Neanderthals gave us a selection of disease genes - [Journal article]

(BBC News, 30th January 2014) - Gene types that influence disease in people today were picked up through interbreeding with Neanderthals, a major study in Nature journal suggests.

Journal article: Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

They passed on variants involved in type 2 diabetes, Crohn's disease and - curiously - smoking addiction.

Genome studies reveal that our species (Homo sapiens) mated with Neanderthals after leaving Africa.

But it was previously unclear what this Neanderthal DNA did and whether there were any implications for human health.

Between 2% and 4% of the genetic blueprint of present-day non-Africans came from Neanderthals.

By screening the genomes of 1,004 modern humans, Sriram Sankararaman and his colleagues identified regions bearing the Neanderthal versions of different genes.

That a gene variant associated with a difficulty in stopping smoking should be found to have a Neanderthal origin is a surprise.

It goes without saying that there is no suggestion our evolutionary cousins were puffing away in their caves.

Instead, the researchers argue, this mutation may have more than one function, so the modern effect of this marker on smoking behaviour may be one impact it has among several.

Researchers found that Neanderthal DNA is not distributed uniformly across the human genome, instead being commonly found in regions that affect skin and hair.

This suggests some gene variants provided a rapid way for modern humans to adapt to the new cooler environments they encountered as they moved into Eurasia. When the populations met, Neanderthals had already been adapting to these conditions for several hundred thousand years.

The stocky hunters once covered a range stretching from Britain to Siberia, but went extinct around 30,000 years ago as Homo sapiens was expanding from an African homeland.

Neanderthal ancestry was found in regions of the genome linked to the regulation of skin pigmentation.

"We found evidence that Neanderthal skin genes made Europeans and East Asians more evolutionarily fit," said Benjamin Vernot, from the University of Washington, co-author of a separate study in Science journal.

Genes for keratin filaments, a fibrous protein that lends toughness to skin, hair and nails, were also enriched with Neanderthal DNA. This may have helped provide the newcomers with thicker insulation against cold conditions, the scientists suggest.

"It's tempting to think that Neanderthals were already adapted to the non-African environment and provided this genetic benefit to (modern) humans," said Prof David Reich, from Harvard Medical School, co-author of the paper in Nature.

But other gene variants influenced human illnesses, such as type 2 diabetes, long-term depression, lupus, billiary cirrhosis - an autoimmune disease of the liver - and Crohn's disease. In the case of Crohn's, Neanderthals passed on different markers that increase and decrease the risk of disease.

Asked whether our ancient relatives actually suffered from these diseases too, or whether the mutations in question only affected the risk of illness when transplanted to a modern human genetic background, Mr Sankararaman said: "We don't have the fine knowledge of the genetics of Neanderthals to answer this," but added that further study of their genomes might shed light on this question.

Joshua Akey, from the University of Washington, an author of the Science publication, added: "Admixture happened relatively recently in evolutionary terms, so you wouldn't expect all the Neanderthal DNA to have been washed away by this point.

"I think what we're seeing to a large extent is the dying remains of this extinct genome as it is slowly purged from the human population."

However, some regions of our genomes were discovered to be devoid of Neanderthal DNA, suggesting that certain genes had such harmful effects in the offspring of modern human-Neanderthal pairings that they have indeed been flushed out actively and rapidly through natural selection.

"We find that there are large regions of the genome where most modern humans carry little or no Neanderthal ancestry," Mr Sankararaman told BBC News.

"This reduction in Neanderthal ancestry was probably due to selection against genes that were bad - deleterious - for us."

The Neanderthal-deficient regions encompass genes that are specifically expressed in the testes, and on the X (female sex) chromosome.

This suggests that some Neanderthal-modern human hybrids had reduced fertility and in some cases were sterile.

"It tells us that when Neanderthals and modern humans met and mixed, they were at the very edge of being biologically compatible," said Prof Reich.

Another genome region that lacked Neanderthal genes includes a gene called FOXP2, which is thought to play an important role in human speech.

Joshua Akey said his team's results were compatible with there having been multiple pulses of interbreeding between modern humans and Neanderthals.

Evidence of interbreeding among early Hominins - [Journal article]

http://digitaljournal.com

(Iflscience.com, 25, November 2013) - The evolutionary tree for modern humans is a bit of a mess - humans haven’t had a close relative on this planet for over 10,000 years, but there used to be several other closely related species living at the same time.

Genetic analyses on bone fragments from Neanderthals and Denisovans has given us new insight into our not-so-distant evolutionary past. The results indicate that not only did Denisovans and Neanderthals interbreed with modern Homo sapiens, but they also mated with an unidentified fourth hominin group. This information was presented to evolutionary geneticists last week for a meeting of the Royal Society.

Neanderthals emerged about 200,000 years ago and remains have been found throughout Europe, stretching into central Asia. While Neanderthals weren’t as cognitively advanced as Homo sapiens who emerged around the same time, they were probably the first hominins known to wear clothing, bury dead, and form languages. It has been traditionally thought that the last common ancestor of Homo sapiens and Neanderthals existed around 400,000 years ago, though new research suggests it could have been earlier.

Denisovans are an extinct group of hominins that are part of our evolutionary lineage. Our knowledge of them comes from bone fragments found in a cave that date back about 30,000-50,000 years. Though genetic analysis had been done a couple years ago, the results weren’t really clear. New techniques have yielded much more complete genetic sequences and two new studies have released different yet related results.

There is evidence of certain populations of humans alive today getting as much as 4% of their DNA from Denisovans, though there is some debate surrounding it. Additionally, there are people with ancestries outside of Africa that could have gotten about 2% of their genomes from Neanderthals, though there is some speculation with this as well.

Right now, the identity of this fourth early human group remains a mystery. They could have come from Asia, but that has not yet been made certain. Future research will hopefully identify this unknown population and help us better understand all of the different evolutionary inputs that make us who we are.

Related references:

Journal article: A Draft Sequence of the Neandertal Genome

Journal article: A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Bird alarm: Great tits use predator-specific calls - [Journal article]

http://upload.wikimedia.org

(BBC News, 22, November 2013) - Great tits use different alarm calls for different predators, according to scientists in Japan.

Journal article: Communication about predator type by a birdusing discrete, graded and combinatorial variation in alarm calls

A researcher analysed the birds' calls and found that they made "jar" sounds for snakes and combinations of "chicka" sounds for crows and martens.

This, he claims, is the first demonstration that birds can put into their alarm calls information about the predator that is threatening them.

The findings are published in the journal Animal Behaviour.

In the short clip available on the Animal Behaviour website, you can hear the three calls: the "chicka" call for crow; a "chicka" call for marten, which incorporates a "trill" that the birds do not use for crows, and finally "jar" call for snake.

Since snakes are particularly dangerous predators for the birds, the researchers think great tits might have evolved this very distinct snake alarm call.

Where is Language Located in the Brain? There are Two Sides to this Story - [Journal Article]

(BPS Research Digest, 21, November 2013) - Simple facts about the brain are rare, but one of them is that for most people language function is located mainly in their left brain hemisphere. The stats vary according to the measures used, but this is the situation for around 95 per cent of right-handers and approximately 75 per cent of left-handers. When it comes to the brain though, few things are straight-forward.

Journal article: Bilateral representation of language: A critical review and analysis of some unusual cases.

If we dig deeper, as Byron Bernal and Alfredo Ardila have done for a new review paper, we find a more complex, two-sided story. The extent to which language is dominated by the left hemisphere is not fixed. It increases through childhood and adolescence, and then this trend reverses in old age, with signs of greater sharing of language function across the brain hemispheres in later life. 

Moreover, by characterising people in binary fashion as having their language abilities housed either in their left or right hemisphere, we ignore those people for whom language is a genuinely "bilateral function," meaning that both brain hemispheres are substantially involved.

As Bernal and Ardila point out, a dramatic demonstration of this comes from the Wada test, named after  Japanese neurologist Juhn Atsushi Wada. With the patient awake, anaesthetic is injected into the neck or head on one side to effectively shut down function in that side of the brain. Speech and language comprehension tests are conducted first with one hemisphere silenced, then the other.

Looking at the results from 1,799 Wada tests, most of which were conducted with epilepsy patients prior to surgery, Bernal and Ardila found that 10 per cent of right-handers and 27 per cent of left-handers (and the ambidextrous) showed evidence that their language function was supported by both brain hemispheres.

The way that bilateral language function manifests in the Wada test varies from patient to patient. In some, shutting down one hemisphere has no effect on their language abilities, while shutting down the other only partially interferes with language. In other patients, shutting down one hemisphere completely impairs language, while shutting down the other also has a partial adverse effect. And in a final group, shutting down either hemisphere results in only a partial impairment to language.

The reason for these different patterns, Bernal and Ardila explain, is that there are various ways that language function can be shared between the hemispheres. Using brain scans from real life case studies, they show how in some people all functions of language are shared between the left and right brain, whereas for other people some sub-functions of language are bilateral, but not others. 

For instance, the faculties involved in language comprehension might be bilateral, but the faculties of language production are not, or vice versa (similar dissociations can be found for processing sound and meaning). Related to this, some people show evidence that the different steps of language function are distributed sequentially between the hemispheres (e.g. one stage processed on one side, the next stage on the other), so there is no redundancy, whereas other people show a kind of parallel arrangement where both hemispheres are able to perform the same steps of language processing.

We need to be cautious when extrapolating from patient studies to healthy people because it's possible that the brain has altered its function to adapt to disease. This caveat aside, Bernal and Ardila's fascinating review is a reminder of the brain's complexity. The factoid that in most people language is left-lateralized conceals a messy reality. "It is a frequent understanding that language lateralization is a matter of all or nothing," write Bernal and Ardila. "However, language dominance is mostly a matter of hemispheric advantage for a specific multi-modular cognitive function: language. As such, language in a strict sense is up to a certain point a bilateral brain function."

Unusual Animal Intelligence - [Magazine article]

(Iflscience.com, 22, October 2013) - Before 1960 most of the work surrounding animal intelligence was centred around behaviour, with famous experiments such as Pavlov’s dogs and Thorndike’s operant conditioning. After 1960, the field began to shift to understand animal cognition and there has been much debate whether animals have an actual consciousness. 

The full extent of what animals think may never be known, but we already have seen amazing intelligence from some unlikely sources.

Crows

Crows are insanely intelligent creatures. They are able to recognize human faces and hold a grudge against the ones they don’t like. In order to study the crows they had to be collected and properly tagged. The scientists who handled the birds quickly fell out of favor with the crows. The next time the researchers entered the enclosure they were greeted by the crows dive bombing and attacking them. If the same researchers came back wearing a mask that the crows hadn’t seen before, they were left alone. It also appears that the crows conspire with one another and share information about which humans they don’t like. Crows who were absent when a particular researcher had handled the other birds would still respond with hostility upon seeing the scientist at a later date.

Their amazing intelligence is not always used to start fights -  they are skilled at using tools in order to retrieve food or solve problems. Crows readily use sticks, rocks, and wires to retrieve food from hidden places. If the proper tool is not at their disposal, they can actually make one to suit the job. What's more, these crows can use tools better than many primates.

Aesop’s “The Crow and the Pitcher” fable describes crows’ ingenuity. A crow wanted a drink of water, but was unable to reach down into the pitcher. Rather than give up, it dropped pebble after pebble into the pitcher until the water rose high enough for it to have a drink. It is a 2600-year-old story of tenacity. Modern scientists have decided to test the fable and found that it was scientifically accurate. 

Dolphins

“So long, and thanks for all the fish.”

Dolphins have long been celebrated as some of the most clever animals in the world. Their brains are extremely large for their body size, have a neocortex (where higher function takes place) much more intricate than humans and the region of the brain that is in charge of self awareness is enlarged when compared to other animals. 

Dolphins live in social societies and communication is integral to its success. They do not have vocal cords as humans do, but use a combination of clicks, squeaks, creaks, and buzzes to talk to their fellow cetaceans, though scientists have not been able to discern an actual language yet. Body language is also an important communication tool Dolphin whistles are unique to individuals and are developed in the first month of life.

It was recently discovered that dolphins remember the signature call of their friends, even if they hadn’t seen each other in over 20 years. This might help explain how dolphins can leave and join different pods so easily over the course of their lifetime.

Dolphins are so intelligent that India has recently put a ban on their captivity. India’s Ministry of the Environment and Forests has labeled cetaceans as "non-human persons" and released a statement saying they are not to be captured for entertainment purposes by any person or institution, whether they are public or private.

Pigs

While it might be surprising to some pigs are quite intelligent and many would compare that intellect to be on the same level as dolphins and higher apes. 

Part of this intellect might be because large chunks of pig genome are virtually identical to humans, though our last common ancestor died out 100 million years ago. Pigs love to become couch potatoes and would rather eat, drink, smoke, and watch TV than be active; not unlike many people.

When introduced to a mirror, they were initially fascinated by the pig in the reflection and tried to interact by nudging and vocalizing. While they could see food in the mirror, they tried looking behind the mirror only to end up hungry. The next time the mirror was presented, they were not interested in their own image, but instead used the reflection to find the bowl of food behind them in under 30 seconds. 

Pigs can also be trained to learn tricks fairly easily. However, if at first they don’t succeed, getting the courage to try again is a long process, especially if the pig got hurt in the attempt. Researchers speculate that the memory of the failure is a big hurdle to overcome for many pigs. Failures in training and living conditions can affect a pig's mood, as the animals are capable of having and expressing complex emotions.

Elephants

Elephants are the largest mammals on land, and it turns out that they have the brains to back up the brawn. 

It was recently discovered that with absolutely no training elephants understand when humans point. While standing in between two identical buckets, but one was filled with food, the elephants immediately chose the one that the human had gestured. While it is remarkable that elephants are able to spontaneously understand this body language, it becomes even more impressive since many great apes are not capable of the same level of understanding.

Captive elephants had no greater advantage than wild elephants with little human interaction, leading the scientists to believe that this is an innate response, and pointing on some level may exist in elephant populations.

In a different study highlighting the intelligence of these pachyderms a group of elephants competed against a group of humans in a teamwork exercise. Not only did the elephants beat the humans in the exercise, but they were able to do it using techniques that the researchers had not previously considered.

 

Altruism or manipulated helping? Altruism may have origins in manipulation - [Article]

(Phys.org, 19, Aug 2013) - Manipulation is often thought of as morally repugnant, but it might be responsible for the evolutionary origins of some helpful or altruistic behaviour, according to a new study.

Journal article: Evolution of manipulated behavior (apologies, article not live at time of publishing)

In evolutionary biology, manipulation occurs when an individual, the manipulator, alters the behaviour of another individual in ways that is beneficial to the manipulator but may be detrimental to the manipulated individual. Manipulation not only occurs in humans and animals but also at the cellular level, such as among cells in a multicellular organism, or in parasites, which can alter the behaviour of their hosts. 

Consider the case of the parasitic roundworm (Myrmeconema neotropicum), which once ingested by the tropical ant (Cephalotes atratus) in Central and South America, causes the ant to grow a bright red abdomen, mimicking berries. This bright abdomen constitutes a phenotype manipulated by the roundworm. Birds eat the "berries," or infected ants, and then spread the parasite in their droppings, which are subsequently collected by foraging Cephalotes atratus and fed to their larva, and the cycle of manipulated behaviour begins anew.

In the study published this week in the journal American Naturalist, the researchers developed a mathematical model for the evolution of manipulated behaviour and applied it to maternal manipulation in eusocial organisms, such as ants, wasps, and bees, which form colonies with reproductive queens and sterile workers. In the model, mothers produce two broods, and they manipulate the first-brood offspring to stay in the maternal site and help raise the second brood. 

Mothers can do this by disrupting the offspring's development in some way, for example through poor feeding or aggressive behaviour. Manipulated offspring of the first-brood stay and help to raise the second brood. Alternatively, first-brood offspring can resist manipulation and leave.

The researchers show that an offspring's resistance to manipulation may often fail to evolve, if the costs of resistance are high. In a sense, then, helping or altruistic behaviour is coerced through manipulation.

"The evidence in so-called primitive eusociality, where helping is often coerced through aggression or differential feeding, appears consistent with these results," said lead author Mauricio Gonzalez-Forero, who conducted the study while a graduate research assistant at the National Institute for Mathematical and Biological Synthesis.