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How we got bigger, more vulnerable brains

This article is taken from European research magazine Horizon as part of our partnership to share natural environment science stories with readers of More than a Dodo. For more on the development of the brain see our Brain Diaries exhibition site.

One of the major features that distinguishes humans from other primates is the size of our brains, which underwent rapid evolution from about two to three million years ago in a group of our ancestors in Africa called the Australopithecines. During this period, the human brain grew almost three-fold to reach its current size. Scientists know this from skull remains, but have puzzled over how it happened…

This year, the mystery was partially solved by Professor Pierre Vanderhaeghen at the Flanders Institute for Biotechnology in Belgium. Prof. Vanderhaeghen, who was conducting his work as part of the GENDEVOCORTEX project, went on a hunt for the genes that drove the growth of human brains.

Scientists had suspected that brain expansion began in our human ancestors when they evolved genes that are switched on in the foetus, when a lot of key brain development occurs. Prof. Vanderhaeghen therefore looked for genes present in human foetal tissue, but missing from our closest living relatives, apes.

His lab discovered 35 hominid – present only in apes and humans – genes that were active in foetal brain tissue. They then became intrigued by three specific genes – all similar to NOTCH genes, an ancient gene family involved in sending messages between cells and that are present in all animals. They found that the three new genes, collectively named NOTCH 2NL, were created by a “copy and paste error” of an original NOTCH gene.

This error created entirely new proteins which likely helped our ancestors’ cerebral cortex to balloon. This is the part of our brain responsible for our language, imagination and problem-solving abilities. Scientists at the University of California, Santa Cruz, have also identified the NOTCH 2NL genes in DNA from Homo sapiens’ extinct cousins – the Neanderthals and Denisovans.

(The NOTCH 2NL) genes are only present in humans today. They were also present in Neanderthal DNA, but not in chimpanzees
Prof. Vanderhaeghen

Evolution
These genes control the growth rate and differentiation of brain stem cells – the starter cells that multiply and give rise to all neurons in our brain – causing them to seed more nerve cells, which in turn helped to expand brain size. The genes likely led to more neurons and brain tissue in our ancestor’s descendants – including Neanderthals, Denisovans, and modern humans.

Prof. Vanderhaeghen’s research could also help to provide new insights into brain disorders. The US researchers linked genetic faults in DNA that were very similar to NOTCH 2NL, to children born with enlarged brains or small brains. Many of the new human-specific genes are located in a small area of our genome that plays an important role in brain size, according to Prof. Vanderhaeghen.

As DNA in this area closely resembles another part of the genome where it was originally cut and pasted from millions of years ago, errors are more likely, said Prof. Vanderhaeghen. “Patients who have (inherited) deletions in this area tend to be at risk of developing schizophrenia, whereas patients with duplications are more at risk of autistic spectrum disorder,” he said.

Prof. Vanderhaeghen is now studying some 20 of the remaining human-only genes to see how they contributed to the evolution of the human brain.

Something like 40-50% of the Neanderthal genome can still be found in people today.
Prof. Svante Pääbo, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

The use of genetics to study human evolution in this way is helping to transform our understanding of how our own species compared to our ancestors. Traditionally, scientists have studied extinct species by looking at the fossilised remains of their bones. This was how they discovered the existence of Neanderthals, the extinct human species that lived across Europe and much of Asia before vanishing around 40,000 years ago.

In the last decade, however, scientists have begun to look at the DNA inside these bones. Professor Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, has led the way in sequencing DNA of these extinct humans from small bone fragments.

This allows scientists to compare modern human DNA with that of extinct humans, rather than just living relatives like chimps. Already, the work has revealed some surprising findings – our own species appears to have interbred with some of these ancient relatives during our history.

Ancient humans
Scientists have found that the DNA of every person outside Africa is 1-2% Neanderthal, meaning that these extinct human relatives had offspring with our own ancestors.

An international consortium of researchers is sequencing the 3 billion bases that make up the genome of our closest relative – the Neanderthal. The sequence is generated from DNA extracted from three Croatian Neanderthal fossils using novel methods developed for this project. Image credit – Frank Vinken for Max Planck Society

“Different people tend to carry different pieces of the Neanderthal genome,” said Prof. Pääbo, who is undertaking a project called 100 Archaic Genomes to decipher the DNA of ancient human individuals. “Something like 40-50% of the Neanderthal genome can still be found in people today,” he said.

According to Prof. Pääbo, we retained some of this DNA because it offered an advantage to our ancestors. “Some (of this retained DNA) has to do with the immune system, presumably helping us to fight off infectious diseases.”

The power of genetics to unravel the history of human evolution took a new twist in 2010 after Prof. Pääbo’s lab sequenced DNA from a finger bone fragment found by a Russian archaeological team in a remote Siberian cave.

The analysis revealed the bone belonged to a previously unknown human relative, now called Denisovans after Denisova Cave where the bone was found. This mysterious ancient human species lived at around the same time as Neanderthals, but further east into Asia.

Last year, Prof. Pääbo’s group published DNA sequences from a tooth found in the cave – the fourth ever Denisovan discovered. We now know Denisovan DNA carries more variation than Neanderthal DNA, leading scientists to conclude that they were more widespread than the better-known Neanderthals.

Denisovans left a more impressive stamp on some of us than Neanderthals, according to Prof Pääbo. Their DNA can be found in people across Asia today, while indigenous peoples of Papua New Guinea and Australia may carry up to 5%. Tibetans also carry some Denisovan DNA in their genomes, which has helped them adapt to life at high altitudes where there is little oxygen in the atmosphere.

Prof. Pääbo and his colleagues will soon publish their third high-quality genome – where almost the entire DNA sequence is intact – of a Neanderthal from Siberia. A deciphered genome of this quality allows for better DNA comparisons and could tell us more about the evolution of important genes – such as those linked to the development and function of the brain. It will add yet another puzzle piece to help us understand the history of our closest extinct relatives, according to Prof. Pääbo.

“There may even be other forms of extinct humans out there to be discovered by studying the DNA of the (ancient) bones we find,” he said.

Top image: The skull of a Australopithecus sediba, a species of Australopithecines, who were our ancestors and whose brains started to grow two to three million years ago. Image credit – Australopithecus sediba by Brett Eloff, courtesy Profberger and Wits University is licensed under CC BY-SA 4.0.

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This post Genetic error led humans to evolve bigger, but more vulnerable, brains was originally published on Horizon: the EU Research & Innovation magazine | European Commission.

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Argonauts: astronauts of the sea

by Mark Carnall, Life Collections manager

Cephalopods are a remarkable group of molluscs that includes nautilus, octopuses, cuttlefish and various groups of ‘squid’. The other major groups of molluscs includes more familiar shelled animals such as gastropods (snails and slugs), bivalves, and chitons, as well as some less familiar forms.

In natural history museums, molluscs are normally represented by shell collections because the hard shelly parts are easier to preserve and store than the soft tissue. This creates a bias against the soft-bodied cephalopods, such as squids, octopuses and cuttlefish, because aside from the cuttlebones of cuttlefish and the thin gladius in squids there aren’t many hard parts that can be preserved to represent these animals in dry collections. For octopuses it’s normally only the beak and microscopic radulae, a toothed tongue-like structure, that can be preserved. But there is one notable exception: the eggcases of argonauts.

Model of Argonauts argo. Image: Mark Carnall
Model of Argonauta argo. Image: Mark Carnall

Argonauts, four* species of octopuses in the genus Argonauta, are unusual in that they produce a paper-thin eggcase, sometimes referred to as a shell. Unlike a true shell it’s not attached to the body of the argonaut, but secreted by two specialised webbed arms. The eggcases themselves are sometimes called paper nautiluses because they resemble the spiral shells of nautiluses, but they are structurally and functionally very different.

External morphology of a female paper nautilus (Argonauta argo) with egg case. Poli, Giuseppe Saverio. Testacea utriusque Siciliae. (1791-1827).
External morphology of a female paper nautilus (Argonauta argo) with eggcase. Poli, Giuseppe Saverio. Testacea utriusque Siciliae. (1791-1827). http://biodiversitylibrary.org/page/44020354

Argonaut eggcases wash on up shorelines around the world and have been known for centuries. But it’s only comparatively recently that the origin and use of these cases has been described. When eggcases containing live argonauts were first encountered it was supposed that argonauts were reusing empty shells created by another animal, much like hermit crabs repurpose gastropod shells.

Pioneering research by marine biologist Jeaneatte Villepreux-Power in the 19th century led to observations of Octopus and Argonauta, confirming that the eggcases are made and repaired by female argonauts. It wasn’t until 2010 that we understood how argonauts use these cases to float in the ocean. It turns out that they ‘bob’ their shells to gulp a pocket of air. Then, using their second pair of arms, they trap the air in the top of the shell and dive releasing enough air to maintain the required buoyancy.

Only female argonauts make the eggcases, so the free-floating males are tiny in comparison. In addition to providing a home for female argonauts, these structures are used to brood embryos in. One eggcase was described with nearly 50,000 embryos attached to the inside of the shell.

Preparation showing series of argonaut egg cases of varying sizes.

Thanks to their oddity and beauty these eggcases are common in museum collections, but they represent one of the marvels of evolution. Unlike many bottom-dwelling octopuses, female argonauts have evolved this amazing structure to function as an underwater craft to allow them to leave the ocean floor and inhabit the open oceans: the true astronauts of the sea.

To celebrate the pioneering work of Jeaneatte Villepreux-Power, these amazing animals, their eggcases, and a selection of museum specimens are on display in the Museum’s Presenting… case until the 3 July 2018.

Mark writes more about these ‘astronauts of the sea’ on the Guardian’s Lost Worlds Revisited blog.

* Tens of species of living argonauts have been described, however four are currently recognised with a few dubious species.

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Life’s big bang?

by Harriet Drage and Scott Billings

You may have heard of the Cambrian Explosion, an ‘event’, starting roughly 540 million years ago, when all the major animal groups suddenly appear in the fossil record, an apparent explosion of life and evolution.

But was there really an evolutionary explosion of all these animal groups, or is the lack of evidence from earlier periods due to some peculiarity of the fossilisation process? The debate has rumbled on for a number of years.

Now, a new study from our research team, the University of Oxford’s Department of Zoology, and the University of Lausanne, claims that the early Cambrian saw the origins and evolution of the largest and most important animal group on Earth – the euarthropods – in a paper which challenges two major pictures of animal evolution.

Euarthropoda contains the insects, crustaceans, spiders, trilobites, and a huge diversity of other forms alive and extinct. They comprise over 80 percent of all animal species on the planet and are key components of all of Earth’s ecosystems, making them the most important group since the dawn of animals over 500 million years ago.

Exceptionally preserved soft-bodied fossils of the Cambrian predator and stem-lineage euarthropod Anomalocaris canadensis from the Burgess Shale, Canada. Top left: Frontal appendage showing segmentation similar to modern-day euarthropods. Bottom right: Full body specimen showing one pair of frontal appendages (white arrows) and mouthparts consisting of plates with teeth (black arrow) on the head. Images: A. Daley.

A team based at the museum, and now at Lausanne, conducted the most comprehensive fossil analysis ever undertaken on early euarthropods, to try and establish whether these animals really did emerge in the early Cambrian period, or whether fossilisation just didn’t occur in any earlier periods.

In an article published today in the Proceedings of the National Academy of Sciences they show that, taken together, the total fossil record does show a gradual radiation of euarthropods during the early Cambrian, 540-500 million years ago, challenging other ideas that suggest either a rapid explosion of forms, or a much slower evolution that has not been preserved in the fossil record.

Each of the major types of fossil evidence has its limitation and they are incomplete in different ways, but when taken together they are mutually illuminating
Professor Allison Daley

Reconstruction of the Cambrian predator and stem-lineage euarthropod Anomalocaris canadensis, based on fossils from the Burgess Shale, Canada. Reconstruction by Natalia Patkiewicz.

By looking at a huge range of fossil material the researchers ruled out the possibility that Pre-Cambrian rocks older than around 541 million years would not have preserved early euarthropods. The only plausible explanation left is that the origins of this huge animal group didn’t evolve until about 540 million years ago, an estimate which also matches the most recent molecular dating.

The timing of the origin of Euarthropoda is very important as it affects how we view and interpret the evolution of the group and its effects on the planet. By working out which groups developed first we can trace the evolution of physical characteristics, such as limbs.

Exploring all the evidence like this allows us to make an informed estimate about the origins of key animal groups, leading to a better understanding of the evolution of early life on Earth.

Model of the Cambrian stem lineage euarthropod Peytoia, based on fossils from the Burgess Shale. Top left: Closeup of the mouth parts and frontal appendages. Bottom right: Overall view of the body. Model and image: E. Horn.

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Deal or no deal

Melinopterus

by Darren Mann, Head of Life Collections

In a previous article on this blog I reported the discovery, in an insect collection, of the 21st British specimen of the ‘Regionally Extinct’ dung beetle Melinopterus punctatosulcatus. And since then, I’ve been on the hunt for more…

Heading out to numerous other museum collections I discovered more specimens, all collected in the same locality – Deal in Kent. In Ipswich Museum there are six, collected by C. Morley in 1896; there are two in the Natural History Museum, London, collected by G.C. Champion; and in the Museum of Zoology, Cambridge there are two collected by G.C. Hall in 1883.

Ipswich Museum
A view through the microscope of Melinopterus punctatosulcatus held in the collections of Ipswich Museum, collected by C. Morley in 1896

But the earliest and most recent finds are both in the National Museum of Scotland – one from May 1871, in the G.R. Waterhouse collection, and one from 1923, in the T. Hudson-Beare collection. So now we know of 42 specimens of this beetle with data and we know that the species occurred at Deal for about 50 years. But why are there no records after this time?

The Deal sandhills in Kent were famous for their insects, but even as long ago as 1900 entomologists* were discussing the negative impact of “summer camping-out stations and the modern craze for the ‘Royal and Ancient Game of Golf'” on beetles and butterflies in the area.

Today, most of the sandhills are gone and there are no grazing animals other than a few rabbits. Most of the surrounding land is either developed as a golf course or under agricultural management. So, is the possible local extinction of this dung beetle due to habitat loss and a lack of dung?

Deal
Deal, Kent: the original locality for Melinopterus punctatosulcatus, with remnants of the sandhills in the distance

To try and answer this question, naturally I went looking for poop in Deal. In a field in Sandwich Bay I could hear sheep bleating in the distance, although poo was scarce. Eventually I found a few old plops and inside were ten Calamosternus granarius, a small dung beetle. This was good, but my main target was Melinopterus punctatosulcatus.

Melinopterus punctatosulcatus edit
A specimen from the Museum of Melinopterus punctatosulcatus, previously listed as ‘Regionally Extinct’ in Britain, but now rediscovered in Deal, Kent

I probed the poop further. To my delight, crowded in the remaining squishy bit were four other species. On close inspection, one of these was hairy, so a male, and much darker than its close relatives. It fitted perfectly with my expectations for Melinopterus punctatosulcatus after seeing so many examples in museum collections. Success! This beetle, misidentified in museum collections for so long, and not seen since the 1920s in Deal, is indeed hanging on in Kent.

Disappointingly, after a further few days of searching, only a handful more specimens were seen. This suggests that either the species exists at low population levels, or that it was it was not the peak emergence period when I was there. Nonetheless, a species not recorded anywhere in the UK for over 70 years is actually still here.

Now hopefully we can encourage local land owners to help conserve this all-important dung fauna and flora.

* Walker, J.J. 1900. The Coleoptera and Hemiptera of the Deal Sandhill. Entomologist Monthly Magazine 36: 94-101.

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Who shot the Dodo?

By Scott Billings, Digital Engagement Officer

If ever the Oxford Dodo were to have squawked, its final squawk may have been the saddest and loudest. For the first time, the manner of death of the museum’s iconic specimen has been revealed: a shot to the back of the head.

This unexpected twist in the long tale of the Oxford Dodo has come to light thanks to a collaboration between the Museum and the University of Warwick. WMG, a cutting-edge manufacturing and technology research unit at Warwick, employed its forensic scanning techniques and expertise to discover that the Dodo was shot in the neck and back of the head with a 17th-century shotgun.

Mysterious particles were found in the specimen during scans carried out to analyse its anatomy. Further investigation of the material and size of these particles revealed them to be lead shot pellets of a type used to hunt wildfowl during the 1600s.

The Oxford Dodo specimen, as it has come to be known, originally came to the University of Oxford as part of the Tradescant Collection of specimens and artefacts compiled by father and son John Tradescant in London in the 17th century. It was thought to have been the remains of a bird recorded as being kept alive in a 17th-century London townhouse, but the discovery of the shotgun pellets cast doubt on this idea, leaving the bird’s origins more mysterious than ever.

Dodos were endemic to the island of Mauritius in the Indian Ocean. The first European accounts of the bird were made by Dutch explorers in 1601, after they rediscovered the island in 1598. The last living bird was sighted in 1662.

The story of the Oxford Dodo is especially significant because it represents the most complete remains of a dodo collected as a living bird – the head and a foot – and the only surviving soft tissue anywhere in the world.

This discovery reveals important new information about the history of the Oxford Dodo, which is an important specimen for biology, and through its connections with Lewis Carroll and Alice’s Adventures in Wonderland of great cultural significance too.
– Professor Paul Smith, Museum director

The Oxford Dodo represents the only soft tissue remains of dodo in the world. This iconic specimen was taken from the Museum to WMG at the University of Warwick for CT scanning.

WMG’s CT scans show that this famous symbol of human-caused extinction was shot in the back of the head and the neck, and that the shot did not penetrate its skull – which is now revealed to be very thick.

The discovery of such a brutal demise was quite a surprise as the scans were actually focused on discovering more about the Dodo’s anatomy, as well as how it lived and died. This work will continue, but we now have a new mystery to solve: Who shot the Dodo?

What’s the next step? It is possible that the isotope of lead in the shot could be analysed and traced to a particular ore field. This might tell us what country it was mined in, and perhaps what country is was made in, and ultimately reveal who shot the Dodo.

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A genetic map of Britain

Our Settlers exhibition tells the story of the peopling of Britain, from the arrival of the earliest modern humans over 40,000 years ago to the population of the present day. At the centre of the exhibition is a genetic map of Britain – the first of its kind to be produced of anywhere in the world. But what exactly does this map show us and how was it created? Brian Mackenwells from the Wellcome Centre for Human Genetics explains…

While maps can be used to show us where we need to go, the one at the heart of the People of the British Isles study was used to show us where we’ve been. Researchers from the Wellcome Centre for Human Genetics wanted to reach back through time by looking at our genetic code.

We obviously can’t travel back a hundred years and sequence people’s DNA, so the next best thing is to sequence the genome of people whose grandparents were all from the same rural area. This is because people in rural areas at that time had a tendency not to travel very far, so the researchers guessed that the genes of their descendants would be like (slightly jumbled) snapshots of the genetic history of the area they were from.

This video, commissioned from Oxford Sparks especially for the exhibition, expands on this idea.

So the People of the British Isles researchers sequenced the DNA of just over 2,000 people and set to work analysing it all. The scientists looked for individuals with common genetic patterns and grouped them together. They had no idea where the individuals were actually from; the system just grouped people whose small genetic variations seemed to be the most similar to each other.

Here’s an example of the process. Imagine you were presented with a list of colours like these and asked to group them.

You would probably group them something like this:

There would be a ‘sort of red’ group, a ‘sort of green’ group, and a ‘sort of blue’ group. This is what the pattern-matching system was trying to do with genetic codes: make clusters of people who seemed to be similar to each other based on very small genetic variations.

But the really surprising bit came next. We took each individual in the study and plotted them on a map of Britain based on the location of their grandparents, using a symbol to denote which genetic cluster they had been placed in.

We weren’t sure what to expect. Would the symbols be spread out randomly over the map,  or would there be groupings? What might the groupings mean?

The result was striking: the genetic clusters are, for the most part, linked to quite specific geographical areas, as you can see in the final map here.

The People of the British Isles genetic map of Britain was the first map of its kind of anywhere in the world. Each marker represents a participant in the study, and the different symbols represented different genetic clusters. It’s clear that the genetic clusters are connected with geography.

What is this map revealing to us? When we compared these different groups to the unique genetic markers of different European populations, working with archaeologists and geographers, we were able to start to understand the meaning of the map. You can clearly see the genetic footprints left by historical migration and events from hundreds of years ago. The video below explains more about this.

The locations of many of the clusters correspond to regions controlled by known historical tribes and kingdoms. The map also shows how places like Northern Ireland and Western Scotland seem to share a genetic heritage.

You can learn more about the map, and the things we’ve learned from it, at the Settlers exhibition until the 16 September 2018.