? Mammalian genomes harbor a diverse set of genomic "fossils" of past viral infections called "endogenous viral elements" (EVEs). A study published in Genome Biology led by Jie Cui of Duke-NUS Graduate Medical School in Singapore, Edward Holmes of the University of Sydney and Zhang, found that bird species had 6-13 times fewer EVE infections in their past than mammals. This finding is consistent with the fact that birds have smaller genomes than mammals. It also suggests birds may either be less susceptible to viral invasions or better able to purge viral genes.

When did colorful feathers evolve? Elaborate, colorful feathers are thought to be evolutionarily advantageous, giving a male bird in a given species an edge over his competitors when it comes to mating. Zhang's flagship paper in Science, which is further analyzed by Matthew Greenwold and Roger Sawyer from the University of South Carolina in a companion study in BMC Evolutionary Biology, found that genes involved in feather coloration evolved more quickly than other genes in eight of 46 bird lineages. Waterbirds have the lowest number of beta keratin feather genes, landbirds have more than twice as many, and in domesticated pet and agricultural bird species, there are eight times more of these genes.

What happens to species facing extinction or recovering from near-extinction? Birds are like the proverbial canaries in the coal mine because of their sensitivity to environmental changes that cause extinction. In a Genome Biology study led by Shengbin Li, Cheng Cheng and Jun Yu from Xi'an Jiaotong University and Jarvis, researchers analyzed the genomes of species that have recently gone nearly extinct, including the crested ibis in Asia and the bald eagle in the Americas. They found genes that break down environmental toxins have a higher rate of mutations in these species and there is lower diversity of immune system genes in endangered species. In a recovering crested ibis population, genes involved in brain function and metabolism are evolving more rapidly. The researchers found more genomic diversity in the recovering population than was expected, giving greater hope for species conservation.

The Start of Something Bigger

This sweeping genome-level comparison of an entire class of life is being powered by frozen bird tissue samples collected over the past 30 years by museums and other institutions around the world. Samples are sent as fingernail-sized chunks of frozen flesh mostly to Duke University and University of Copenhagen for DNA separation. Most of the genome sequencing and critical initial analyses of the genomes have then been conducted by the BGI in China.

The avian genome consortium is now creating a database that will be made publicly available in the future for scientists to study the genetic basis of complex avian traits.

Setting up the pipeline for the large-scale study of whole genomes -- collecting and organizing tissue samples, extracting the DNA, analyzing its quality, sequencing and managing torrents of new data -- has been a massive undertaking. But the scientists say their work should help inform other major efforts for the comprehensive sequencing of vertebrate classes. To encourage other researchers to dig through this 'big data' and discover new patterns that were not seen in small-scale data before, the avian genome consortium has released the full dataset to the public in GigaScience, and in NCBI, ENSEMBL and CoGe databases.

Under the leadership of Dave Burt, the National Avian Research Facility at the Roslin Institute and Edinburgh University, UK, has created genome browser databases based on the ENSEMBL model for 48 species.

The full set of papers in Science and other journals can be accessed at http://www.sciencemag.org/content/346/6215/1308.

Story Source:
The above story is based on materials provided by Duke University. Note: Materials may be edited for content and length.


Duke University. "'Big Bang' of bird evolution mapped: Genes reveal deep histories of bird origins, feathers, flight and song." ScienceDaily. ScienceDaily, 11 December 2014. <www.sciencedaily.com/releases/2014/12/141211142136.htm>.