Vertebrate animal evolution, new study

This video says about itself:

22 January 2016

The evolution of fish began about 530 million years ago during the Cambrian explosion. Early fish from the fossil record are represented by a group of small, jawless, armoured fish known as ostracoderms. Jawless fish lineages are mostly extinct. An extant clade, the lampreys, may approximate ancient pre-jawed fish. The first jaws are found in Placoderm fossils. The diversity of jawed vertebrates may indicate the evolutionary advantage of a jawed mouth. It is unclear if the advantage of a hinged jaw is greater biting force, improved respiration, or a combination of factors. The evolution of fish is not studied as a single event since fish do not represent a monophyletic group but a paraphyletic one (by exclusion of the tetrapods).

From the University of Konstanz in Germany:

Evolutionary biologists solve puzzle of evolutionary relationships among vertebrates

July 24, 2017

Using the largest and most informative molecular phylogenetic dataset ever analysed, evolutionary biologists were able to construct a new phylogenetic tree of jawed vertebrates. This new tree resolves several key relationships that have remained controversial, including the identification of lungfishes as the closest living relatives of land vertebrates. The evolution of jawed vertebrates is part of our own history since humans belong to the tetrapods more specifically we are mammals, or, even more specifically, primates. The study utilised a novel set of newly developed analyses for building and reconstructing, large-scale genomic datasets. In the future, this method might also be used to reconstruct the evolutionary relationships among other enigmatic groups of organisms that await resolution. The research was done as part of a large collaborative work between several laboratories, with evolutionary biologists Dr Iker Irisarri and Professor Axel Meyer from the University of Konstanz among the principal investigators. Their research results will be published in the journal Nature Ecology & Evolution at Monday, 24 July 2017.

Fishes, amphibians, mammals, snakes, turtles, lizards, crocodiles and birds are all groups of animals that include thousands of species and are morphologically very different from each other. These animal lineages show huge differences in species richness, life history, behaviour and many other aspects of their biology. Notwithstanding these differences, they all possess a backbone and jaws. Since their origin about 470 million years ago, jawed vertebrates have diversified extraordinarily: they include more than 68,000 described species, not counting those that went extinct. Some of them evolved key innovations that enabled their ancestors during the Devonian age to leave water and conquer terrestrial environments on all continents. They even learned to fly more than once.

The evolution of jawed vertebrates is also part of our own history as humans. Understanding the evolutionary relationships between jawed vertebrates has thus been one of the major unsolved puzzles in biology. Despite decades of investigations, attempting to determine how some of these animal groups are related to each other has remained difficult. Estimating a robust tree that depicts evolutionary relationships is the first requirement for understanding the evolution, and also of jawed vertebrates. Their history includes astonishing examples of repeated evolution such as flight (in birds and bats) and echolocation (bats and whales). However, such convergences can only be recognised if the relationships among organisms are estimated with confidence.

The study reconstructs a new phylogenetic tree of jawed vertebrates using the largest and most informative dataset ever analysed. A total of 7,189 genes from 100 species are employed, providing one million nucleotides each to retrace their evolutionary history. Inferring evolutionary relationships by means of statistical methods could be viewed as “molecular archaeology,” as the signals left by evolution in the DNA of our genomes are used to reconstruct events that happened millions of years ago.

The new tree of jawed vertebrates resolves several key relationships that have remained controversial despite decades of research, including the identification of lungfishes as the closest living relatives of land vertebrates, the close association of turtles with crocodilians and birds (the Archosaurs), or the relationships among amphibian groups (salamanders, frogs, caecilians) (supporting the Batrachia hypothesis). The phylogenetic tree was time-calibrated using fossils as anchors, which allowed testing of temporal relationship of diversification with major geological events. For example, two major groups of birds and mammals had been hypothesised to have diversified as a consequence of the extinction of dinosaurs (67 million years ago). The new study invalidates this hypothesis by showing that both groups are in fact much older.

The strength of the study is a novel set of approaches for analysing new, large-scale genomic datasets. The newly developed analytical pipeline solves the most important challenges posed by the new genomic-scale data set and could thus be used to reconstruct the evolutionary relationship of other enigmatic groups of organisms that await resolution.

Turkish regime bans evolution science from schools

This video from the USA says about itself:

But Bruh, Evolution is Just a Theory…Happy Darwin Day!

12 February 2017

Out of 34 surveyed countries, guess where the United States ranked in the public acceptance of evolution?

Correction at the 3-minute and 19-second mark: I said 32 European countries, Turkey, and the US. I meant to say 31 European countries, Japan, Turkey, and the US.

The USA is 33rd out of 34 countries in that survey.

Translated from Dutch NOS TV today:

Turkey eliminates ‘controversial and complex’ evolution science in schools

Turkey has removed evolution science from school programs throughout the country. …

Evolution science used to be part of third-grade biology courses in secondary schools in Turkey. …

The measure had been announced before and led to criticism from Turkish academics. They pointed out to the government in Ankara that strictly religious Saudi Arabia is the only country in the world where evolution science is not taught.

Though the Erdogan regime in Turkey is in a proxy war in Libya with the Saudi absolute monarchy, and is on the brink of a military conflict with the Saudi regime about Qatar, that still does not seem to stop Erdogan from emulating Saudi anti-science fanaticism. Or maybe Erdogan emulates the party of ex-South Korean president, creationist and dictator’s daughter Ms Park, impeached because of her corruption.

Or maybe it is influence of the Turkish millionaire businessman known as “Harun Yahya” (real name: Adnan Oktar).

“Harun Yahya” may sound somewhat less anti-science than many Christian creationists, as he does not attack scientific evidence that some fossils of animals or plants are hundreds of millions years old; while Christian creationists tend to claim that life on earth is just a few thousand years old. Nevertheless, “Yahya” is as anti-evolution as American fellow creationism. In Saudi Arabia, important ally of the USA, and theocratic dictatorial monarchy, teaching evolution is illegal.

In Dutch daily NRC Handelsblad of 20 March 2010, Dirk Vlasblom and others argue that neither “Harun Yahya” nor the Saudi state represent the mainstream of Islamic thought on evolution since Charles Darwin published his Origin of Species.

Translated from Vlasblom’s article; about late 19th century Muslim scholars Al-Afghani and Hussein Al-Jisr, quoting Mohammed M. Ghaly, a contemporary Islamic scholar:

Al-Jisr was much better informed about evolution theory than Al-Afghani, Ghaly says:

“Al-Afghani said that evolutionists believe that a flea in the course of centuries can transform itself into an elephant. Al-Jisr said that according to this theory, humans, like other animals, have evolved via natural selection and that it is not impossible that humans and apes have a common ancestor. He gave the evolution theory the benefit of the doubt and concluded that it does not conflict with the Qur’an, as long as space remains within the theory for God as the ultimate Creator. The creation story in the Qur’an is quite brief, said Al-Jisr, and is intended to affirm belief in God, not for scientific information.

This religious opinion (fatwa) was taken over by scholars from Turkey, from Syria and throughout the Arabic speaking world.”


Al-Jisr wanted his “approval” of Darwin to show that Islam as a rational religion is the ally of all true science, and that Islamic belief is superior to, in his eyes, dogmatic Christianity. That position was welcomed by the Ottoman Sultan Abdul Hamid

Sultan Abdul Hamid II

who wanted progress for his empire like in other countries. He gave Al-Jisr an important award in 1891.

Al-Afghani changed his mind as well. In his book Khatirat (ideas), he wrote around 1900 that evolution theory is indeed compatible with Islam.”

The article says that Al-Jisr’s views are still the mainstream view among Muslims, though conservatives attack them.

‘Jellyfish, not sponges, oldest animals’

This video says about itself:

23 October 2015

Put the comb jelly in the spotlight and watch it groove. The sea creatures turn into pulsating rainbows of movement under the right lighting, no disco ball needed.

From Vanderbilt University in the USA:

Forget sponges: The earliest animals were marine jellies

April 10, 2017

Summary: One of the longest-running controversies in evolutionary biology has been, ‘What was the oldest branch of the animal family tree?’ Was it the sponges, as had long been thought, or was it the delicate marine predators called comb jellies? A powerful new method has been devised to settle contentious phylogenetic tree-of-life issues like this and it comes down squarely on the side of comb jellies

When cartoonist and marine-biology teacher Steve Hillenburg created SpongeBob SquarePants in 1999, he may have backed the wrong side of one of the longest-running controversies in the field of evolutionary biology.

For the last decade, zoologists have been battling over the question, “What was the oldest branch of the animal family tree?” Was it the sponges, as they had long thought, or was it a distinctly different set of creatures, the delicate marine predators called comb jellies? The answer to this question could have a major impact on scientists’ thinking about how the nervous system, digestive tract and other basic organs in modern animals evolved.

Now, a team of evolutionary biologists from Vanderbilt University and the University of Wisconsin-Madison have devised a new approach designed specifically to settle contentious phylogenetic tree-of-life issues like this. The new approach comes down squarely on the side of comb jellies.

The method and its application to this and 17 other controversial phylogenetic relationships was published online on Apr. 10 by the journal Nature Ecology & Evolution in an article titled “Resolution of contentious relationships in phylogenomic studies can be driven by one or a handful of genes.”

For nearly a century, scientists organized the animal family tree based in large part on their judgement of the relative complexity of various organisms. Because of their comparative simplicity, sponges were considered to be the earliest members of the animal lineage. This paradigm began to shift when the revolution in genomics began providing vast quantities of information about the DNA of an increasing number of species. Evolutionary biologists started to apply this wealth of information to refine and redefine evolutionary relationships, creating a new field called phylogenomics. In most cases, the DNA data helped clarify these relationships. In a number of instances, however, it gave rise to controversies that intensified as more and more data accumulated.

In 2008, one of the early phylogenomic studies fingered the comb jellies (aka ctenophores) as the earliest members of the animal kingdom, rather than sponges. This triggered an ongoing controversy with the latest round being a massive study published last month that marshalled an unprecedented array of genetic data to support the sponges’ position as the first animal offshoot.

“The current method that scientists use in phylogenomic studies is to collect large amounts of genetic data, analyze the data, build a set of relationships and then argue that their conclusions are correct because of various improvements they have made in their analysis,” said Antonis Rokas, Cornelius Vanderbilt Professor of Biological Sciences, who devised the new approach with Vanderbilt postdoctoral scholar Xing-Xing Shen and Assistant Professor Chris Todd Hittinger from the University of Wisconsin-Madison. “This has worked extremely well in 95 percent of the cases, but it has led to apparently irreconcilable differences in the remaining 5 percent.”

Rokas and his collaborators decided to focus on 18 of these controversial relationships (seven from animals, five from plants and six from fungi) in an attempt to figure out why the studies have produced such strongly contradictory results. To do so, they got down into the weeds, genetically speaking, and began comparing the individual genes of the leading contenders in each relationship.

“In these analyses, we only use genes that are shared across all organisms,” Rokas said. “The trick is to examine the gene sequences from different organisms to figure out who they identify as their closest relatives. When you look at a particular gene in an organism, let’s call it A, we ask if it is most closely related to its counterpart in organism B? Or to its counterpart in organism C? And by how much?”

These analyses typically involve hundreds to thousands of genes. The researchers determined how much support each gene provides to one hypothesis (comb-jellies first) over another (sponges first). They labeled the resulting difference a “phylogenetic signal.” The correct hypothesis is the one that the phylogenetic signals from the most genes consistently favor.

In this fashion, they determined that comb jellies have considerably more genes which support their “first to diverge” status in the animal lineage than do sponges.

Another contentious relationship the researchers addressed was whether crocodiles are more closely related to birds or turtles. They found that 74 percent of the shared genes favor the hypothesis that crocodiles and turtles are sister lineages while birds are close cousins.

In the course of their study, they also discovered that in a number of contentious cases one or two “strongly opinionated genes” among all the genes being analyzed appear to be causing the problem because the statistical methods that evolutionary biologists have been using are highly susceptible to their influence.

In some cases, such as the controversies over the origins of flowering plants and modern birds, they determined that the removal of even a single opinionated gene can flip the results of an analysis from one candidate to another. In cases like this, the researchers were forced to conclude that the available data is either inadequate to support a definitive conclusion or it indicates that the diversification occurred too rapidly to resolve.

“We believe that our approach can help resolve many of these long-standing controversies and raise the game of phylogenetic reconstruction to a new level,” Rokas said.

Ancient bird Archaeopteryx and Donald Trump

This video says about itself:

23 May 2014

In 1860 in Germany, an unusual fossil was found that shocked the world. It seemed to be a strange combination of a dinosaur and a bird. It was the 150 million-year-old fossil of Archaeopteryx. The skeleton looked like a normal two-legged meat-eating dinosaur, but it had one very special feature: feathers. Its feathers are how it got its name, which means “ancient wing”.

By Peter Frost in Britain:

Archaeopteryx takes to the skies

Friday 24th March 2017

The fossil which proved the evolutionary link between dinosaurs and birds is on tour. PETER FROST explains why this scientific discovery is still relevant today

CHARLES DARWIN published his earth-shattering book On the Origin of Species in 1859. The book outlined the theory of evolution that is still, despite its compelling evidence, being argued about today, especially in the United States bible belt and even in President Donald Trump’s White House.

Part of Darwin’s argument predicted finding fossil evidence for the transitional stage between dinosaurs and what would become birds. At the time of his writing, Darwin predicted that evidence would be uncovered to prove his theory. Critics scoffed and noted the absence of any fossil evidence.

Then in 1861, just two years after his book was published, the fossil of a single feather was uncovered in the limestone layers of Solnhofen in Bavaria, southern Germany. It was clear evidence for the transitional fossil between dinosaurs and birds that Darwin had predicted. The great scientist was vindicated, to the dismay of his critics.

That same year more proof arrived when the first complete specimen of Archaeopteryx was discovered. That first skeleton, later to be known as “the London specimen,” was unearthed near Langenaltheim, Germany. It finally proved the link between dinosaurs and birds.

The fossil was given to local physician Karl Haberlein in return for medical services. Over the years, ten more fossils of Archaeopteryx have surfaced all in the same limestone layers of Solnhofen.

These fossil archaeopteryx have since become key evidence for the origin of birds, the transitional fossils debate and the confirmation of evolution.

The original German fossil was purchased by Britain in 1863 for £700 and was kept initially at the British Museum. When the Natural History Museum opened in South Kensington in 1881, the fossil became one of its most important exhibits.

Until this year it had never left the museum, but since March 18 it has been the star exhibit in a travelling exhibition at the National Museum of Nature and Science in Tokyo.

At first glance the fossil might seem to be just a ragtag assortment of bones, but on closer inspection you can understand why Archaeopteryx is so interesting and important.

Today, the thin limestone slabs that contain the bones of this pivotal creature are considered priceless. If one ever came to auction it would sell for millions of pounds.

The delicate stone has been carefully reinforced using a strong plastic resin but is still incredibly delicate. Museums officials are satisfied the iconic fossil will come to no harm in transit or during its time on display in Japan.

The Archaeopteryx fossil has beautiful impressions of feathers and wings — like a bird. But then it also displays the claws, the long bony tail and the serrated teeth more normally associated with dinosaurs.

Archaeopteryx was roughly the size of a small chicken, with broad wings that were rounded at the ends and a long tail compared to its body length.

Its feathers were very similar in structure to modern-day bird feathers. Unlike modern birds, Archaeopteryx had small teeth as well as a long bony tail, features which the species shared with other dinosaurs of the time.

Directors of modern dinosaur films may have used their computers to make Archaeopteryx into a soaring elegant flyer — something like a giant condor. In reality, it was probably an ungainly beast capable only of flapping flight from one low shrub to another.

In a world where more and more fundamentalist religious views are arguing against the science of evolution, it is important that the convincing evidence of fossils is made as widely known as possible.

President Trump and Vice-President Mike Pence were asked for their thoughts on evolution and Darwin. Pence told Congress he believed in teaching creationism in schools to balance out the theory of evolution.

In answer to a journalists question, he replied: “Do I believe in evolution? I embrace the view that God created the heavens and the Earth, the seas and all that’s in them.”

Pence wants the biblical story of creation taught in biology class alongside evolution.

With backwoodsman Trump as president, it will certainly happen.

Sadly the pair of them are in good company as many people in the United States agree with them.

While the majority of people in Europe and in many other parts of the world accept evolution, the United States lags behind.

Today, four in every 10 adults in the US believe that humans have existed in our present form since the beginning of time. In many religious groups, that number is even higher.

Perhaps then it is good news that the remarkable Archaeopteryx fossil is making the journey to Tokyo as just one of 300 exhibits from the collection of London’s Natural History Museum.

The travelling exhibition features all sorts of objects, including many animals that inspired Darwin directly and demonstrate the truth of evolution.

The artefacts range from a lion from the royal menagerie to an exquisite glass model of an octopus. All have a fascinating science backstory.

“Science is a global endeavour fuelled by wonder and curiosity. So it has been an ambition for us to share these extraordinary treasures with a wider audience,” Natural History Museum director Sir Michael Dixon told us.

“They are the essence of the scientific exploration that inspired pioneers and continues today at the Natural History Museum.”

Other destinations for this exciting touring exhibition beyond Japan will be announced in due course, but I doubt they will be welcome in Trump and Pence’s Washington.

Computer game on evolution of bird flight

This video from the USA says about itself:

Flap to the Future – American Robin

7 February 2017

HELFUL TIP: I play through the level twice. Skip to 3:02 for former personal best time.

Wowza, wowza! A bird game! Of course I’m going to play it longer than I should.

Cornell Lab of Ornithology sent out an email today about this game, so I tried it out and maybe got somewhat good at the American Robin stage. It’s a super easy stage assuming you have a good path routed and can pull off a few tight maneuvers. Though my time is very beatable, I’ll leave it as is since it seems that my new best times aren’t being posted on the leaderboards for some reason. I could always go back and restart my file to have a new best time posted, but I really don’t want to lose the random generated name I currently have on my account. I’ll just have to deal with my initial 05:30.17 minute clear time on the leaderboards.

EDIT: The leaderboards are now functional beyond the initial completion of a level! However, I accidentally reset my game like an idiot, and as such, Lilac-feathered Friendly Heron will forever be displayed with mediocre completion times.

My current mobile name is now Agile Tourmaline-backed Heron, and my current PC name is Least-bearded Fluffheron.

From the Cornell Lab of Ornithology in the USA:

Video Game Lets You Scamper, Glide, and Flap Through the Evolution of Flight

Skip through time and explore how birds mastered the skies with our new video game. Start as an earthbound dinosaur and then feel the thrill of feathered wings and flapping flight. Then jump ahead 100 million years from now to imagine the future of flight. The game is free, mobile-friendly, and runs in a web browser. There’s no app download necessary—just an interest in dinosaurs, flight, or video games. Visit Bird Academy to play (and—bonus—find out your very own fanciful bird name).

Horse evolution, new study

This video says about itself:

7 August 2015

The “evolution of the horse” occurred over a period of 50 million years, transforming the small, dog-sized, forest-dwelling “Eohippus” into the modern horse. Paleozoologists have been able to piece together a more complete outline of the evolutionary lineage of the modern horse than of any other animal.

The horse belongs to the order Perissodactyla, the members of which all share hooved feet and an odd number of toes on each foot, as well as mobile upper lips and a similar tooth structure. This means that horses share a common ancestry with tapirs and rhinoceroses. The perissodactyls arose in the late Paleocene, less than 10 million years after the Cretaceous–Paleogene extinction event. This group of animals appears to have been originally specialized for life in tropical forests, but whereas tapirs and, to some extent, rhinoceroses, retained their jungle specializations, modern horses are adapted to life on drier land, in the much harsher climatic conditions of the steppes. Other species of “Equus” are adapted to a variety of intermediate conditions.

The early ancestors of the modern horse walked on several spread-out toes, an accommodation to life spent walking on the soft, moist grounds of primeval forests. As grass species began to appear and flourish, the equids’ diets shifted from foliage to grasses, leading to larger and more durable teeth. At the same time, as the steppes began to appear, the horse’s predecessors needed to be capable of greater speeds to outrun predators. This was attained through the lengthening of limbs and the lifting of some toes from the ground in such a way that the weight of the body was gradually placed on one of the longest toes, the third.

From Science News:

Horse evolution bucks evolutionary theory

Speciation events not accompanied by big changes in teeth and body size


A cautionary tale in evolutionary theory is coming straight from the horse’s mouth. When ancient horses diversified into new species, those bursts of evolution weren’t accompanied by drastic changes to horse teeth, as scientists have long thought.

A new evolutionary tree of horses reveals three periods when several new species emerged, scientists report in the Feb. 10 Science. The researchers found that changes in teeth morphology and body size didn’t change very much during these periods of rapid speciation.

“This knocks traditional notions that rapid diversification of new species comes with morphological diversification as well,” says paleontologist Bruce MacFadden of the University of Florida in Gainesville. “This is a very sophisticated and important paper.”

The emergence of several new species in a relatively short time is often accompanied by the evolution of special new traits. Classic notions of evolution say that these traits — such as longer teeth with extensive enamel — are adaptive, enabling an animal to succeed in a particular environment. In horses, the evolution of such teeth might permit a shift from browsing on leafy, shrubby trees to grazing on grasses in open spaces with windblown dust and grit.

“You can’t live on a grassland as a grazer and have short teeth,” says MacFadden, an expert in horse evolution. “You’ll wear your teeth down and that’s not a recipe for success as a species.”

Similarly, a big change in body size can indicate a move to a new environment. Animals that live in forests tend to be smaller and more solitary than the larger herd animals that live in open grasslands.

Paleontologist Juan Cantalapiedra and colleagues compiled decades of previous work to create an evolutionary tree of 138 horse species (seven of which exist today), spanning roughly 18 million years. The tree reveals three major branchings of new species: a North American burst between 15 million and 18 million years ago, and two bursts coinciding with dispersals into Eurasia about 11 million and 4.5 million years ago.

The researchers expected to see evidence of an “adaptive radiation,” major changes in teeth and body size that allowed the new horse species to succeed. But rates of body size evolution didn’t differ much in sections of the family tree with low and high speciation rates. And rates of change in tooth characteristics were actually lower in sections of the tree with fast speciation rates, the team reports.

“It’s very tempting to see some change in body size, for example, and say, ‘Oh, that’s adaptive radiation,’” says Cantalapiedra, of the Leibniz Institute for Evolution and Biodiversity Science at the Museum für Naturkunde in Berlin. “But that’s not what we see.”

Cantalapiedra and his collaborators speculate that during the periods of rapid speciation, the environment was so expansive and productive that there just wasn’t a lot of competition to drive the evolution of adaptive traits. Perhaps, for example, North American grasslands were so rich and dense that there was enough energy for various species to evolve without having to develop traits that gave them an edge.

That scenario might be special to horses, says MacFadden, but it might not. Similarly, classic adaptive radiation scenarios might be true in many cases, but as this work shows, not always.

Tiger tail seahorses, new research

This 2013 video shows baby tiger tail seahorses, one day old.

From Science News:

Genome clues help explain the strange life of seahorses

by Cassie Martin

4:30pm, December 14, 2016

A seahorse’s genetic instruction book is giving biologists a few insights into the creature’s odd physical features and rare parenting style.

Researchers decoded a male tiger tail seahorse’s (Hippocampus comes) genome and compared it to the genomes of other seahorses and ray-finned fishes. The analysis revealed a bevy of missing genes and other genetic elements responsible for enamel and fin formation. The absence of these genes may explain their tubelike snouts, small toothless mouths, armored bodies and flexible square tails, the team reports online December 14 in Nature.

Although H. comes may be short a few genes, the seahorse has a surplus of other genes important for male pregnancy — a trait unique to seahorses, sea dragons and pipefish. These genetic differences suggest the tiger tail seahorse has evolved more quickly than its relatives, the researchers conclude.