Millions of years before humans invented sonar, bats and toothed whales had mastered the biological version of the same trick – echolocation. By timing the echoes of their calls, one group effortlessly flies through the darkest of skies and the other swims through the murkiest of waters. It’s amazing enough that two such different groups of mammals should have evolved the same trick but that similarity isn’t just skin deep.
The echolocation abilities of bats and whales, though different in their details, rely on the same changes to the same gene – Prestin. These changes have produced such similar proteins that if you drew a family tree based on their amino acid sequences, bats and toothed whales would end up in the same tight-knit group, to the exclusion of other bats and whales that don’t use sonar.
This is one of the most dramatic examples yet of ‘convergent evolution’, where different groups of living things have independently evolved similar behaviours or body parts in response to similar evolutionary pressures.
It is one of a growing number of studies have shown that convergence on the surface – like having venom, being intelligent or lacking enamel – is borne of deeper genetic resemblance. But this discovery is special in a deliciously ironic way. It was made by two groups of scientists, who independently arrived at the same result. The first authors even have virtually identical names. These are people who take convergence seriously!
In the White Sands National Park of New Mexico, there are three species of small lizard that all share white complexions. In the dark soil of the surrounding landscapes, all three lizards wear coloured coats with an array of hues, stripes and spots. Colours would make them stand out like a beacon among the white sands so natural selection has bleached their skins. Within the last few thousand years, the lesser earless lizard, the eastern fence lizard and the little striped whiptail have all evolved white forms that camouflage beautifully among the white dunes.
Erica Bree Rosenblum from the University of Idaho has found that their white coats are the result of changes to the same gene, Mc1r. All of these adaptations arose independently of one another and all of them reduce the amount of the dark pigment, melanin, in the lizards’ skin. It’s a wonderful example of convergent evolution, where the same environmental demands push different species along the same evolutionary paths. But Rosenblum has also found that there are many ways to break a gene.
Each of the three lizards has a different mutation in their Mc1r gene, that has crippled it in diverse ways. These differences may seem slight, but they affect how dominant and widespread the white varieties are, and how likely they are to branch off into new species of their own. Even when different species converge on the same results – in this case, whitened skin – and even when the same gene is responsible, their evolutionary paths can still be very different.
The Mc1r gene encodes a protein called the melanocortin 1 receptor (MC1R). It’s a messenger that sits astride the cell’s membrane and transmits messages across it. It triggers a sequence of events that stimulates the production of the dark pigment melanin. In this way, it affects the skin colour of many animals and faulty copies of the gene tend to result in lighter colours. In humans, for example, around 80% of redheads owe their hair colour to common faulty variant of Mc1r.
In each of the White Sands lizards, just one of the MC1R protein’s many amino acids has been swapped (red circles above), and it’s a different one in each species. All three amino acids lie within the part of the protein that straddles the cell membrane. These regions are important for keeping the protein together, and for channelling signals from one side of the membrane to another.
In science, we don’t often get to talk about male repression, but a new discovery gives us just such a chance. It turns out that ovaries can only remain ovaries by constantly suppressing their ability to become male. Silence a single gene, and adult ovaries turn into testes. That adult tissues can be transformed in this way would be surprising enough, but doing so by changing a single gene is truly astonishing.
As embryos, our gonads aren’t specific to either gender. Their default course is a female one, but they can be diverted through the action of a gene called SRY that sits on the Y chromosome. SRY activates another gene called Sox9, which sets off a chain reaction of flicked genetic switches. The result is that premature gonads develop into testes. Without SRY or Sox9, you get ovaries instead.
But Henriette Uhlenhaut from the European Molecular Biology Laboratory has found that this story is woefully incomplete. Maleness isn’t just forced onto developing gonads by the actions of SRY – it’s permanently kept at bay by another gene called FOXL2.
Today, a new paper published in Nature adds another chapter to the story of FOXP2, a gene with important roles in speech and language. The FOXP2 story is a fascinating tale that I covered in New Scientist last year. It’s one of the pieces I’m proudest of so I’m reprinting it here with kind permission from Roger Highfield, and with edits incorporating new discoveries since the time of writing.
The FOXP2 Story (2009 edition)
Imagine an orchestra full of eager musicians which, thanks to an incompetent conductor, produces nothing more than an unrelieved cacophony. You’re starting to appreciate the problem faced by a British family known as KE. About half of its members have severe difficulties with language. They have trouble with grammar, writing and comprehension, but above all they find it hard to coordinate the complex sequences of face and mouth movements necessary for fluid speech.
Thanks to a single genetic mutation, the conductor cannot conduct, and the result is linguistic chaos. In 2001, geneticists looking for the root of the problem tracked it down to a mutation in a gene they named FOXP2. Normally, FOXP2 coordinates the expression of other genes, but in affected members of the KE family, it was broken.
It had long been suspected that language has some basis in genetics, but this was the first time that a specific gene had been implicated in a speech and language disorder. Overeager journalists quickly dubbed FOXP2 “the language gene” or the “grammar gene”. Noting that complex language is a characteristically human trait, some even speculated that FOXP2 might account for our unique position in the animal kingdom. Scientists were less gushing but equally excited – the discovery sparked a frenzy of research aiming to uncover the gene’s role.
Several years on, and it is clear that talk of a “language gene” was premature and simplistic. Nevertheless, FOXP2 tells an intriguing story. “When we were first looking for the gene, people were saying that it would be specific to humans since it was involved in language,” recalls Simon Fisher at the University of Oxford, who was part of the team that identified FOXP2 in the KE family. In fact, the gene evolved before the dinosaurs and is still found in many animals today: species from birds to bats to bees have their own versions, many of which are remarkably similar to ours. “It gives us a really important lesson,” says Fisher. “Speech and language didn’t just pop up out of nowhere. They’re built on very highly conserved and evolutionarily ancient pathways.”
Two amino acids, two hundred thousand years
The first team to compare FOXP2 in different species was led by Wolfgang Enard from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. In 2001, they looked at the protein that FOXP2 codes for, called FOXP2, and found that our version differs from those of chimpanzees, gorillas and rhesus macaques by two amino acids out of a total of 715, and from that of mice by three. This means that the human version of FOXP2 evolved recently and rapidly: only one amino acid changed in the 130 million years since the mouse lineage split from that of primates, but we have picked up two further differences since we diverged from chimps, and this seems to have happened only with the evolution of our own species at most 200,000 years ago.
The similarity between the human protein FOXP2 and that of other mammals puts it among the top 5 per cent of the most conserved of all our proteins. What’s more, different human populations show virtually no variation in their FOXP2 gene sequences. Last year, Enard’s colleague Svante Pääbo made the discovery that Neanderthals also had an identical gene, prompting questions over their linguistic abilities (see “Neanderthal echoes below).
“People sometimes think that the mutated FOXP2 in the KE family is a throwback to the chimpanzee version, but that’s not the case,” says Fisher. The KEs have the characteristically human form of the gene. Their mutation affects a part of the FOXP2 protein that interacts with DNA, which explains why it has trouble orchestrating the activity of other genes.
There must have been some evolutionary advantage associated with the human form of FOXP2, otherwise the two mutations would not have spread so quickly and comprehensively through the population. What this advantage was, and how it may have related to the rise of language, is more difficult to say. Nevertheless, clues are starting to emerge as we get a better picture of what FOXP2 does – not just in humans but in other animals too.
During development, the gene is expressed in the lungs, oesophagus and heart, but what interests language researchers is its role in the brain. Here there is remarkable similarity across species: from humans to finches to crocodiles, FOXP2 is active in the same regions. With no shortage of animal models to work with, several teams have chosen songbirds due to the similarities between their songs and human language: both build complex sequences from basic components such as syllables and riffs, and both forms of vocalisation are learned through imitation and practice during critical windows of development.
All bird species have very similar versions of FOXP2. In the zebra finch, its protein is 98 per cent identical to ours, differing by just eight amino acids. It is particularly active in a part of the basal ganglia dubbed “area X”, which is involved in song learning. Constance Scharff at the Max Planck Institute for Molecular Genetics in Berlin, Germany, reported that finches’ levels of FOXP2 expression in area X are highest during early life, which is when most of their song learning takes place. In canaries, which learn songs throughout their lives, levels of the protein shoot up annually and peak during the late summer months, which happens to be when they remodel their songs.
So what would happen to a bird’s songs if levels of the FOXP2 protein in its area X were to plummet during a crucial learning window? Scharff found out by injecting young finches with a tailored piece of RNA that inhibited the expression of the FOXP2 gene. The birds had difficulties in developing new tunes and their songs became garbled: they contained the same component “syllables” as the tunes of their tutors, but with syllables rearranged, left out, repeated incorrectly or sung at the wrong pitch.
The cacophony produced by these finches bears uncanny similarities to the distorted speech of the afflicted KE family members, making it tempting to pigeonhole FOXP2 as a vocal learning gene – influencing the ability to learn new communication sounds by imitating others. But that is no more accurate than calling it a “language gene”. For a start, songbird FOXP2 has no characteristic differences to the gene in non-songbirds. What’s more, among other species that show vocal learning, such as whales, dolphins and elephants, there are no characteristic patterns of mutation in their FOXP2 that they all share.
Instead, consensus is emerging that FOXP2 probably plays a more fundamental role in the brain. Its presence in the basal ganglia and cerebellums of different animals provides a clue as to what that role might be. Both regions help to produce precise sequences of muscle movements. Not only that, they are also able to integrate information coming in from the senses with motor commands sent from other parts of the brain. Such basic sensory-motor coordination would be vital for both birdsong and human speech. So could this be the key to understanding FOXP2?
New work by Fisher and his colleagues supports this idea. In 2008, his team engineered mice to carry the same FOXP2 mutation that affects the KE family, rendering the protein useless. Mice with two copies of the dysfunctional FOXP2 had shortened lives, characterised by motor disorders, growth problems and small cerebellums. Mice with one normal copy of FOXP2 and one faulty copy (as is the case in the affected members of the KE family) seemed outwardly healthy and capable of vocalisation, but had subtle defects.
For example, they found it difficult to acquire new motor skills such as learning to run faster on a tilted running wheel. An examination of their brains revealed the problem. The synapses connecting neurons within the cerebellum, and those in a part of the basal ganglia called the striatum in particular, were severely flawed. The signals that crossed these synapses failed to develop the long-term changes that are crucial for memory and learning. The opposite happened when the team engineered mice to produce a version of FOXP2 with the two characteristically human mutations. Their basal ganglia had neurons with longer outgrowths (dendrites) that were better able to strengthen or weaken the connections between them.
A battery of over 300 physical and mental tests showed that the altered mice were generally healthy. While they couldn’t speak like their cartoon equals, their central nervous system developed in different ways, and they showed changes in parts of the brain where FOXP2 is usually expressed (switched on) in humans.
Their squeaks were also subtly transformed. When mouse babies are moved away from their nest, they make ultrasonic distress calls that are too high for us to hear, but that their mothers pick up loudly and clearly. The altered Foxp2 gene subtly changed the structure of these alarm calls. We won’t know what this means until we get a better understanding of the similarities between mouse calls and human speech.
For now, the two groups of engineered mice tentatively support the idea that human-specific changes to FOXP2 affect aspects of speech, and strongly support the idea that they affect aspects of learning. “This shows, for the first time, that the [human-specific] amino-acid changes do indeed have functional effects, and that they are particularly relevant to the brain,” explains Fisher. “FOXP2 may have some deeply conserved role in neural circuits involved in learning and producing complex patterns of movement.” He suspects that mutant versions of FOXP2 disrupt these circuits and cause different problems in different species.
Pääbo agrees. “Language defects may be where problems with motor coordination show up most clearly in humans, since articulation is the most complex set of movements we make in our daily life,” he says. These circuits could underpin the origins of human speech, creating a biological platform for the evolution of both vocal learning in animals and spoken language in humans.
Holy diversity, Batman
The link between FOXP2 and sensory-motor coordination is bolstered further by research in bats. Sequencing the gene in 13 species of bats, Shuyi Zhang and colleagues from the East China Normal University in Shanghai discovered that it shows incredible diversity. Why would bats have such variable forms of FOXP2 when it is normally so unwavering in other species?
Zhang suspects that the answer lies in echolocation. He notes that the different versions seem to correspond with different systems of sonar navigation used by the various bat species. Although other mammals that use echolocation, such as whales and dolphins, do not have special versions of FOXP2, he points out that since they emit their sonar through their foreheads, these navigation systems have fewer moving parts. Furthermore, they need far less sensory-motor coordination than flying bats, which vocalise their ultrasonic pulses and adjust their flight every few milliseconds, based on their interpretation of the echoes they receive.
These bats suggest that FOXP2 is no more specific to basic communication than it is to language, and findings from other species tell a similar tale. Nevertheless, the discovery that this is an ancient gene that has assumed a variety of roles does nothing to diminish the importance of its latest incarnation in humans.
Since its discovery, no other gene has been convincingly implicated in overt language disorders. FOXP2 remains our only solid lead into the genetics of language. “It’s a molecular window into those kinds of pathways – but just one of a whole range of different genes that might be involved,” says Fisher. “It’s a starting point for us, but it’s not the whole story.” He has already used FOXP2 to hunt down other key players in language.
The executive’s minions
FOXP2 is a transcription factor, which activates some genes while suppressing others. Identifying its targets, particularly in the human brain, is the next obvious step. Working with Daniel Geschwind at the University of California, Los Angeles, Fisher has been trying to do just that, and their preliminary results indicate just what a massive job lies ahead. On their first foray alone, the team looked at about 5000 different genes and found that FOXP2 potentially regulates hundreds of these.
Some of these target genes control brain development in embryos and its continuing function in adults. Some affect the structural pattern of the developing brain and the growth of neurons. Others are involved in chemical signalling and the long-term changes in neural connections that enable to learning and adaptive behaviour. Some of the targets are of particular interest, including 47 genes that are expressed differently in human and chimpanzee brains, and a slightly overlapping set of 14 targets that have evolved particularly rapidly in humans.
Most intriguingly, Fisher says, “we have evidence that some FOXP2 targets are also implicated in language impairment.” Last year, Sonja Vernes in his group showed that FOXP2 switches off CNTNAP2, a gene involved in not one but two language disorders – specific language impairment (SLI) and autism. Both affect children, and both involve difficulties in picking up spoken language skills. The protein encoded by CNTNAP2 is deployed by nerve cells in the developing brain. It affects the connections between these cells and is particularly abundant in neural circuits that are involved in language.
Verne’s discovery is a sign that the true promise of FOXP2′s discovery is being fulfilled – the gene itself has been overly hyped, but its true worth lies in opening a door for more research into genes involved in language. It was the valuable clue that threw the case wide open. CNTNAP2 may be the first language disorder culprit revealed through FOXP2 and it’s unlikely to be the last.
Most recently, Dan Geschwind compared the network of genes that are targeted by FOXP2 in both chimps and humans. He found that the two human-specific amino acids within this executive protein have radically altered the set of genetic minions that it controls.
The genes that are directed by human FOXP2 are a varied cast of players that influence the development of the head and face, parts of the brain involved in motor skills, the growth of cartilage and connective tissues, and the development of the nervous system. All those roles fit with the idea that our version of FOXP2 has been a lynchpin in evolving the neural circuits and physical structures that are important for speech and language.
The FOXP2 story is far from complete, and every new discovery raises fresh questions just as it answers old ones. Already, this gene has already taught us important lessons about evolution and our place in the natural world. It shows that our much vaunted linguistic skills are more the result of genetic redeployment than out-and-out innovation. It seems that a quest to understand how we stand apart from other animals is instead leading to a deeper appreciation of what unites us.
Box – Neanderthal echoes
The unique human version of the FOXP2 gives us a surprising link with one extinct species. Last year, Svante Pääbo’s group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, extracted DNA from the bones of two Neanderthals, one of the first instances of geneticists exploring ancient skeletons for specific genes. They found that Neanderthal FOXP2 carries the same two mutations as those carried by us – mutations accrued since our lineage split from chimps between 6 and 5 million years ago.
Pääbo admits that he “struggled” to interpret the finding: the Neanderthal DNA suggests that the modern human’s version of FOXP2 arose much earlier than previously thought. Comparisons of gene sequences of modern humans with other living species had put the origins of human FOXP2 between 200,000 and 100,000 years ago, which matches archaeological estimates for the emergence of spoken language. However, Neanderthals split with humans around 400,000 years ago, so the discovery that they share our version of FOXP2 pushes the date of its emergence back at least that far.
“We believe there were two things that happened in the evolution of human FOXP2,” says Pääbo. “The two amino acid changes – which happened before the Neanderthal-human split – and some other change which we don’t know about that caused the selective sweep more recently.” In other words, the characteristic mutations that we see in human FOXP2 may indeed be more ancient than expected, but the mutated gene only became widespread and uniform later in human history. While many have interpreted Pääbo’s findings as evidence that Neanderthals could talk, he is more cautious. “There’s no reason to assume that they weren’t capable of spoken language, but there must be many other genes involved in speech that we yet don’t know about in Neanderthals.”
When Walt Disney created Mickey Mouse in 1928, he understood the draw that anthropomorphic mice would have. But even Walt’s imagination might have struggled to foresee the events that have just taken place in a German genetics laboratory. There, a group of scientists led by Wolfgang Enard have “humanising” a gene in mice to study its potential relevance for human evolution.
The gene in question is the fascinating FOXP2, which I have written extensively about before, particularly in a feature for New Scientist. FOXP2 was initially identified as the gene behind an inherited disorder that affected language and grammar skills. Subsequently hailed as a “language gene”, it proved to be anything but. The gene, and its encoded protein, is incredibly conserved among animals, even among those without sophisticated communication skills. The chimp version differs from our own by just two amino acids; the mouse adds a single change on top of that.
The two amino acids that have cropped up since our split from chimps are unique to us and there’s plenty of evidence that they’re the result of intense natural selection. There has always been the tantalising possibility that these changes were crucial for the evolution of our speech and language skills but until now, no one really understood their purpose. No human has ever been found with mutations at these crucial positions. Obviously, genetically manipulating humans or chimps is out of the question, but the fact that the mouse version is so similar gave Enard a unique opportunity.
He tweaked the mouse Foxp2 so that it produced a protein with the two human-specific amino acids. The resulting mice couldn’t speak like their cartoon equals, but their calls were subtly altered, their central nervous system developed in different ways, and they showed changes in parts of the brain where FOXP2 is usually expressed (switched on) in humans. Simon Fisher, who first discovered the important role of FOXP2 and contributed to the study, says, “This shows, for the first time, that the [human-specific] amino-acid changes do indeed have functional effects, and that they are particularly relevant to the brain.”
The success of termites and other social insects hinges on their complex social systems, where workers sacrifice the ability to raise their own young in order to serve the colony and its queen – the only individual who reproduces. But this social order can be thrown into chaos by knocking out a single gene, and one that originally had a role in that other characteristic termite ability – eating wood.
Judith Korb from the University of Osnabrueck in Germany found that the queen termite relies on a gene called Neofem2 to rule over her subjects. Korb worked with the termite Cryptotermes secundus, and searched for genes that were strongly activated in quens but not kings or workers. Her search singled out Neofem2 and she used a technique called RNA interference (RNAi) to deactivate the gene in the queens of eight colonies.
Cryptotermes workers all have the ability to become royalty, but only if the current monarchs die. Until then, they keep their reproductive rights at bay. If queens are physically removed, the remaining workers start a war of succession, headbutting each other to try and establish their dominance. Those that butt most frequently ascend to the head job. And that’s exactly the behaviour that Korb saw when she nullified Neofem2.
The queen herself was unaffected, but her subjects became unruly. The frequency of butting bouts tripled in the day after the gene was silenced, something that didn’t happen in 24 control colonies where the queen’s genes were left unaltered. Cutting out this single gene made the workers behave as though their colony was queenless.
The world of genetics is filled with stories that are as gripping as the plot of any thriller. Take the IRGM gene – its saga, played out over millions of years, has all the makings of a classic drama. Act One: setting the scene. By duplicating and diverging, this gene thrived in the cells of most mammals as a trinity of related versions that played vital roles in the immune system.
Act Two: tragedy strikes. About 50 million years ago, in the ancestors of today’s apes and monkeys, the entire IRGM cluster was practically deleted, leaving behind a sole survivor. Things took a turn for the worse – a parasitic chunk of DNA called Alu hopped into the middle of the remaining gene, rendering it useless. IRGM was, for all intents and purposes, dead and it remained that way for over 25 million years of evolution.
Act Three: the uplifting ending. The future looked bleak, but IRGM’s fortunes were revived in the common ancestor of humans and great apes. Out of the blue, a virus inserted itself into this ancient genome in just the right place to resurrect the long-defunct gene. A fall from grace, a tragic demise and an last-minute resurrection – what more could you ask for from a story?
This twisting tale lies hidden in the genomes of the world’s mammals and it was discovered and narrated by Cemalettin Bekpen from the University of Seattle. To reconstruct the evolutionary story of the IRGM gene, Bekpen searched for it in a variety of different species.
(Oh come on – you try to find an image to illustrate this story!)