The plant family Corsiaceae, new research

This video is called Liliaceae plant family, description, examples, info.

From the Journal of Biogeography:

Ancient Gondwana break-up explains the distribution of the mycoheterotrophic family Corsiaceae (Liliales)

19 FEB 2015



Many plant families have a disjunct distribution across the southern Pacific Ocean, including the mycoheterotrophic family Corsiaceae, which provides a prime example of this biogeographical pattern. A better grasp of the family’s evolutionary relationships is needed to understand its historical biogeography. We therefore aimed to (1) test the uncertain monophyly of Corsiaceae, (2) define its phylogenetic position, and (3) estimate divergence times for the family, allowing us to assess whether the distribution of the family is the result of vicariance.


Southern South America and Australasia.


We analysed various combinations of mitochondrial and nuclear data to address the monophyly, phylogenetic position and age of Corsiaceae. To test its monophyly, we used a three-locus data set including most monocot orders, and to infer its exact phylogenetic position, we used a five-locus extended data set. We corroborated these findings using an independent plastome dataset. We then used a two-locus dataset with taxa from all monocot orders, and a three-locus dataset containing only taxa of Liliales, to estimate divergence times using a fossil-calibrated uncorrelated lognormal relaxed-clock approach.


Corsiaceae is a monophyletic family and the sister group of Campynemataceae. This clade is the sister group of all other Liliales. The crown age of Corsiaceae is estimated to be 53 Ma (95% confidence interval 30–76 Ma).

Main conclusions

Corsiaceae is an ancient family of mycoheterotrophic plants, whose crown age overlaps with the plate-tectonic split of Gondwana, consistent with a vicariance-based explanation for its current distribution.

See also here.

Worst ever ice age and first animals, 715 million years ago

This video is called Precambrian Ediacaran Life Before the Cambrian Explosion 600 million years ago.

From the BBC:

Earth was a frozen snowball when animals first evolved

715 million years ago the entire planet was encased in snow and ice. This frozen wasteland may have been the birthplace of complex animals

Presented by Kate Ravilious

The ice brought Earth to a standstill. Where there were once waves lapping onto a tropical shore and warm waters teeming with life, there was just the whistling of the wind and a cold barren landscape, covered in ice as far as the eye could see. Even at the equator – the warmest place on Earth – the average temperature was a frigid -20°C, equivalent to modern-day Antarctica. Most life was wiped out, and the creatures that did survive huddled in small pockets of open water, where hot springs continued to bubble up.

This was “Snowball Earth” – a deep freeze that began around 715 million years ago and held Earth in its icy grip for a good 120 million years. “There are no other comparable glacial periods on Earth. This one was really quite catastrophic,” says Graham Shields of University College London in the UK.

However, some scientists now believe that this crushing catastrophe drove one of the most incredible steps in evolution: the development of the first animals, and a dramatic flourishing of life known as the Cambrian explosion.

Around 540 million years ago, a host of exotic creatures suddenly appeared. They included giant woodlouse-like creatures known as trilobites, the five-eyed Opabinia, and the spiny slug-like Wiwaxia. Suddenly, Earth leapt from being dominated by single-celled bacteria to a world teeming with exotic multicellular creatures, all in a geological blink of an eye.

This video shows a reconstruction of the extinct animal Opabinia.

The Cambrian explosion remains a puzzle

For Charles Darwin, trying to demonstrate his theory of natural selection, this sudden burst of evolution was a major problem. “The case must at present remain inexplicable; and may be truly urged as a valid argument against the views here entertained,” he wrote in On the Origin of Species in 1859.

To this day the Cambrian explosion remains a puzzle. But maybe a planet-encasing icy catastrophe could help explain it.

The evidence for a Snowball Earth first emerged in the early 1990s. Unexpectedly, geologists discovered evidence of glaciers – such as stones that had clearly been carried on ice rafts and then dropped – in the tropics. Since then, a growing body of evidence has shown that the global deep freeze began around 715 million years ago, and lasted nearly 120 million years.

Exactly how far the ice extended is still debated. Some argue that the entire Earth was encased in ice, with just a few small pockets of open water where hot springs bubbled up. Others believe that a belt of open water remained around Earth’s equator.
Regardless of how far the ice stretched, most scientists agree that the Snowball formed suddenly. It was probably caused by rapid weathering of Earth’s continents, which sucked carbon dioxide – a planet-warming greenhouse gas – out of the atmosphere and caused temperatures to plummet. There were two distinct pulses of extreme glaciation, interspersed with a 20-million-year warm period. Finally, around 660 million years ago, Earth’s volcanoes topped up the atmospheric carbon dioxide enough to haul the climate out of its frozen state.

So why on Earth would this period of extreme cold cause life to switch gear so rapidly? Maybe, say many geologists, because it pumped lots of life-giving oxygen into the air.

The idea is that the ice gave a boost to microscopic plants, which released oxygen as a waste product. During the Snowball, the glaciers would have worn huge amounts of phosphorus-rich dust away from the underlying rocks. Then, when the ice retreated at the end of the Snowball, rivers washed this dust into the oceans, where it fed the microbes.

“High phosphorus levels would have increased biological productivity and organic carbon burial in the ocean, leading to a build-up of atmospheric oxygen,” says Noah Planavsky of Yale University in New Haven, Connecticut. In 2010 he identified a massive spike in phosphorus levels in sediments from around the world, just as Snowball Earth was ending.

That was suggestive, but in 2014 Planavsky found more direct evidence. His team estimated oxygen levels prior to Snowball Earth, by studying chromium – which exists in different states depending on the amount of oxygen in the air – in ancient rocks. Until 800 million years ago, atmospheric oxygen levels were just one-hundredth of today’s levels.

Planavsky thinks that is far too low to support complex animal life. “In modern low-oxygen environments there is less ecosystem complexity and a more limited range of animal behaviours,” says Planavsky. “So it is reasonable to expect that an oxygen rise would pave the way for animal and ecosystem diversification.”

But there’s a problem with that idea. Experiments published in 2014 showed that some animals can survive with much less oxygen than previously thought. Sponges, one of the oldest kinds of animal, need just 0.5% of modern oxygen levels. That suggests oxygen wasn’t enough of a trigger.

In recent years another idea has come to prominence. Maybe it was the ice itself that drove the evolutionary leap, says Richard Boyle of the University of Southern Denmark in Odense. “There are no animals more complex than a sponge prior to the last of the Snowball glaciation events, and in my opinion this is not coincidence,” says Boyle.

For Boyle the real puzzle isn’t the appearance of multicellular animals. Instead, it’s the rise of cellular differentiation – cells with specific roles like liver, muscle and blood. These specialised cells allowed animals to become much more intricate. “What sets animals apart from plants and fungi is this irreversible cellular differentiation, which, for instance, is what allows animals to have more cell types,” says Boyle.

It’s hard to see how this could have evolved, because specialised cells lose the ability to reproduce on their own. Instead they have to be distinctly self-sacrificing, cooperating with other cells in the body for the greater good of the animal. Only the specialised reproductive cells, the sperm and eggs, get to create a new generation.

By contrast, plants don’t just rely on specialist sex cells to reproduce. They can also reproduce themselves from cuttings taken from their stems or roots. “You can’t take a cutting from an animal,” says Boyle. He thinks the severity of Snowball Earth may have pushed animal cells to abandon this flexibility, and specialise.

“During the Snowball period, life will have been confined to small geothermally heated areas, and will have experienced frequent extinctions and population crashes,” says Boyle. The populations that did survive were often reduced to just a handful of organisms. Boyle suggests that these little groups of survivors were often closely related, encouraging them to cooperate more than usual.

Biologists have long known that animals are more likely to help close relatives, because by doing so they can benefit their own genes, which the relative will also carry. For example, wild animals are likely to adopt orphans that are related to them, but not orphans that are unrelated. Boyle thinks that Snowball Earth may have forced cells to behave altruistically. “Until that point, the cost of being an animal cell had been too high,” he says.

Boyle’s notion is controversial and other scientists are sceptical. “Boyle’s melt-hole idea for the origin of animals is fun,” says palaeontologist Nick Butterfield of the University of Cambridge, UK. “But most geologists don’t buy the idea of a hard Snowball Earth anymore, so the isolated hot-spring refugia ponds wouldn’t have actually existed.”

Butterfield argues that life probably retreated to the open waters of the tropics during Snowball times, but otherwise carried on as normal.

It would really help to find some definitive fossils to resolve this. Unfortunately, the fossil record is very patchy in such ancient rocks. So far, the oldest definitive fossils of complex animals date to around 560 million years ago. That could fit with either hypothesis.

Genetics doesn’t help much either. By working backwards through the animal family tree and estimating rates of genetic change, scientists have estimated that the first animals are likely to have emerged around 750 million years ago. But these “molecular clock” estimates are notoriously unreliable.

Nonetheless, recent discoveries hint that animal life may have started to gain a foothold during Snowball Earth. In 2014, Malcolm Wallace of the University of Melbourne in Australia discovered strange clumps of fossils in remote regions of Australia and Namibia. In the remains of ancient reefs, Wallace found bubble-shaped fossils up to 3cm across. Many of the bubbles appeared to interconnect into a network of finger-like strands.

“These fossils are big and complex, but they don’t really fit exactly into any of the animal phyla,” says Wallace. They date from around 700 million years ago, soon after Earth first became a Snowball.

So Wallace and his colleagues think they may have found the precursors to animals – very early sponge-like creatures, which lived in low-oxygen waters and represented a halfway stage between single-celled microbes and multicellular animals. And they think it is no coincidence that these animal precursors appear right after the first major Snowball glaciation.

“Intuitively, you might think that Snowball Earth would hinder evolution, and yet animals appear soon after the big glaciations,” says Wallace. “It seems clear that these big glaciations have disrupted the Earth’s ocean-atmosphere system in some way that was favourable for complex life to develop.”

Boyle agrees that this kind of primitive animal life may have evolved before the end of Snowball Earth, but he argues that this wasn’t the crucial step. Instead, the key threshold is when individual cells forgo their ability to reproduce, and instead take on specific roles within an animal.

So far, animals more complex than sponges, with specialised organs that do different jobs, have only been found in rocks laid down after the Snowball. Boyle predicts that they will never be found in older rocks, certainly not in rocks laid down before the Snowball. “If such fossils are found then my hypothesis will be proven incorrect,” he says.

Butterfield agrees that such ancient animal fossils may never turn up, but that could simply be because they haven’t been preserved. He now suspects that Boyle, Planavsky and Wallace have got the whole story backwards. Instead of the ice creating complex animals, he suggests that the first animals appeared 750 million years ago and transformed the planet, cooling the climate. “I think there is a good case to be made for the evolution of animals actually triggering the glaciations,” says Butterfield.

“Animals have an enormous capacity to modify physical environments,” says Butterfield. So he thinks the first animals upset the delicate balance of ocean chemistry, with knock-on effects for the rest of the planet.

Animals can certainly have big effects on the planet. For instance, burrowing animals like worms can break up rocks faster. The resulting rock dust reacts with carbon dioxide in the air, and the minerals produced get washed into the oceans – removing the carbon dioxide from the air. Meanwhile, marine animals boost oxygen levels by eating the remains of dead organisms, which would otherwise consume oxygen. Butterfield also thinks animals may have driven the evolution of new microscopic plants that sank faster, taking carbon dioxide with them.

There is some evidence that the first animals could have thrown Earth into a deep freeze. In 2011, Eli Tziperman of Harvard University in Cambridge, Massachusetts and his colleagues modelled the chemical cycles in the ocean. They found that the evolution of new marine organisms could have helped transport more carbon to the ocean floor and forced a major change in climate. “It’s certainly not unreasonable to suggest that the evolution of animals initiated glaciation,” says Butterfield.

Right now there’s not enough information to decide whether animals created Snowball Earth, or Snowball Earth triggered animal evolution. But either way, the two events are linked.

They are also a sobering reminder of how quickly conditions on Earth can change. Our planet has been just right for us for thousands of years, but there is no reason to believe it will stay that way.

Right now our appetite for fossil fuels is hotting things up dangerously fast. But a large asteroid impact, like the one that did for the dinosaurs, would throw up enough dust to block sunlight and cause a dangerous chill. And because today’s oceans are cooler than they were in the dinosaurs’ time it’s conceivable that the oceans would freeze and Earth would revert to a Snowball state.

Whether our planet goes hot or cold, it will be a seriously bumpy ride. Maybe we should learn from those early animal cells, and learn to work together.

Methane didn’t warm ancient Earth, new simulations suggest. Alternative explanation needed for why planet didn’t freeze despite dim sun: here.

Flowering plants evolution and Charles Darwin

This video is called Blooming flowers, amazing nature!

From the BBC:

The abominable mystery: How flowers conquered the world

Charles Darwin was baffled by the speed with which flowers evolved and spread. Now genetics could solve the mystery

It was, Charles Darwin wrote in 1879, “an abominable mystery”. Elsewhere he described it as “a most perplexing phenomenon”. Twenty years after the publication of his seminal work The Origin of Species, there were still aspects of evolution that bothered the father of evolutionary biology. Chief among these was the flower problem.

Flowering plants from gardenias to grasses, water lilies to wheat belong to a large and diverse group called the angiosperms. Unlike almost all other types of plants, they produce fruits that contain seeds. What worried Darwin was that the very earliest samples in the fossil record all dated back to the middle of the Cretaceous period, around 100 million years ago, and they came in a bewilderingly wide variety of shapes and sizes. This suggested flowering plants had experienced an explosive burst of diversity very shortly after their origins – which, if true, threatened to undermine Darwin’s entire model of gradual evolution through natural selection.

In fact recently published research has revealed that angiosperms evolved relatively gradually after all. Yet this still leaves a number of key questions. The roughly 350,000 known species of flowering plants make up about 90% of all living plant species. Without them, we would have none of our major crops including those used to feed livestock, and one of the most important carbon sinks that mop up our carbon dioxide emissions would be missing. How and where did they originate? And, perhaps more importantly, why did they become so spectacularly successful?

This 2012 video is about research into the origins of flowering plants.

Darwin was an undoubted expert on origins. His remarkable insights helped establish a framework for the way new species form – and he was adamant that the process was slow and gradual.

“As natural selection acts solely by accumulating slight, successive, favourable variations, it can produce no great or sudden modification; it can act only by very short and slow steps,” he wrote in The Origin of Species.

But Darwin was painfully aware that there were apparent exceptions to his slow and steady rule. The angiosperms were a particular source of frustration. Angiosperms simply didn’t exist for most of Earth’s history. Early forests were populated by bizarre primitive tree-like plants closely related to the club mosses and horsetails that are a very minor part of today’s plant communities. Later a group called the gymnosperms – plants with unenclosed seeds such as the conifers – took over. And then came the angiosperms.

Early in the 19th century, scientists like Adolphe-Théodore Brongniart began collating everything that was then known about fossil plants. Work like this highlighted the fact that a huge variety of angiosperms – often called the “higher plants” or dicotyledons in the 19th century – popped up all too suddenly in the middle of the Cretaceous geological period.

“[The] sudden appearance of so many Dicotyledons… appears to me a most perplexing phenomenon to all who believe in any form of evolution, especially to those who believe in extremely gradual evolution,” Darwin wrote to Swiss naturalist Oswald Heer in 1875.

He was well aware the sudden appearance of flowering plants was more than just perplexing. It also provided his critics with ammunition against his evolutionary model.

Darwin did suggest a solution, however. Angiosperms, he said, may have evolved gradually in a remote region of the world as yet unexplored by scientists. By the middle of the Cretaceous, something caused them to spill out of their homeland and rapidly spread across the world. This, reasoned Darwin, would give the misleading impression to researchers working in Europe and North America that a wide variety of flowering plant species had all evolved at the same time. Aware of the lack of evidence to back up his theory, Darwin described it as “wretchedly poor”.

In fact, his speculation has since proved to be partly correct. Angiosperms that predate the middle Cretaceous specimens by tens of millions of years have begun to turn up in rocks from China. But Darwin didn’t get the details entirely right because very rare early angiosperms have been found in Europe and the US too.

“Our knowledge has greatly increased since the end of the 19th century,” says Laurent Augusto at the National Institute for Agricultural Research in Bordeaux, France. Palaeobotanists may not yet agree on precisely where and when flowering plants first evolved, but their appearance in the fossil record much earlier than was previously known means they are no longer a problem for Darwin’s theory of gradual evolution. Other debates about them, especially concerning their spectacular diversity, remain active, however.

“Our world is an angiosperm world,” says Augusto. “In many ecosystems they dominate in species and in biomass – this angiosperm ecological dominance remains unexplained.”

This video from the USA is called Floral Beaks and Flower Evolution.

Clues to the ultimate origins of flowering plants are to be found on New Caledonia, a small island about 1,600 kilometres east of Australia. Here, around the time that Darwin was agonising over his angiosperm problem, botanists discovered a plant called Amborella. Careful study over the last century has shown it to be the sole survivor of one of the very earliest branches of the angiosperm evolutionary tree. This means its relationship to all living flowers is bit like that of the duck-billed platypus to all living mammals: it might look unassuming, but Amborella can tell us more than even the most elaborate orchid about how the angiosperms first evolved.

Last year, the plant finally spilled some of its secrets. The Amborella Genome Project unveiled a draft version of the plant’s genome. The first angiosperms must have evolved from one of the gymnosperm species that dominated the world at the time. The Amborella genome suggests that the first angiosperms probably appeared when the ancestral gymnosperm underwent a ‘whole genome doubling‘ event about 200 million years ago.

Genome doubling occurs when an organism mistakenly gains an extra copy of every one of its genes during the cell division that occurs as part of sexual reproduction. The extra genetic material gives genome doubled organisms the potential to evolve new traits that can provide a competitive advantage. In the case of the earliest angiosperms, the additional genetic material gave the plants the potential to evolve new, never-before-seen structures – like flowers. The world’s flora would never be the same again.

The Amborella genome results strongly suggest that flowers have been a defining feature of the angiosperms from very early on in their evolution. Could the flowers themselves help explain why the angiosperms became so diverse?

Darwin was certainly open to the possibility. While he was wrestling with the problem posed by the seemingly sudden appearance of the angiosperms, he received a letter from Gaston de Saporta, a French biologist who said the apparent evidence of the 19th century fossil record suggesting the plant group appeared suddenly need not be a problem for Darwin’s theory of gradual evolution. It simply showed that angiosperms were an unusual exception to his general rule. Flowering plants and their insect pollinators evolved together, reasoned Saporta, and this ‘co-evolution’ drove both groups to diversify unusually rapidly.

“Your idea … seems to me a splendid one,” responded an enthusiastic Darwin. “I am surprised that the idea never occurred to me, but this is always the case when one first hears a new and simple explanation of some mysterious phenomenon.”

But the theory runs into trouble today, says Augusto. Early angiosperms may have had flowers, but we now know from fossils that those first flowers were very plain – and probably not that attractive to pollinators. By the time the big, bold flowers that entice insects appeared, the angiosperms were already diverse.

Another theory, advanced by Frank Berendse and Marten Scheffer at Wageningen University in the Netherlands in 2009, rests on the fact that the angiosperms are much more productive than gymnosperms like the conifers. Perhaps they simply outcompeted rival plants by growing faster and gobbling up the lion’s share of the nutrients, they suggested.

“Our paper was meant to be a bit provocative,” says Berendse, to encourage botanists and those who study fossil plants to work together more closely on explaining the spectacular rise of the angiosperms.

In fact, the two had already begun working together. Earlier in 2009, a team led by Tim Brodribb at the University of Tasmania in Hobart, Australia, published the first in a series of papers exploring angiosperm evolution by examining fossil leaves. They found that their leaves gained many more veins during the Cretaceous, which would have provided them with more water for photosynthesis, and allowed them to grow more rapidly.

“That provided very strong support for our ideas,” says Berendse. But as with the flower hypothesis, problems remain with the nutrient-based theory. For instance, while individual angiosperm leaves are more efficient at photosynthesising than conifer needles, conifers may be able to compensate because their needles collectively have a much larger surface area than that of the leaves of an average angiosperm tree.

Unfortunately, there are no simple explanations for the diversity and ecological dominance of the flowering plants. “Very probably no single theory can explain the massive rise of the angiosperms,” admits Berendse.

It’s more likely, says Augusto, that several factors played a role, with each being more or less important in specific places and times. For instance, Berendse’s productivity theory may apply in the tropical belts, where rich soils could give nutrient-hungry angiosperms a vital edge over gymnosperms, but it might not explain what’s going on in regions with poor soils, where angiosperms are potentially starved of the nutrients they need. And the simple flowers of early angiosperms may have done little for the evolution of the group, but when elaborate flowers finally appeared they probably did help drive the plant group to take over the world.

That is, if they really did take over the world. It might seem odd to suggest otherwise when there are something like 350,000 known angiosperm species and not many more than 1000 gymnosperms, most of which are conifers. But there’s more to success than diversity, says Brodribb. Many of the few conifers species that do survive are super-abundant.

“In the northern hemisphere conifers rule the vast boreal and much of the temperate zone,” says Brodribb. He adds that the angiosperms have not become ecologically dominant in many of these regions. This might be because the soils there are too poor for them to establish a nutritional advantage, in keeping with Berendse’s ideas, or perhaps it’s because temperatures drop too low for them to survive. But why even in 350,000 attempts the angiosperms haven’t come up with species that can overcome these problems and outcompete those northern conifers is another unsolved mystery.

Today’s plant scientists understandably have a better handle on the origins of flowering plants than Darwin did, but they are still struggling to explain the group’s diversity, and why despite this it has failed to become dominant in some parts of the world.

Augusto, at least, is confident that answers will eventually be found, in part because these mysteries continue to fascinate researchers. And while there is little doubt this fascination stems in part from the ecological and economic importance of angiosperms today, perhaps it is also partly down to Darwin and his way with words. “I think the ‘abominable mystery’ quote does contribute to the general interest in angiosperms,” adds Augusto.

Songbirds’ bill colours are about social life, not sex

This 2013 video from the USA is called Bird Feeding Adaptations: How Beaks are Adapted to What Birds Eat.

From the Journal of Evolutionary Biology:

Carotenoid-based bill coloration functions as a social, not sexual, signal in songbirds (Aves: Passeriformes)


Many animals use coloration to communicate with other individuals. While the signalling role of avian plumage colour is relatively well studied, there has been much less research on coloration in avian bare parts.

However, bare parts could be highly informative signals as they can show rapid changes in coloration. We measured bill colour (a ubiquitous bare part) in over 1600 passerine species and tested whether interspecific variation in carotenoid-based coloration is consistent with signalling to potential mates or signalling to potential rivals in a competitive context.

Our results suggest that carotenoid bill coloration primarily evolved as a signal of dominance, as this type of coloration is more common in species that live in social groups in the non-breeding season, and species that nest in colonies; two socio-ecological conditions that promote frequent agonistic interactions with numerous and/or unfamiliar individuals.

Additionally, our study suggests that carotenoid bill coloration is independent of the intensity of past sexual selection, as it is not related to either sexual dichromatism or sexual size dimorphism. These results pose a significant challenge to the conventional view that carotenoid-based avian coloration has evolved as a developmentally costly, condition-dependent sexual signal. We also suggest that bare part ornamentation may often signal different information than plumage ornaments.

Bird evolution, new research

This video says about itself:

The phylogeny of wing assisted incline running

12 January 2011

WAIR is ubiquitous among a number of avian orders, as displayed. This is not a complete sample of bird orders – the members of other orders likely perform WAIR as well. If you find video evidence, let us know!

From daily The Guardian in Britain:

Sprouting feathers and lost teeth: scientists map the evolution of birds

Mass genome sequencing reveals avian family tree – and how imitative birdsong gives birds genetic similarities to humans

A remarkable international effort to map out the avian tree of life has revealed how birds evolved after the mass extinction that wiped out the dinosaurs into more than 10,000 species alive today. More than 200 scientists in 20 countries joined forces to create the evolutionary tree, which reveals how birds gained their colourful feathers, lost their teeth, and learned to sing songs.

The project has thrown up extraordinary similarities between the brain circuits that allow humans to speak and those that give some birds song: a case of common biology being arrived at via different evolutionary routes.

Some birds are shown to have unexpectedly close relationships, with falcons more closely related to parrots than [to] eagles or vultures, and flamingoes more closely related to pigeons than [to] pelicans. The map also suggests that the earliest common ancestor of land birds was an apex predator, which gave way to the prehistoric giant terror birds that once roamed the Americas.

This video about Pleistocene prehistory in North America is called Terror Bird vs. Wolves.

“This has not been done for any other organism before,” Per Ericson, an evolutionary biologist at the Swedish Museum of Natural History in Stockholm, told the journal Science. “It’s mind-blowing.”

The scientists began their task by analysing fingernail-sized pieces of frozen flesh taken from 45 bird species, including eagles, woodpeckers, ostriches and parakeets, gathered by museums around the world over the past 30 years. From the thawed-out tissue, they extracted and read the birds’ whole genomes. To these they added the genomes of three previously sequenced species. It took nine supercomputers the equivalent of 400 years of processor time to compare all the genomes and arrange them into a comprehensive family tree.

Members of the project, named the Avian Phylogenomics Consortium, published the family tree and their analysis on Thursday in eight main papers in the journal Science, and in more than 20 others in different scientific journals.

The rise of the birds began about 65m years ago. A mass extinction – probably caused by an asteroid collision – wiped out most of the larger-bodied dinosaurs, but left a few feathered creatures. The loss of so many other species freed up vast ecological niches, giving these animals an unprecedented chance to diversify.

Comparisons of the birds’ genomes with those of other animals pointed researchers towards a host of genes involved with the emergence of coloured feathers. While feathers may first have emerged for warmth, colourful plumage may have played a part in mating success. Researchers at the University of South Carolina found that waterbirds had the lowest number of genes linked to feather coloration, while domesticated pets and agricultural birds had eight times as many.

Further analysis of the genomes revealed that the common ancestor of all living birds lost its teeth more than 100m years ago. Mutations in at least six key genes meant that the enamel coating of teeth failed to form around 116m years ago. Tooth loss probably began at the front of the jaw and moved to the rear as the beak developed more fully.

“Ever since the discovery of the fossil bird Archaeopteryx in 1861, it has been clear that living birds are descended from toothed dinosaurs. However, the history of tooth loss in the ancestry of modern birds has remained elusive for more than 150 years,” said Mark Springer at the University of California, Riverside.

Birdsong has evolved more than once. Despite sharing many of the same genes, parrots and songbirds gained the ability to learn and copy sounds independently from hummingbirds. More striking is that the group of 50 or so genes that allow some birds to sing is similar to those that give humans the ability to speak. “This means that vocal learning birds and humans are more similar to each other for these genes in song and speech areas in the brain than other birds and primates are to them,” said Erich Jarvis at Duke University in North Carolina.

The common genes are involved in making fresh connections between brain cells in the motor cortex and those that control muscles used to make sounds.

The common genes are involved in making fresh connections between brain cells in the motor cortex and those that control muscles used to make sounds.

This video is called Penguin Fail – Best Bloopers from Penguins Spy in the Huddle (Waddle all the Way).

Penguins must withstand the cold and go without food for months on end, making fat storage a crucial factor in survival. The Adélie penguin were seen to have eight genes involved with metabolism of fatty lipids, though the emperor had only three.

The birds lost their ability to fly but their wings became supremely adapted to underwater acrobatics. Writing in the journal GigaScience, Li’s team describes 17 genes that have driven the re-shaping of penguins’ forelimbs. Mutations in one of those genes, called EVC2, causes Ellis-van Creveld syndrome, a genetic disorder that causes short-limb dwarfism and short ribs in people.

The first penguins evolved about 60m years ago, but the emperors and Adélies have markedly different histories. The Adélie penguin population grew rapidly 150,000 years ago as the climate warmed, but crashed by 40% when a cold and dry glacial period arrived 60,000 years ago.

The emperor penguins fared better, their numbers hardly changing, pointing to a better ability to handle the harsh environment.

Huge genetic analysis of 48 bird species confirms ‘big bang’ in bird diversity after dinosaurs went extinct: here.

The genomes of modern birds reveal how they emerged and evolved after the mass extinction that wiped out dinosaurs 66 million years ago, reports Smithsonian Science: here.

How some snakes became venomous, new research

This video is called The Evolution of Venom – Who is The Most Poisonous? [Full Documentary]

From the University of Texas at Arlington in the USA today:

Team proposes new model for snake venom evolution

17 hours ago

Technology that can map out the genes at work in a snake or lizard‘s mouth has, in many cases, changed the way scientists define an animal as venomous. If oral glands show expression of some of the 20 gene families associated with “venom toxins,” that species gets the venomous label.

But, a new study from The University of Texas at Arlington challenges that practice, while also developing a new model for how snake venoms came to be. The work, which is being published in the journal Molecular Biology and Evolution, is based on a painstaking analysis comparing groups of related genes or “gene families” in tissue from different parts of the Burmese python, or Python molurus bivittatus.

A team led by assistant professor of biology Todd Castoe and including researchers from Colorado and the United Kingdom found similar levels of these so-called toxic gene families in python oral glands and in tissue from the python brain, liver, stomach and several other organs. Scientists say those findings demonstrate much about the functions of genes before they evolved into venoms. It also shows that just the expression of genes related to venom toxins in oral glands of snakes and lizards isn’t enough information to close the book on whether something is venomous.

“Research on venom is widespread because of its obvious importance to treating and understanding snakebite, as well as the potential of venoms to be used as drugs, but, up until now, everything was focused in the , where venom is produced before it is injected,” Castoe said. “There was no examination of what’s happening in other parts of the snake’s body. This is the first study to have used the genome to look at the rest of that picture.”

Learning more about venom evolution could help scientists develop better anti-venoms and contribute to knowledge about gene evolution in humans.

Castoe said that with an uptick in genetic analysis capabilities, scientists are finding more evidence for a long-held theory. That theory says highly toxic venom proteins were evolutionarily “born” from non-toxic genes, which have other ordinary jobs around the body, such as regulation of cellular functions or digestion of food.

“These results demonstrate that genes or transcripts which were previously interpreted as ‘toxin genes’ are instead most likely housekeeping genes, involved in the more mundane maintenance of normal metabolism of many tissues,” said Stephen Mackessy, a co-author on the study and biology professor at the University of Northern Colorado. “Our results also suggest that instead of a single ancient origin, venom and venom-delivery systems most likely evolved independently in several distinct lineages of reptiles.”

Castoe was lead author on a 2013 study that mapped the genome of the Burmese python. Pythons are not considered venomous even though they have some of the same genes that have evolved into very toxic venoms in other species. The difference is, in highly venomous snakes, such as rattlesnakes or cobras, the venom gene families have expanded to make many copies of those shared genes, and some of these copies have evolved into genes that produce highly toxic venom proteins.

“The non-venomous python diverged from the snake evolutionary tree prior to this massive expansion and re-working of venom gene families. Therefore, the python represents a window into what a snake looked like before venom evolved,” Castoe said. “Studying it helps to paint a picture of how these gene families present in many vertebrates, including humans, evolved into deadly toxin encoding genes.”

Jacobo Reyes-Velasco, a graduate student from Castoe’s lab, is lead author on the new paper. In addition to Castoe and Mackessy, other co-authors are: Daren Card, Audra Andrew, Kyle Shaney, Richard Adams and Drew Schield, all from the UT Arlington Department of Biology; and Nicholas Casewell, of the Liverpool School of Tropical Medicine.

The paper is titled “Expression of Venom Gene Homologs in Diverse Python Tissues Suggests a New Model for the Evolution of Snake Venom.” It is available online here.

The research team looked at 24 gene families that are shared by pythons, cobras, rattlesnakes and Gila monsters, and associated with venom. The traditional view of venom evolution has been that a core venom system developed at one point in the evolution of snakes and lizards, referred to as the Toxicofera, and that the evolution of highly venomous snakes, known as caenophidian snakes, came afterward. But little explanation has been given for why evolution picked just 24 genes to make into highly toxic venom-encoding genes, from the 25,000 or so possible.

“We believe that this work will provide an important baseline for future studies by venom researchers to better understand the processes that resulted in the mixture of toxic molecules that we observe in venom, and to define which molecules are of greatest importance for killing prey and causing pathology in human snakebite victims,” Casewell said.

When they looked at the python, the team found several common characteristics among the venom-related gene families that differed from other genes. Compared with other python gene families, venom are “expressed at lower levels overall, expressed at moderate-high levels in fewer tissues and show among the highest variation in expression level across tissues,” Castoe said.

“Evolution seems to have chosen what genes to evolve into venoms based on where they were expressed (or turned on), and at what levels they were expressed,” Castoe said.

Based on their data, the new paper presents a model with three steps for venom evolution. First, these potentially venomous genes end up in the oral gland by default, because they are expressed in low but consistent ways throughout the body. Then, because of natural selection on this expression in the oral gland being beneficial, tissues in the mouth begin expressing those genes in higher levels than in other parts of the body. Finally, as the venom evolves to become more toxic, the expression of those genes in other organs is decreased to limit potentially harmful effects of secreting such toxins in other body tissues.

The team calls its new model the Stepwise Intermediate Nearly Neutral Evolutionary Recruitment, or SINNER, model. They say differing venom levels in snakes and other animals could be traced to the variability of where different species, or different genes within a species, are along the continuum between the beginning and end of the SINNER model.

Castoe said the next step in the research would be to examine the genome of highly venomous snakes to see if the SINNER model bears out. For now, he and the rest of the team hope that their findings about the presence of venom-related in other parts of the python change some thinking on what species are labeled as venomous.

“What is a venom and what species are venomous will take a lot more evidence to convince people now,” Castoe said. “It provides a brand new perspective on what we should think of when we look at those oral glands.”

Human evolution, alcohol and chemistry

This video is called African Animals Getting Drunk From Ripe Marula Fruit.

By Bob Yirka today:

Study shows pre-human ancestors adapted to metabolize ethanol long before humans learned about fermentation

19 hours ago

(—A team of researchers in the U.S. has found evidence to support the notion that our pre-human ancestors were able to metabolize ethanol long before our later ancestors learned to take advantage of fermentation—to create alcoholic beverages. In their paper published in Proceedings of the National Academy of Sciences, the team describes how they genetically sequenced proteins from modern primates and used what they found to work backwards to discover just how long ago our ancestors have been able to metabolize ethanol.

Humans have been consuming beverages that make them tipsy, drunk and/or sick for a very long time, of that there is little doubt. But why do we have the ability to metabolize ethanol in the first place? That’s what the team set out to answer. They began by sequencing an enzyme called ADH4—it’s what’s responsible for allowing us to metabolize ethanol. Other have it as well, but not all metabolize ethanol as well as we do. By sequencing ADH4 found in a 28 including 17 that were primates, the team was able to create a family tree of sorts based on ethanol metabolizing ability. The team then tested those sequences for their metabolizing ability by synthesizing nine kinds of the ADH4 enzyme. Doing so showed the researchers that most early primates had very little ability to metabolize ethanol for most of their early history.

Then, about 10 million years ago, some of the ancestors of modern humans suddenly were able to do a much better job of it, while others that diverged and led to apes such as orangutans, did not. This discovery led the team to wonder what might have occurred to cause this to come about. They note that other evidence has shown that around this same time, the planet cooled slightly, making life a little more difficult for our tree dwelling ancestors. They suggest they began climbing down out of the trees to eat the fruit that fell, which gave them a food advantage and a reason for developing the ability to metabolize —otherwise they would have become too drunk from eating the fermenting fruit to defend themselves or live otherwise normal lives. If true, the theory would also offer a major clue as to why our became terrestrial.

Explore further: Study unlocks secret of how fruit flies choose fruit with just the right amount of ethanol

More information: Hominids adapted to metabolize ethanol long before human-directed fermentation, PNAS, Matthew A. Carrigan, DOI: 10.1073/pnas.1404167111


Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate–ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol.

‘AMERICANS ARE DRINKING THEMSELVES TO DEATH’ “Alcohol is killing Americans at a rate not seen in at least 35 years, according to new federal data. Last year, more than 30,700 Americans died from alcohol-induced causes, including alcohol poisoning and cirrhosis, which is primarily caused by alcohol use.” [WaPo]