Tiny molecules drove the evolution of the vertebrates

Blogging on Peer-Reviewed ResearchThe spinal column that runs down your back is an identity badge that signifies your membership among the vertebrates – animals with backbones. Vertebrates have arguably the most complex bodies and genomes of any animal group and certainly, our lineage has come a long way from its last common ancestor.

TigerThe closest evolutionary cousins of the vertebrates are simple aquatic creatures such as the jawless lancelets and the sac-like, immobile sea squirts. How did these simple body plans diversify into the vast array of sophisticated forms wielded by today’s fish, amphibians, reptiles and mammals?

Gene number

Many scientists have suggested that the answer lies in the number of our genes. At three different points, the vertebrate genome (its full suite of genes) experienced a massive jump in size as huge chunks of genes – possibly the entire lot – were duplicated. The first of these coincided with the origins of the group itself and the second happened alongside the rise of the first jawed fish, setting them and their descendants aside from more ancient jawless forms like the lampreys.

So far, there seems to be a tidy connection between gene number and complexity, but the third round of duplication is a bit of a stumbling block. It happened at some point during the evolution of the bony fishes and while this group proceeded to radiate into a multitude of different shapes, their basic body plan stayed essentially the same. No big jump in complexity there.

Indeed, as the full genome sequences of more and more species are revealed, it’s becoming clear that the basic genetic toolkit that controls the development of animal bodies is remarkably consistent across the kingdom. Even the genome of a sea anemone, one of the simplest and most ancient animals on Earth, is strikingly similar to that of vertebrates.

In this light, it’s looking increasingly unlikely that the advent of new genes can account for the large rise in vertebrate complexity. Now, Alysha Heimberg and colleagues from Dartmouth College have proposed a new theory, centred around tiny molecules called microRNAs.

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Chimps have more adaptive genetic changes than humans

According to new research, chimpanzee genes have shown more adaptive changes than those of humans. The media widely reported the results as evidence that chimps are ‘more evolved’ than humans. But as I discuss here, these headlines are putting words into the researchers’ mouths.

Chimps have more adaptive genetic changes than humansSince the time when humans and chimps evolved from our common ancestor, our species appears to have come on by leaps and bounds. We walk on two legs, we speak using languages and while there is no doubt that chimps are intelligent, there is even less doubt that our brainpower outclasses theirs.

For years, scientists have assumed that our advanced abilities must be reflected in our genetics. After all, traits like intelligence and language give us great adaptive advantages. They should therefore be mirrored by similarly large changes in the human genome, compared to the chimp one.

Not so. Researchers at the University of Michigan sifted through the human and chimp genomes for signs of positive selection – the process where natural selection firmly embeds new mutations because of the advantages they provide. They found that the chimp genome contains 50% more positively-selected genes than the human one.

While earlier studies have compared individual human and chimp genes, this is the first to do a proper census. Margaret Bakewell and colleagues looked at almost 14,000 genes in both species.

The project was given a valuable push by the recent publication of the fully-sequenced rhesus macaque genome. The macaque – a type of monkey – is an evolutionary cousin of both humans and chimps, and provides a useful comparison.

Humans may have fewer adaptive changes than chimps because our population sizes have traditionally been smaller.If the team found a difference in the human and chimp genes, the macaque version can tell them which version is closest to the ancestral one. Previously, scientists had to make do with the mouse, a much more distantly related animal. The macaque’s presence gives the analysis greater accuracy.

Bakewell failed to find any noticeable differences in the function of positively-selected genes in humans and chimps. Both species even had similar proportions of positive changes among the genes that control the brain and nervous systems.

The reasons for this surprising result are unclear, but Bakewell feels that population sizes may hold the answer. For most of their evolution, chimpanzees have enjoyed a larger population size than humans have. It’s only recently that our numbers have ballooned to unfeasible proportions.

According to evolutionary theory, beneficial genetic changes are more quickly established in a population if it is larger. But in smaller groups, random genetic changes can trickle down through generations without being properly weeded out. This ‘genetic drift’ could explain why humans have fewer positively-selected genes than chimps do.

An alternative theory is that many of the human genetic changes that provide us with the greatest advantages may be relatively new developments. It is only recently in our history that we spread around the world from our origins in Africa, and as such, new genetic innovations may not have become established in the population as a whole.

A third theory, which I’m putting forward myself, is that the genetic changes responsible for our most human traits, may lie among stretches of DNA missed by this study. Recently, a study showed that one of the most important ‘genes’ in human evolution lies within our so-called junk DNA and controls the development of our brains. Clearly, we still have much to learn.

Evolution is not about progress.Nonetheless, the study helpfully shows that evolution is not necessarily about progress. It’s not an inexorable march toward some gleaming future. It’s about change, regardless of direction or result.

Somewhere along the line, the word ‘evolved’ started to gain a false value. It became an indicator of positive progress, so that claiming to be ‘more evolved’ than a peer is to claim superiority.

A huge number of newspapers and magazines reported this story under the headline of ‘Chimps more evolved than humans’. And while that may be technically reasonable, the inferences made were anything but.

The inherent values placed upon the phrase ‘more evolved’ clearly emerged in the reaction to the story. Some suggested that humans were obviously ‘less evolved’ given for reasons ranging from pollution to capitalism. Meanwhile, creationists and ID-supporters smelled blood in the water, and claimed that such as blatantly preposterous conclusion proved that evolution was nonsense.

Of course, no such conclusions were actually made by the study itself. In the light of the proper progress-free meaning of the word ‘evolution’, hese results are not preposterous, but fascinating. We should use them to drive a nail in the coffin of phrases like ‘evolutionary race’ or ‘more evolved’, at least in its value-laden non-scientific sense.

Reference: Bakewell, Shi & Zhang. 2007. More genes underwent positive selection in chimpanzee evolution than in human evolution. PNAS 104: 7489-7494.

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Non-coding DNA drove human brain evolution by making nerve cells stickier

Most of our genome is made up of the poorly named ‘junk DNA’. New research shows that these sequences may have been vital in the evolution of human brains, by allowing our neurons to make better contacts with each other.

DNA, and little of it is 'junk'.Two months ago, a group of scientists found that the gene that has evolved fastest since our evolutionary split from chimpanzees is found in our so-called ‘junk DNA’. DNA is a code that tells our cells how to build their molecular workforce – proteins.

But the vast majority of our DNA sequence is never translated into proteins. While some considered this ‘junk’ DNA to be meaningless, recent research has shown that it makes important contributions to our most human of organs – our brains.

Now, Shyam Prabhakar and James Noonan at the Lawrence Berkeley National Laboratory have found further proof of the link between non-coding DNA and our mental evolution.

They studied over 110,000 stretches of DNA called ‘conserved non-coding sequences’ (CNSs), that are largely similar in a wide variety of animals. Of these sequences, 992 showed large numbers of changes that were specific to humans.

This number is much higher than would be expected if these DNA regions were drifting aimlessly in the evolutionary river. Their frequency is the mark of natural selection – these sequences must have changed for a reason.

To discover what this reason might have been, Prabhakar and Noonan looked at which genes these CNSs were in, and what they do in the body. They found that a large proportion of the genes in question were involved in the adhesion of neurons (nerve cells).

These genes are vital for the growth and development of our brains and allow neurons to make connections with each other, and with their surrounding framework of supportive cells.

The duo found a similar number of CNSs with chimpanzee-specific changes and many of these were also involved in nerve cell adhesion. But there was hardly any overlap between the chimp-specific and human-specific sequences.

Both lineages have developed nerve cells that make better contacts with each other, but have done so in separate ways using different genes.

It is possible that human and chimp brains have evolved different mental abilities to satisfy different evolutionary pressures. Identifying the precise role of the human-specific CNSs will help to test this possibility and it is the next big challenge facing Prabhakar and Noonan.

In the meantime, this research once again shows that non-coding DNA, far from being useless junk, was vitally important for the evolution of the human brain and its many unique abilities. Subtle changes in these sequences separate us from even our closest animal relatives.

Prabhakar, Noonan, Paabo & Rubin. 2006. Science 314: 786.
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Hidden ‘junk’ gene separates human brains from chimpanzees

Scientists used to believe that 98.5% of our DNA is junk and serves no useful purpose. But new discoveries are showing that this assumption is wrong. We now know that one of the most important genes that separates humans from chimpanzees lies among this supposed junk.

 

We’ve all found gems hidden among junk before – the great album you own but never listened to, the book on your shelf that you never read, or the boot sale item that’s worth a fortune. Geneticists are no different. Last month, Katherine Pollard and Sofie Salama discovered that one of the most important genes in human evolution has been lying in plain sight, hidden within a pile of genetic junk.

Humans and chimps share over 98.5% of our DNA.

Humans and our closest cousins, chimpanzees, evolved from a common ancestor, and we famously share anywhere from 96-99% of our DNA. This similarity suggests an obvious question: what are the key genetic differences that separate us from chimps? The search for these differences is now possible because the entire human and chimp genomes have been sequenced. The genomes represent each species’ entire DNA repertoire and by comparing them, Pollard and Salama sought to hunt down the genetic innovations that shaped our very humanity.

The duo and their colleagues at the University of California, Santa Cruz, clocked the rate of evolution in different parts of the human genome. They specifically looked for bits that had remained relatively stable for eons, but had exploded into evolutionary action since we and chimps diverged form our common ancestor.

They found 47 such areas which they appropriately named ‘human accelerated regions’ or HARs. And among these, a clear winner emerged – HAR1, a stretch of DNA that had changed 18 times faster than expected since the human and chimp dynasties split. HAR1 is part of a gene called HAR1F, and when the duo homed in on its location, they were in for a shock.

Hidden gems

98.5% of our DNA is apparently junk

HAR1F is part of our so-called ‘junk DNA’. DNA is a code that becomes useful when it is deciphered into messages written in a related molecule called RNA. RNA messages then act as recipes for building the molecular workforce of our bodies, proteins. But 98.5% of our genes do not code for proteins.

This poorly-named ‘junk DNA’ produces RNA messages that are never translated. For a time, they were largely thought to be ignored by evolutionary forces, and while some research hinted at an active function, actual details about their roles have remained elusive.

Over the last decade or so, geneticists have come to appreciate that certain stretches of ‘junk DNA’ may actually be vitally important. The discovery of HAR1F provides massive evidence that this line of thought is correct. In fact, 47 out of the 49 HARs were found among junk DNA and many of these lie next to genes that code for proteins involved in brain development.

Pollard and Salama believe that HAR1F and its colleagues control when, where and how these brain development genes are switched on, effectively redeploying our protein arsenal in interesting ways. When they looked at the brains of embryos, they found that HAR1F showed up between the second and fifth months of development. It is found in special brain cells called Cajal-Retzius cells, which control the migration of neurons from their birthplace to other parts of the brain.

It is unsurprising that one of the fastest evolving genes in our collection affects the brain or that many of the other HARs also control brain development. After all, our large brains (three times larger than a chimp’s) are arguably our most defining attribute. But this study suggests that evolution fashioned our brains not by substituting in new proteins but by creatively changing the formation and tactics of the existing squad.

The evidence has never been stronger that the previously over-looked 98.5% of our genome is far from junk. Instead, this is an area littered with hidden gems that are essential to being human.

Reference: Pollard, Salama, Lambert, Lambot, Coppens, Pedersen, Katzman, King, Onodera, Siepel, Kern, Dehay, Igel, Ares, Vanderhaeghen & Haussler. 2006. Nature. Epub ahead of print.

Related posts on DNA and chimp/human evolution:
Non-coding DNA drove brain evolution by making nerve cells stickier
Chimps have more adaptive genetic changes than humans
Opinion: Not so unique – the chimpanzee Stone Age, and our place among intelligent animals
Chimps show that actions spoke louder than words in language evolution
Orang-utan study suggests that upright walking may have started in the trees

 

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