Category Archives: Mammals

Genome sequencing mountain gorillas reveals the genetic impact of inbreeding

Our genetic cousins, mountain gorillas, have been the subject of ongoing conservation efforts for decades. Despite this there are fewer than 900 left in the wild because of poaching and habitat destruction. Now, genetic sequencing has revealed the toll these constant threats have taken on their genome.

Our research, published in Science, reveals a striking loss of genetic diversity, but also finds more to be optimistic about than expected.

Man-made threats

Gorillas are classified into two species: one in West Africa (Gorilla gorilla) and one to the east (Gorilla beringei) in the centre of the continent. Mountain gorillas are a subspecies of the eastern gorilla species, and differ from the others in that their habitat ranges to high altitudes. This has consequences for their diet and physiology – for example, they have thicker and longer fur, which helps them survive the colder temperatures and the wetter, mistier environment.

The number of mountain gorillas living in the Virunga volcanic mountain range (on the borders of Rwanda, Uganda and the Democratic Republic of Congo) dropped to around 253 in 1981. Since then, conservation efforts have bolstered numbers there to approximately 480. There is another colony of about 400 of mountain gorillas about 30 km to the north. This adds up to only around 880 mountain gorillas surviving in the wild.

Our new research is based on blood samples collected from wild-born gorillas and is the first whole genome study; previous studies have used DNA from fecal samples or looked at much smaller sequences.

Chronic decline

Analysis of the genome data revealed that as well as suffering a dramatic collapse in numbers during the last century, mountain gorillas had already experienced a long decline going back many thousands of years. These events have resulted in a very substantial loss of genetic diversity and more inbreeding than expected: it turns out that two mountain gorillas are typically identical at more than a third of their genetic sequence – the comparable number for most humans is only a few percent.

Inbreeding increases the threat from disease and environmental change by reducing mountain gorillas’ ability to adapt. It also means they carry a larger burden of harmful mutation than other gorilla species.

Silver lining

However there is a silver lining: many of the most severely harmful mutations are less common in mountain gorillas than in other gorilla subspecies, and appear to have been purged. These are mutations that disrupt the operation of a gene by prematurely terminating the protein it produces. Such mutations are expected to be more problematic than other others which may only alter the protein slightly, and some of them will be very harmful or even lethal if the protein is doing an essential job in the body.

To see why severely harmful mutations can be reduced as a result of inbreeding, consider that in a large population someone carrying such a mutation is less likely to meet and have children with another carrier. The mutation is able to persist because we have two copies of every gene, meaning it is usually only present in one copy in offspring. The lethal effect is masked by a working copy and can be passed on. However in an inbred population, carriers are more likely to meet others with the same mutation, meaning their children are more likely to have two copies, with lethal consequences for the children and preventing the mutation from being passed on.

As great apes, mountain gorillas are close evolutionary cousins of humans, so understanding their evolution also provides some insights into our own. For example, it is believed that our own ancestors also experienced severe reductions in population size at least once during human evolution, and other close relatives such as the Neanderthals went extinct in this way. Mountain gorillas thus provide an opportunity to study how humans might have adapted genetically to this condition.

Justice for poachers

It is also hoped that the detailed, whole-genome sequence data gathered through this research will aid conservation efforts in a practical way. Now that a genome-wide map of genetic differences between populations is available, it will be possible to identify the origins of gorillas that have been illegally captured or killed. This will enable more gorillas to be returned to the wild and will make it easier to bring prosecutions against those who poach gorillas for souvenirs and bush meat.

So, despite the threats they face, there are reasons to be optimistic about the future for mountain gorillas, if conservation efforts can be sustained and further encroachment on their habitat resisted. This research suggests that although low in genetic diversity, they have not yet crossed a point of no return. They can continue to survive and will return to larger numbers if we help them.

This article was originally published on The Conversation.
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Why is CRISPR the Science Buzzword of Early 2015?

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CRISPR isn’t just the cutting edge of genetic modification – it is re-framing our understanding of evolution.

What is CRISPR?

CRISPR is a DNA sequence that can do something most other genes can’t. It changes based on the experience of the cell it’s written in. It works because of a natural ability for cells to rewrite their own genetic code, first discovered in 1987. The name CRISPR was coined in 2002, and it stands for “clustered regularly interspaced short palindromic repeats”. They function as a method of inserting recognizable DNA of questionable or dangerous viruses into DNA strands so that the offspring of the cell can recognize what its ancestors have encountered and defeated in the past. By inserting a CRISPR-associated protein into a cell along with a piece of RNA code the cell didn’t write, DNA can be edited.A 2012 breakthrough involved, in part, the work of Dr. Jennifer A. Doudna. Doudna and the rest of the team at UC Berkley were the first to edit human DNA using CRISPR. Recently, in March 2015, she warned this new genome-editing technique comes with dangers and ethical quandaries, as new tech often does. Dr. Doudna in a NYT article, she called for a planet-wide moratorium on human DNA editing, to allow humanity time to better understand the complicated subset of issues we all now face.

CRISPR-related tech insn’t only about editing human genes, though. It affects cloning and the reactivation of otherwise extinct species. It isn’t immediately clear what purpose this type of species revival would have without acknowledging the scary, rapidly increasing list of animals that are going extinct because of human activity. Understanding and utilizing species revival could allow humans to undo or reverse some of our environmental wrongs. The technique may be able to revive the long lost wooly mammoth by editing existing elephant DNA to match the mammoth‘s, for instance. Mammoths likely died out due to an inability to adapt to natural climate change which caused lower temperatures in their era, and are a non-politically controversial choice but the implications for future environmentalism are promising.

Each year, mosquitoes are responsible for the largest planetary human death toll. Editing DNA with CRISPR bio-techniques could help control or even wipe out malaria someday. The goal of this controversial tech is to make the mosquito’s immune system susceptible to malaria or make decisions about their breeding based on how susceptible they are to carrying the disease. The controversy around this approach to pest and disease control involves the relatively young research behind Horizontal Gene Transfer, where DNA is passed from one organism to an unrelated species. A gene that interferes with the ability of mosquitoes to reproduce could end up unintentionally cause other organisms to have trouble reproducing. This info is based on the work of , , http://www.biorxiv.org/content/early/2014/12/27/013276

Even more controversial are the startups claiming they can create new life forms, and own the publishing rights. Austen Heinz’ firm is called Cambrian Genomics which grows genetically-controlled and edited plants. The most amazing example is the creation of a rose species that literally glows in the dark. Cambrian is collaborating with the rose’s designer, a company called Glowing Plant, whose projects were eventually banned from kickstarter for violating a rule about owning lifeforms. Eventually, Heinz wants to let customers request and create creatures: http://www.sfgate.com/business/article/Controversial-DNA-startup-wants-to-let-customers-5992426.php#photo-7342819

The final example in an ongoing list of 2015 breakthroughs involving CRISPR is this CRISPR-mediated direct mutation of cancer genes in the mouse liver might be able to combat cancer. It’s the second cancer-related breakthrough in 2015 that affects the immune system, the first was on Cosmos about a week back: Accidental Discovery Could Turn Cancer Cells Into Cancer-Attacking Immune Cells.

Other Related Cosmoso.net articles:

Pre-Darwinian Theory of Heredity Wasn’t Too Far Off

Wooly Mammoth Poised to be the First De-Extincted Animal, Son~!

Jonathan Howard
Jonathan is a freelance writer living in Brooklyn, NY

Reintroduce lynx? Fine, but we must control the apex predator

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The lynx: a short-tailed felid weighing up to six times more than your domestic moggy. This large carnivore once roamed the British Isles 1,300 ago but, due to habitat destruction, overhunting of its prey and purposeful killing by humans, the species was driven to extinction in the UK. Now, there are plans to reintroduce this species to three sites in England and Scotland. But what are the chances of a success?

The International Union for Conservation of Nature (IUCN) has strict guidelines for reintroducing species into the wild. One of the key recommendations they make is that the main causes of the historical decline must be addressed to ensure success of the reintroduction.

In terms of the threats to lynx, we now have stringent land management policies in place so it is unlikely that the cat’s preferred forested habitat will be destroyed. The previous decline in the prey base (notably deer) is also not a problem today – in fact, many would agree that we have too many deer due to the lack of natural predators. But it is unclear to what extent the last threat – the purposeful killing by humans – is under control.

The human factor

Previous research has noted that the main cause of death among carnivores that have been reintroduced is due to humans. Although attitudes towards carnivores are generally positive in the UK, they become more negative among the people that could be adversely affected by these species and it is these people who have the power to kill. These are the farmers, gamekeepers and hunters (all of whom are allowed to own guns) who will be sharing their land with this species and may be worried about the damage that lynx can cause.

Are we ready for the lynx? Ask the people with guns.
David Cheskin/PA

The IUCN clearly states:

Any translocation will impact and be impacted by human interests. Social, economic and political factors must be integral to translocation feasibility and design. These factors will also influence implementation and often require an effective, multi-disciplinary team, with technical and social expertise representing all interests.

Much research to date has looked into the biological factors surrounding the potential success of reintroducing lynx (eg. here, here and here), but far less attention has been focused on these important social, economic or political aspects. And it is the human dimension that will play a large part in dictating whether this project succeeds or fails.

It is therefore worrying that amongst the main proponents of the lynx reintroduction, only one social scientist is listed on its team of experts (the rest being biologists). This is not uncommon amongst species reintroduction projects: the Scottish Beaver Trial reintroduction team also does not have a social scientist.

Given the widespread call among conservationists to include more social science into wildlife management schemes, it is disheartening to see that more is not being done in this country to integrate the human aspects of conservation into environmental projects.

Consider the negative

Although I cannot deny that the lynx would bring positive effects to this country by reducing deer populations (which might have additional benefits for young trees), we cannot disregard the potential negatives. Lynx can occasionally kill livestock, which could have economic and psychological costs.

Some of the strongest opposition to reintroducing the lynx comes from the deer community.
Red deer image via www.shutterstock.com

The frequency of predation may be low, but this has not stopped the continual persecution of reintroduced predators in other parts of the world, such as the Mexican wolf. It is therefore crucial that we do not underestimate the potential for opponents of the lynx reintroduction to negatively impact the success of the project.

Research in other areas of Europe has shown that attitudes towards lynx are, in general, positive. It is likely that this is the case in the UK too, and I am sure that many British people would love to have lynx wandering the countryside again. Like the Scottish Wildlife Trust, I too feel that we have a moral and ecological case to bring this species back, but until more extensive work is undertaken to address the threat of human persecution, I do not hold out much hope for this felid’s future in the UK.

This article was originally published on The Conversation.
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Prehistoric Hippo Was Closely Related to Whales

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Perhaps one of the strangest stories of evolution is that of the whales – the descendants of wolf-like creatures who roamed the Earth eons ago. Proteins in their genomes once coded for legs, and their fins are actually shaped like hands with wrists, reminders of their long, proud mammalian lineage. It seems strange – why did animals whose long ago descendants crawl out of the sea onto dry land, return to the sea? The obvious answer is survival, adapting to an ever changing world. As to how, the short answer would be that it simply didn’t happen overnight. The modern hippopotamus, whose name literally means “water horse,” is actually a distant relative of the whale, a four-legged mammal that spends much of its life in the water. The hippo family shares a number of ancestors that adapted to living in water for the long term. Now, a recent fossil expedition in Africa has unearthed what paleontologists suspect may have been one of the first hippos to have roamed the Earth.

The first hippo, paleontologists estimate, based on the size of the newly excavated animal from a Kenya rock bed, was likely a little larger than a modern horse, just a little smaller than modern hippos, and weighing several hundred pounds.

“They are slender hippos, very thin hippos,” said Fabrice Lihoreau, a paleontologist at the University of Montpellier in France who co-authored the new paper.

This newly discovered creature, known as Epirigenys lokonensis, also had its evolutionary roots in Africa, as the study confirmed. The genetic evidence suggests that the common ancestor shared by hippos and whales existed some 53 million years ago. Epirigenys first roamed the Earth a mere 15 million years ago – with only a few known specimens found in between.

The current hypothesis is that one of the prehistoric ancestors of hippos were a family of semi-aquatic mammals, the anthrocotheres, which appeared around 40 million years ago. At one time, these ancient beasts were prevalent across the globe, with fossils found everywhere from North America to Asia. However, any ancestry it had to hippos was never identified.

The inspiration for this dig began at Kenya’s Nairobi Museum, where Lihoreau and his colleagues stumbled upon one small exhibit in the collections – a rather unusual jaw belonging to an anthrocothere. This particular jawbone had been discovered at the Turkana Basin, a fossil-rich rock formation in Kenya, where the rock layers carry a myriad of fossils dating all the way back to the Cretaceous Period and leading right up into the present day. Among the fossils in these rocks are our own recent ancestors, the Homo erectus and the Neanderthals. The exact location where the jawbone was located was a large body of water 28 million years ago, containing a plethora of crocodilian fossils. Unfortunately, the rock’s thickness made digging difficult, where they risked damaging the fossils.

While they hunted for new potential locations, the researchers took notice of a small spot called Lokone Hill with considerably softer rock that could easily be removed with acid, making the excavation much easier. The first few finds were of several uncovered teeth, which they confirmed had come from a new species of anthrocothere, previously unknown to science, and newly discovered at the Lokone Hill, found alongside sets of molars and incisors, the trademarks that this certainly belonged to a mammal. Most promising perhaps, was that the molars bore a striking similarity to the teeth found in modern-day hippos – bearing a prominent pattern that looked like a bladed three-leaf, not too different from a maple leaf shape. The new species earned its name Epirigenys lokonensis, a rough translation from Latin into “original hippo from the Lokone,” according to Lihoreau.

It was this molar pattern which linked the E. lokonensis as the hippo’s direct ancestor. (the teeth of mammals, particularly herbivorous ones, are so distinct from each other that any discovered patterns found on the molars almost act as a fingerprint for the species.) Paleontologists who are lucky enough to find one can establish a clear lineage between an extinct creature and its closest living descendants.

E. lokonensis weighed only about 220 pounds according to Lihoreau’s estimate, which is considerably smaller than the plodding two to three ton hippo that roams the African wetlands today, an aggressive creature that may or may not have earned its fearsome reputation as the most dangerous animal in Africa, known to attack if provoked. Just like their modern ancestors, however, the Lokone hippo lived primarily in the water.

“When you do a safari, you want to see a lion and you want to see an antelope, but these animals come from Asia ” Lihoreau told Live Science in an interview. “They are not really African mammals. This is really an African mammal.”

The paper describing this new species was published yesterday in the journal Nature Communications.

James Sullivan
James Sullivan is the assistant editor of Brain World Magazine and a contributor to Truth Is Cool and OMNI Reboot. He can usually be found on TVTropes or RationalWiki when not exploiting life and science stories for another blog article.

Behavioural study shows that rats know how to repay a favour

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By Gilbert Roberts, Newcastle University

If I scratch your back and you scratch mine, then we’re both better off as a result – so goes the principle of reciprocity, one of the most popular explanations for how co-operative behaviour has evolved. But what if one partner provides a better service than another? A paper by Dolivo and Taborsky shows that Norway rats will only give as good as they get.

As humans, we are familiar with the concept of helping those who help us, whether it is by buying rounds of drinks or expelling diplomats. But demonstrating reciprocity in other species has proved more challenging. Part of the reason for this may be that reciprocity is rarer than might be imagined. But a major factor is the difficulty of establishing an objective means of measuring the costs and benefits of apparently helpful behaviour in the field.

Do as you would have done to you

This is where the laboratory rat comes in. If the economics of behaviour elude field measurement, an attractive alternative is to perform controlled lab experiments. Dolivo and Taborsky trained rats to pull on a stick that drew a food item within reach of a rat in an adjoining cage separated from them by wire mesh.

They then introduced a further treatment in which an experimental rat was placed in a cage with other caged rats on either side. On one side the rat pulled a stick that provided pieces of carrot to the rat in the central cage, while the other pulled a stick that produced banana pieces. In subsequent trials the focal rat had the opportunity to repay the other rats using the same stick apparatus to deliver food items.

Now, the rats had typically turned their noses up at the carrot and showed a strong preference for the more desirable banana. On the basis that the banana-providing rat should therefore be remembered as the superior partner, the authors predicted that in the test phase the focal rat would more readily help provide for banana-purveying rats than for carrot-offering rats. This proved to be the case, so it did seem that the rats that had provided better help in the past received greater rewards, as expected if they were behaving reciprocally.

Behavioural scientists have questioned the extent to which non-human animals have the capacity to engage in reciprocity without being exploited by “cheats” who take advantage of their kindness. It seems that this is cognitively demanding, in terms of bringing together the memories of who did what and judging how to respond.

Dolivo and Taborsky’s latest results show that rats can recall the quality of help provided and by which rat, and adjust their subsequent behaviour so as to invest more time and energy in helping those that helped them. Taken together with the Taborsky group’s prior findings that rats are more likely to help a partner that had helped them before than one that had not helped them at all, these results provide interesting insight into how animals are able to manage the challenges of conditional co-operation.

Not just rats

It is increasingly apparent that we shouldn’t underestimate the ability of animals to engage in reciprocity. For example, a 2006 study by Alicia Melis and colleagues reported that chimpanzees took into account their experience with potential partners when choosing which to recruit for a collaborative venture.

A similar effect is seen among client fish – those species that are co-operatively served by other species of cleaner fish – which will preferentially associate with cleaner fish they have observed behaving in a co-operative manner. So there is evidence that other animals can assess the quality of partners and behave conditionally – a requirement for reciprocity to work.

The latest paper fits within a resurgence of interest in reciprocity, as researchers take up the challenge laid down by critiques questioning its occurrence in non-human animals. For example, the classic case of blood donation among vampire bats has been revisited with a demonstration that the best predictor of donations received was whether donations had been made.

Meanwhile recent experiments with pied flycatchers also appear to demonstrate that birds will help those that have helped them mob owls in their territories.

Good examples of reciprocity in non-human animals may be uncommon but Dolivo and Taborsky’s work supports the view that, where reciprocity does pay, animals can make it work through co-operating conditionally and favouring those partners which provide the best quality help.

This article was originally published on The Conversation.
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Evolution Brought Kindness Before Intelligence

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All too often we imagine our hominid ancestors as hairy and primitive cavemen, living under the law of club and fang – unruly monsters that were more primate than human. The evidence, however, is painting a much different picture. Not only were other species of humans like the Neanderthals and Cro-Magnons capable of crafting tools and speaking languages, but human evolution in general likely brought about compassion and kindness some time before producing the intelligent beings of today.

Throughout history, we’ve thought of ourselves as the products of an evolutionary process grounded in intellect – only the brightest and the strongest spawned descendants, with each successive generation better than the last, the eventual outcome of lifeforms that became gradually more complex. However, according to a new study led by researcher Penny Spikins, from York University, this isn’t an entirely accurate assessment.

According to Spikins, there were at least three groups of the earliest human ancestors that exhibited altruistic behavior, developing some time before early humans showed evidence of intelligence and speech, concepts that are only about 150,000 years old.

“Human evolution is usually depicted as driven by intelligence, with empathy and deeper emotions following,” Spikins said. “However, the evidence suggests it happened the other way round. Evolution made us sociable, living in groups and looking after one another, even before we had language. Our success since then, including the evolution of intelligence, all sprang from that.”

Australopithecines, the species of ape to which Lucy belonged, were the first of our ancestors to walk upright, and lived in South Africa some three million years ago.

They had brains about one third the size of our own and were sometimes described by anthropologists as “killer apes” – a name that conjures up that scene from the beginning of 2001: A Space Odyssey. Spikins bristles at the term, reminding us of the Makapansgat pebble, found inside an African cave back in 1925 – a small stone shaped like a face that an Australopithecine did not carve, but collected and kept in its dwelling:

“What is remarkable is that this pebble was carried several miles back to its cave by an australopithecine. Did it remind them of a baby? It is impossible to tell for sure but this is not the only tantalising sign of something perhaps approaching tenderness.”

Another 1.5 million years after Lucy, and there is archaeological evidence that our close relative Homo ergaster lived in tribes that took care of their sick. There is also the Homo heidelbergensis, which lived about 450,000 years ago, and is thought to have raised disabled children to maturity.

“[Evidence suggests] early humans’ survival would have depended on co-operation,” she said, considering the difficulty that they would have had hunting alone or evading predators. “Aggressive or selfish behaviour would have been very risky.”

Spikins published her research in the new book How Compassion Made Us Human. Another piece of her evidence is a 250,000-year-old axe which was decorated with a fossilized scallop – already, humans seemed to have developed their own sense of aesthetics and beauty that they recognized in nature well before they began cave paintings of their own.

“A uniquely human feeling lies behind both the creation of such finely crafted tools and caring for the vulnerable. It suggests early humans, from two million years ago, were emotionally similar to us.”

“Compassion is perhaps the most fundamental human emotion,” she added, but hardly unique to modern homo sapiens as we might imagine. “It binds us together and can inspire us but it is also fragile and elusive. This apparent fragility makes addressing the evidence for the development of compassion in our most ancient ancestors a unique challenge, yet the archaeological record has an important story to tell about the prehistory of compassion.” Far from clouding our judgment, it made building social networks possible in a dangerous and unpredictable world.

“We have traditionally paid a lot of attention to how early humans thought about each other, but it may well be time to pay rather more attention to whether or not they ‘cared’.”

Spikins was previously involved with research on Neanderthals, published in the Oxford Journal of Archaeology.

While she does not deny that the mountains of the Neander Valley was a harsh climates to grow up in during the Ice Age, with geography that often led to isolation, the small families of Neanderthals were actually fairly close to each other. They buried their dead and their children played games which developed the skills they would later use to function as members of the tribe. Not only did parents care for sick or injured children, but child graves were marked with much more distinction than those of tribal elders.

“There is a critical distinction to be made between a harsh childhood and a childhood lived in a harsh environment,” said Spikins of her work – an important thing to consider when we imagine what our ancestors endured growing up in the Paleolithic Era.

Chimps and gorillas desperately need Ebola vaccine too

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By Meera Inglis, University of Sheffield

There is a side to the Ebola crisis that, perhaps understandably, has received little media attention: the threat it poses to our nearest cousins, the great apes of Africa. At this moment in time Ebola is the single greatest threat to the survival of gorillas and chimpanzees.

The virus is even more deadly for other great apes as it is for humans, with mortality rates approximately 95% for gorillas and 77% for chimpanzees (Pan troglodytes). Current estimates suggest a third of the world’s gorillas and chimpanzees have died from Ebola since the 1990s.

As with humans, these deaths tend to come in epidemics. In 1995, an outbreak is reported to have killed more than 90% of the gorillas in Minkébé Park in northern Gabon. In 2002-2003 a single outbreak of ZEBOV (the Zaire strain of Ebola) in the Democratic Republic of Congo killed an estimated 5,000 Western gorillas (Gorilla gorilla). It’s hard to accurately count such elusive creatures but the WWF estimates there are up to 100,000 left in the wild – so a single Ebola outbreak wiped out a considerable chunk of the world’s gorilla population.

There are of course additional factors behind the declining numbers of Africa’s great apes: illegal trading in wildlife and bushmeat, war, deforestation and other infectious diseases. The world’s remaining wild apes are being increasingly forced into isolated pockets of forest, which impedes their ability to forage, breed and to hide from hunters. There is also a growing body of evidence linking deforestation and subsequent changes in climate to the spread of Ebola and other infectious diseases.

The ranges of the remaining wild ape populations in Africa.
ICUN/Riccardo Pravettoni, GRID-Arendal

Back in 2003 an article on the decline of great apes, written by a team led by primatologist Peter Walsh, predicted that:

Without aggressive investments in law enforcement, protected area management and Ebola prevention, the next decade will see our closest relatives pushed to the brink of extinction.

Sadly, this prediction appears to have come true. Since 2008, the IUCN has listed the Eastern Gorilla (Gorilla beringei) as endangered and the Western Gorillas as critically endangered. If we do not act fast, these may prove to be the last decades in which apes can continue to live in their natural habitat. Unfortunately, there appears to be a lack of political will to implement policies which would bring viable solutions into effect.

We need both short-term solutions to halting the spread of Ebola and long-term ones to prevent future outbreaks. As a short-term strategy, vaccination could prove enormously useful in tackling the Ebola crisis in apes. Unlike for humans, a vaccine for gorillas and apes has been developed which thus far has been proven both safe and effective.

To date though, these trials have not involved “challenging” the vaccinated chimps with the live virus. Across much of Europe, medical research on great apes is either banned or highly restricted because of their cognitive similarity to humans. The question is whether or not we should make an exception in this case.

In the long term, conservation efforts aimed at restoring forest habitat could also help curb the spread of the virus, as larger forested areas would reduce the chances of infected animals coming into contact with one another. In tandem with forest regeneration, greater protection for apes from hunters and strict laws to control bushmeat consumption would also be hugely beneficial, both for apes and for humans.

This article was originally published on The Conversation.
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We’re all mammals – so why do we look so different?

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By Diego Villar Lozano, University of Cambridge

It is easy to distinguish a mouse from a cow. But for members of the same class of mammal, where do such differences begin? In 2011, scientists discovered there were differences in cow and mice blastocysts, the tiny hollow spheres of cells which precede the development of the embryo.

So while adult mammals are easily distinguishable, it was remarkable that the researchers were able to still tell the difference at this extremely early stage of development. This early difference was largely due to the crucial process of gene regulation.

Mammalian species are all quite different in look and size, and have colonised all ecological niches – they can be terrestrial (like humans and mice), aquatic (dolphins and whales) and even aerial (bats). Like humans, all mammals have large, complex genomes – the DNA sequences in our cells. These contain the instructions which are used to construct our bodies and brains. However, the best-understood functional units in our DNA – our genes – take up only 2% of our genome sequence, and are extremely similar across non-marsupial mammals. So what makes us so different?

Classical studies – for example, those by geneticists Mary-Claire King and Allan Wilson, have shown that the major differences between mammalian species lie not in the genes themselves, but where genes are switched on and off – that is, in gene regulation.

She’s the regulatory element.
Off on switch by Shutterstock

Understanding gene regulation in mammals is very challenging. The DNA sequences that regulate our genes – so-called regulatory elements – are painstaking to identify. These sequences are spread across our vast genome, and are largely different for each of our tissues. To decipher gene regulation in mammals, we need to locate them and understand how they change as the animal evolves.

Gene regulation evolves

As evolution progresses and mammalian species diverge, various genes are switched on an off. So which aspects of our genome stay the same and where are the changes taking place?

New experimental and computational tools for DNA sequencing are now making it possible to identify regulatory elements and their activity with unprecedented accuracy and speed. These tools allow us to study gene regulation across mammalian genomes, as has been done for humans and mice, but much less so for recently sequenced genomes, such as those of species with unique adaptations – dolphins or subterranean cancer-resistant naked mole rats among them.

Not your average looker.
Buffenstein/Barshop Institute/UTHSCSA, CC BY

In a recent study published in Cell, we found the extent of gene regulation differences – the “on/off” switching – across mammals was astonishing. It is rare that the DNA sequences that regulate our genes show similar activities across mammals. More commonly, gene regulatory activities change rapidly as mammals evolve (though still over millions of years – for example, humans and chimps are separated by 6m years of evolution), and such differences probably lead to different genes switching on and off.

In fact, a good fraction of the regulatory elements that we identified in each mammalian genome were active in a single mammal (out of the 20 analysed), which suggests that these regulatory elements may be associated with recent evolutionary adaptations unique to a few species.

Repurposing

So how do such vast numbers of newly active regulatory sequences arise? Our findings suggest that, rather than acquiring wholly new DNA sequences that regulate genes, mammals derive most regulatory innovations from existing DNA – sequences shared to some extent by all mammals today and likely present in the ancestral species from which they evolved – but repurposed in a particular species.

This process resembles evolutionary tinkering, where continuous tweaking of existing DNA sequences can result in new patterns of gene regulation. The prevalence of this mechanism, as opposed to the generation of regulatory elements from newly acquired DNA, could in part explain the rapid evolution we see in mammals, and may have been pivotal in allowing mammals to efficiently colonise Earth’s ecosystems. Essentially, continuous modifications in vast mammalian genomes within relatively small populations likely contributed to new evolutionary paths that allowed mammal species to diverge.

Many questions remain. Our results indicate how rapidly gene regulation can change in mammalian genomes, but further work will be required to fully understand the relative importance of the retained and new DNA sequences that regulate our genes, and how they cooperate to create species diversity while maintaining the organ functions found across vertebrates. And our findings could have profound implications for our understanding of human disease – in particular, the mechanisms by which rapidly evolving pathologies, such as cancer, hijack normal gene regulation and alter it to their advantage.

This article was originally published on The Conversation.
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Premiere PBS Series, “EARTH: A New Wild” Looks Dope

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Are you sick of nature shows sidestepping environmental disasters and general negative effects humans cause on the species we come into contact with? PBS has always been a mark of quality programming but this new series has me jazzed up for it’s innovative approach to the discussion of human impact on the environment.

EARTH A New Wild questions society’s conventional approach to nature shows by including humankind’s relationship to the natural world as beautiful locations and exotic species are examined with the production values we’ve come to expect from PBS. It’s a new style that is more appropriate to the ongoing environmental discussion of 2015.

The show is a joint production between National Geographic Studios in association with Passion Planet, the series is hosted by Dr. M. Sanjayan, conservation scientist, who takes viewers on a stunning visual journey to explore how humans are inextricably woven into every aspect of the planet’s natural systems.

The series shows humans and the natural environment interacting by editing footage from 45 shoots in 29 different countries. It shows humans in cohabitation with giant pandas, humpback whales, African lions and Arctic reindeer. Dr. Sanjayan posits that humans must learn to work together with animal and plant life in order to survive as a species.

EARTH A New Wild Premieres tonight, February 4th, at 8/9 Central

Jonathan Howard
Jonathan is a freelance writer living in Brooklyn, NY

Genetic Analysis Shows Polar Bears Migrating To Northern Canada

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As with most animals whose natural habitats are being threatened, polar bears are beginning to travel to the far Northern side of Canada where a lot more plentiful ice is more prevalent.

A US Geological Survey conducted a study in which the team evaluated the local bear population’s genetic makeup. The scientists noticed that starting somewhere in the 1990s, the last three generations of polar bears have been headed in a northern direction where ice is present all year-round. Similarly, Lily Peacock, a USGS wildlife biologist, stated that there have been serious directional movements of bears towards the Canadian Archipelago. Peacock thinks that in the long term, the genetic analysis used by them provides better data.

The genetic analysis can help them estimate both directions and levels of genetic flow, pattern of population as whether it has expanded or contracted. Such genetic flows take place over the course of generations, and would remain undetectable through measures like tracking methods.

At first glance this might seem like simply a natural reaction to climate change, but researchers are concerned that the move further in the northern direction can turn out to be a harmful decision for the species as the bears could become isolated up there. Isolated populations face problems regarding their genetics and how they interact with the weather which makes the species more vulnerable to extinction in the long run.

Kristin Laidre at the University of Washington’s Polar Science Center said that there are many other Arctic species as well that have also shifted due to loss of sea ice and, while many skeptics still feel this is a natural progression of the Earth, most climate change scientists still agree that human contributions to global warming is the being threat to the species. Could this be the end of an era for our furry white friends up North?