Wprawdzie artykuł New Scientist "Why Darwin was wrong about the tree of life" nie jest już publicznie dostępny, ale w sieci można jeszcze znaleźć jego przedruki. Publikuję jeden z nich - być może ta strona stanie się wkrótce jednym z nielicznych miejsc, gdzie będzie można dotrzeć do pełnej treści tej ważnej publikacji.
Ponieważ wyedukowana przez światłe umysły dziennikarzy urbanowo - kotlińskich gadzinówek hołota, jest święcie przekonana, że dyskutuje z ciemnogrodem, warto, by poznała jego przedstawicieli z imienia, nazwiska, rangi i tytułu. Oto oni:
Michael R. Rose - profesor, biolog ewolucyjny, University of California, Irvine
Eric Bapteste biolog ewolucyjny Uniwersytet w Paryżu
John Dupré - filozof nauki, profesor Uniwersytetu w Exeter
Michael Syvanen - University of California
21 January 2009 by Graham Lawton
IN JULY 1837, Charles Darwin had a flash of inspiration. In his
study at his house in London, he turned to a new page in his red
leather notebook and wrote, "I think". Then he drew a spindly sketch
of a tree.
As far as we know, this was the first time Darwin toyed with the
concept of a "tree of life" to explain the evolutionary
relationships between different species. It was to prove a fruitful
idea: by the time he published On The Origin of Species 22 years
later, Darwin's spindly tree had grown into a mighty oak. The book
contains numerous references to the tree and its only diagram is of
a branching structure showing how one species can evolve into many.
The affinities of all the beings of the same class have sometimes
been represented by a great tree. I believe this simile largely
speaks the truth...
The tree-of-life concept was absolutely central to Darwin's
thinking, equal in importance to natural selection, according to
biologist W. Ford Doolittle of Dalhousie University in Halifax, Nova
Scotia, Canada. Without it the theory of evolution would never have
happened. The tree also helped carry the day for evolution. Darwin
argued successfully that the tree of life was a fact of nature,
plain for all to see though in need of explanation. The explanation
he came up with was evolution by natural selection.
Ever since Darwin the tree has been the unifying principle for
understanding the history of life on Earth. At its base is LUCA, the
Last Universal Common Ancestor of all living things, and out of LUCA
grows a trunk, which splits again and again to create a vast,
bifurcating tree. Each branch represents a single species; branching
points are where one species becomes two. Most branches eventually
come to a dead end as species go extinct, but some reach right to
the top--these are living species. The tree is thus a record of how
every species that ever lived is related to all others right back to
the origin of life.
...The green and budding twigs may represent existing species, and
those produced during each former year may represent the long
succession of extinct species
For much of the past 150 years, biology has largely concerned itself
with filling in the details of the tree. "For a long time the holy
grail was to build a tree of life," says Eric Bapteste, an
evolutionary biologist at the Pierre and Marie Curie University in
Paris, France. A few years ago it looked as though the grail was
within reach. But today the project lies in tatters, torn to pieces
by an onslaught of negative evidence. Many biologists now argue that
the tree concept is obsolete and needs to be discarded. "We have no
evidence at all that the tree of life is a reality," says Bapteste.
That bombshell has even persuaded some that our fundamental view of
biology needs to change.
So what happened? In a nutshell, DNA. The discovery of the structure
of DNA in 1953 opened up new vistas for evolutionary biology. Here,
at last, was the very stuff of inheritance into which was surely
written the history of life, if only we knew how to decode it. Thus
was born the field of molecular evolution, and as techniques became
available to read DNA sequences and those of other biomolecules such
as RNA and proteins, its pioneers came to believe that it would
provide proof positive of Darwin's tree of life. The basic idea was
simple: the more closely related two species are (or the more
recently their branches on the tree split), the more alike their
DNA, RNA and protein sequences ought to be.
It started well. The first molecules to be sequenced were RNAs found
in ribosomes, the cell's protein-making machines. In the 1970s, by
comparing RNA sequences from various plants, animals and
microorganisms, molecular biologists began to sketch the outlines of
a tree. This led to, among other successes, the unexpected discovery
of a previously unknown major branch of the tree of life, the
unicellular archaea, which were previously thought to be bacteria.
By the mid-1980s there was great optimism that molecular techniques
would finally reveal the universal tree of life in all its glory.
Ironically, the opposite happened.
The problems began in the early 1990s when it became possible to
sequence actual bacterial and archaeal genes rather than just RNA.
Everybody expected these DNA sequences to confirm the RNA tree, and
sometimes they did but, crucially, sometimes they did not. RNA, for
example, might suggest that species A was more closely related to
species B than species C, but a tree made from DNA would suggest the
reverse.
Which was correct? Paradoxically, both--but only if the main
premise underpinning Darwin's tree was incorrect. Darwin assumed
that descent was exclusively "vertical", with organisms passing
traits down to their offspring. But what if species also routinely
swapped genetic material with other species, or hybridised with
them? Then that neat branching pattern would quickly degenerate into
an impenetrable thicket of interrelatedness, with species being
closely related in some respects but not others.
We now know that this is exactly what happens. As more and more
genes were sequenced, it became clear that the patterns of
relatedness could only be explained if bacteria and archaea were
routinely swapping genetic material with other species--often
across huge taxonomic distances--in a process called horizontal
gene transfer (HGT).
At first HGT was assumed to be a minor player, transferring only
"optional extra" functions such as antibiotic resistance. Core
biological functions such as DNA replication and protein synthesis
were still thought to be passed on vertically. For a while, this
allowed evolutionary biologists to accept HGT without jeopardising
their precious tree of life; HGT was merely noise blurring its
edges. We now know that view is wrong. "There's promiscuous exchange
of genetic information across diverse groups," says Michael Rose, an
evolutionary biologist at the University of California, Irvine.
From tree to web
As it became clear that HGT was a major factor, biologists started
to realise the implications for the tree concept. As early as 1993,
some were proposing that for bacteria and archaea the tree of life
was more like a web. In 1999, Doolittle made the provocative claim
that "the history of life cannot properly be represented as a tree"
(Science, vol 284, p 2124). "The tree of life is not something that
exists in nature, it's a way that humans classify nature," he says.
Thus began the final battle over the tree. Many researchers stuck
resolutely to their guns, creating ever more sophisticated computer
programs to cut through the noise and recover the One True Tree.
Others argued just as forcefully that the quest was quixotic and
should be abandoned.
The battle came to a head in 2006. In an ambitious study, a team led
by Peer Bork of the European Molecular Biology Laboratory in
Heidelberg, Germany, examined 191 sequenced genomes from all three
domains of life--bacteria, archaea and eukaryotes (complex
organisms with their genetic material packaged in a nucleus)--and
identified 31 genes that all the species possessed and which showed
no signs of ever having been horizontally transferred. They then
generated a tree by comparing the sequences of these "core" genes in
everything from E. coli to elephants. The result was the closest
thing yet to the perfect tree, Bork claimed (Science, vol 311, p
1283).
Other researchers begged to differ. Among them were Tal Dagan and
William Martin at the Heinrich Heine University in Düsseldorf,
Germany, who pointed out that in numerical terms a core of 31 genes
is almost insignificant, representing just 1 per cent of a typical
bacterial genome and more like 0.1 per cent of an animal's. That
hardly constitutes a mighty oak or even a feeble sapling--more like
a tiny twig completely buried by a giant web. Dagan dubbed Bork's
result "the tree of 1 per cent" and argued that the study
inadvertently provided some of the best evidence yet that the
tree-of-life concept was redundant (Genome Biology, vol 7, p 118).
The debate remains polarised today. Bork's group continue to work on
the tree of life and he continues to defend the concept. "Our point
of view is that yes, there has been lots of HGT, but the majority of
genes contain this tree signal," Bork says. The real problem is that
our techniques are not yet good enough to tease that signal out, he
says.
Meanwhile, those who would chop down the tree of life continue to
make progress. The true extent of HGT in bacteria and archaea
(collectively known as prokaryotes) has now been firmly established.
Last year, Dagan and colleagues examined more than half a million
genes from 181 prokaryotes and found that 80 per cent of them showed
signs of horizontal transfer (Proceedings of the National Academy of
Sciences, vol 105, p 10039).
Surprisingly, HGT also turns out to be the rule rather than the
exception in the third great domain of life, the eukaryotes. For a
start, it is increasingly accepted that the eukaryotes originated by
the fusion of two prokaryotes, one bacterial and the other archaeal,
forming this part of the tree into a ring rather than a branch
(Nature, vol 41, p 152).
The neat picture of a branching tree is further blurred by a process
called endosymbiosis. Early on in their evolution, eukaryotes are
thought to have engulfed two free-living prokaryotes. One of these
gave rise to the cellular power generators called mitochondria while
the other was the precursor of the chloroplasts, in which
photosynthesis takes place. These "endosymbionts" later transferred
large chunks of their genomes into those of their eukaryote hosts,
creating hybrid genomes. As if that weren't complicated enough, some
early eukaryotic lineages apparently swallowed one another and
amalgamated their genomes, creating yet another layer of horizontal
transfer (Trends in Ecology and Evolution, vol, 23, p 268).
This genetic free-for-all continues to this day. The vast majority
of eukaryote species are unicellular--amoebas, algae and the rest
of what used to be known as "protists" (Journal of Systematics and
Evolution, vol 46, p263). These microscopic beasties have lifestyles
that resemble prokaryotes and, according to Jan Andersson of the
University of Uppsala in Sweden, their rates of HGT are often
comparable to those in bacteria. The more we learn about microbes,
the clearer it becomes that the history of life cannot be adequately
represented by a tree.
Hang on, you may be thinking. Microbes might be swapping genes left,
right and centre, what does that matter? Surely the stuff we care
about--animals and plants--can still be accurately represented by
a tree, so what's the problem?
Well, for a start, biology is the science of life, and to a first
approximation life is unicellular. Microbes have been living on
Earth for at least 3.8 billion years; multicellular organisms didn't
appear until about 630 million years ago. Even today bacteria,
archaea and unicellular eukaryotes make up at least 90 per cent of
all known species, and by sheer weight of numbers almost all of the
living things on Earth are microbes. It would be perverse to claim
that the evolution of life on Earth resembles a tree just because
multicellular life evolved that way. "If there is a tree of life,
it's a small anomalous structure growing out of the web of life,"
says John Dupré, a philosopher of biology at the University of
Exeter, UK.
More fundamentally, recent research suggests that the evolution of
animals and plants isn't exactly tree-like either. "There are
problems even in that little corner," says Dupré. Having uprooted
the tree of unicellular life, biologists are now taking their axes
to the remaining branches.
For example, hybridisation clearly plays an important role in the
evolution of plants. According to Loren Rieseberg, a botanist at the
University of British Columbia in Vancouver, Canada, around 14 per
cent of living plant species are the product of the fusion of two
separate lineages.
Hybrid humans
Some researchers are also convinced that hybridisation has been a
major driving force in animal evolution (see "Natural born
chimeras", and "Two into one"), and that the process is ongoing. "It
is really common," says James Mallet, an evolutionary biologist at
University College London. "Ten per cent of all animals regularly
hybridise with other species." This is especially true in rapidly
evolving lineages with lots of recently diverged species--including
our own. There is evidence that early modern humans hybridised with
our extinct relatives, such as Homo erectus and the Neanderthals
(Philosophical Transactions of the Royal Society B, vol 363, p
2813).
Hybridisation isn't the only force undermining the multicellular
tree: it is becoming increasingly apparent that HGT plays an
unexpectedly big role in animals too. As ever more multicellular
genomes are sequenced, ever more incongruous bits of DNA are turning
up. Last year, for example, a team at the University of Texas at
Arlington found a peculiar chunk of DNA in the genomes of eight
animals--the mouse, rat, bushbaby, little brown bat, tenrec,
opossum, anole lizard and African clawed frog--but not in 25
others, including humans, elephants, chickens and fish. This patchy
distribution suggests that the sequence must have entered each
genome independently by horizontal transfer (Proceedings of the
National Academy of Sciences, vol 105, p 17023).
Other cases of HGT in multicellular organisms are coming in thick
and fast. HGT has been documented in insects, fish and plants, and a
few years ago a piece of snake DNA was found in cows. The most
likely agents of this genetic shuffling are viruses, which
constantly cut and paste DNA from one genome into another, often
across great taxonomic distances. In fact, by some reckonings, 40 to
50 per cent of the human genome consists of DNA imported
horizontally by viruses, some of which has taken on vital biological
functions (New Scientist, 27 August 2008, p 38). The same is
probably true of the genomes of other big animals. "The number of
horizontal transfers in animals is not as high as in microbes, but
it can be evolutionarily significant," says Bapteste.
Nobody is arguing--yet--that the tree concept has outlived its
usefulness in animals and plants. While vertical descent is no
longer the only game in town, it is still the best way of explaining
how multicellular organisms are related to one another--a tree of
51 per cent, maybe. In that respect, Darwin's vision has triumphed:
he knew nothing of micro-organisms and built his theory on the
plants and animals he could see around him.
Even so, it is clear that the Darwinian tree is no longer an
adequate description of how evolution in general works. "If you
don't have a tree of life, what does it mean for evolutionary
biology?" asks Bapteste. "At first it's very scary... but in the
past couple of years people have begun to free their minds." Both he
and Doolittle are at pains to stress that downgrading the tree of
life doesn't mean that the theory of evolution is wrong--just that
evolution is not as tidy as we would like to believe. Some
evolutionary relationships are tree-like; many others are not. "We
should relax a bit on this," says Doolittle. "We understand
evolution pretty well--it's just that it is more complex than
Darwin imagined. The tree isn't the only pattern."
Others, however, don't think it is time to relax. Instead, they see
the uprooting of the tree of life as the start of something bigger.
"It's part of a revolutionary change in biology," says Dupré. "Our
standard model of evolution is under enormous pressure. We're
clearly going to see evolution as much more about mergers and
collaboration than change within isolated lineages."
Rose goes even further. "The tree of life is being politely buried,
we all know that," he says. "What's less accepted is that our whole
fundamental view of biology needs to change." Biology is vastly more
complex than we thought, he says, and facing up to this complexity
will be as scary as the conceptual upheavals physicists had to take
on board in the early 20th century.
If he is right, the tree concept could become biology's equivalent
of Newtonian mechanics: revolutionary and hugely successful in its
time, but ultimately too simplistic to deal with the messy real
world. "The tree of life was useful," says Bapteste. "It helped us
to understand that evolution was real. But now we know more about
evolution, it's time to move on."
Two species become one
It could be time to ditch the old idea that hybrids are sterile
individuals that cannot possibly have played a role in shaping the
history of life on Earth. Hybridisation is a significant force in
animal evolution, according to retired marine biologist Donald
Williamson, formerly of the University of Liverpool, UK. His
conclusion comes from a lifetime studying marine animals such as
starfish, sea urchins and molluscs, many of which lead a strange
double life, starting out as larvae and metamorphosing into adult
forms.
The conventional explanation for metamorphosis is that it evolved
gradually, with the juvenile form becoming specialised for feeding
and the adult for mating, until they barely resembled each other.
Williamson thinks otherwise. He points out that marine larvae have
five basic forms and can be organised into a family tree based on
shared characteristics. Yet this tree bears no relationship to the
family tree of adults: near-identical larvae often give rise to
adults from different lineages, while some closely related adults
have utterly unrelated larvae.
BIOLOGICAL MASH-UP
It's as if each species was randomly assigned one of the larval
forms--which is exactly what Williamson argues happened. He
believes metamorphosis arose repeatedly during evolution by the
random fusion of two separate species, with one of the partners
assuming the role of the larva and the other that of the adult.
If that sounds unlikely, Williamson points out that many marine
species breed by casting their eggs and sperm into the sea and
hoping for the best, giving ample opportunity for cross-species
hybridisation. Normally nothing comes of this, he says, but "once in
a million years it works: the sperm of one species fertilises
another and two species become one". The most likely way for this
biological mash-up to function is if the resulting chimera expresses
its two genomes sequentially, producing a two-stage life history
with metamorphosis in the middle.
This explains many anomalies in marine biology, says Williamson. His
star witness is the starfish Luidia sarsi, which starts life as a
small larva with a tiny starfish inside. As the larva grows, the
starfish migrates to the outside and when the larva settles on the
seabed, they separate. This is perfectly normal for starfish, but in
Luidia something remarkable then happens. Instead of degenerating,
the larva swims off and lives for several months as an independent
animal. "I can't see how one animal with one genome could do that,"
says Williamson. "I think the larval genome and the adult genome are
different."
Natural born chimeras
The idea that microbes regularly swap portions of genetic code with
individuals from another species doesn't seem so far-fetched (see
main story). But could the same process also have shaped the
evolution of multicellular animals? In 1985, biologist Michael
Syvanen of the University of California, Davis, predicted that it
did (Journal of Theoretical Biology, vol 112, p 333). Back then
there was no way to test that claim, but there is now.
Syvanen recently compared 2000 genes that are common to humans,
frogs, sea squirts, sea urchins, fruit flies and nematodes. In
theory, he should have been able to use the gene sequences to
construct an evolutionary tree showing the relationships between the
six animals.
He failed. The problem was that different genes told contradictory
evolutionary stories. This was especially true of sea-squirt genes.
Conventionally, sea squirts--also known as tunicates--are lumped
together with frogs, humans and other vertebrates in the phylum
Chordata, but the genes were sending mixed signals. Some genes did
indeed cluster within the chordates, but others indicated that
tunicates should be placed with sea urchins, which aren't chordates.
"Roughly 50 per cent of its genes have one evolutionary history and
50 per cent another," Syvanen says.
The most likely explanation for this, he argues, is that tunicates
are chimeras, created by the fusion of an early chordate and an
ancestor of the sea urchins around 600 million years ago.
"We've just annihilated the tree of life. It's not a tree any more,
it's a different topology entirely," says Syvanen. "What would
Darwin have made of that?"
Graham Lawton is features editor of New Scientist
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