Frog genome holds out conservation promise

Scientists have published the first genome sequence from an amphibian.

Xenopus tropicalis, the western clawed frog, joins the list of sequenced organisms that includes chicken, horse, rat, yeast, platypus, and human being.

It has about 20,000 genes - about the same as a human - and scientists say it sheds new light on genetic evolution.

Conservationists say analysing the genes could lead to new ways of combating threats such as the often fatal fungal disease chytridiomycosis.

Presenting their results in the journal Science, the researchers also suggest it may lead to better understanding of the threat posed by endocrine-disrupting ("gender-bending") chemicals, to which amphibians are especially sensitive.

Filling the gap

Forty-eight scientists from 20 institutions collaborated on the study, led from the US Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, California.

More detail on the genes that give resistance could have massive implications for captive breeding programmes

Robin Moore Conservation International

"When human genome work was wrapping up around 2002, we were discussing what should be next," JGI's Uffe Hellsten told BBC News.

"At that time there were a couple of furry mammals in the pipeline, and the chicken and at least two fish - but there seemed to be a gaping hole in the branch that constitutes the amphibians, and it seemed logical to fill that hole."

The species chosen - X tropicalis - is a close relative of a standard laboratory animal, the African clawed frog X laevis.

This animal has been a staple of pioneering research in fields such as cell differentiation, the role of ribonucleic acid (RNA) and cloning.

During the 1940s and 50s, their sensitivity to human hormones also led to their use in pregnancy tests.

For this project, X tropicalis was preferred because it reproduces much faster than its more famous cousin.

The chytrid fungus is devastating amphibians numbers around the world

Its genome is also roughly half the size.

That is because at some point in evolutionary history, the lineage leading to X laevis duplicated its DNA, meaning it now carries a double cargo of the double helix.

The team reports that certain regions of the genome, clustered around specific genes, are remarkably similar to equivalent regions in the genomes of chicken and Homo sapiens - despite the fact that their lineages diverged some 360 million years ago.

"When you look at segments of the Xenopus genome, you literally are looking at structures that are 360 million years old," said Dr Hellsten.

"They were part of the genome of the last common ancestor of all birds, frogs, dinosaurs and mammals that ever roamed the Earth."

Immune attack

However, it is the set of genes unique to amphibians that has excited conservationists.

For the last few decades, frogs and - to a lesser extent - salamanders have been hard hit by a water-borne fungus, Batrachochytrium dendrobatidis.

It is spreading across the world and has caused mass deaths in many species. It is implicated as the major factor in several species extinctions.

WHAT ARE AMPHIBIANS?

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• First true amphibians evolved about 250m years ago
• Adapted to many different aquatic and terrestrial habitats
• Present today on every continent except Antarctica
• Undergo metamorphosis, from larvae to adults

Recently, scientists in several institutions have been working on a conservation strategy that would take naturally-occurring anti-chytrid chemicals from species that are immune, and use them to protect others.

Xenopus appear to be immune themselves; and unravelling the genetic blueprint of its chemical defences could perhaps help to accelerate this line of research.

"Xenopus is the genus from which chytrid was first recorded, in [a museum specimen from] 1938, and they seem to be resistant," said Robin Moore, amphibian conservation officer with Conservation International.

"More detail on the genes that give resistance could also have massive implications for captive breeding programmes, helping us select animals that are resistant."

A valuable next step, he added, would be to compare variants of these genes between amphibian species - especially from those that are highly vulnerable to chytrid.

Dr Hellsten also suggested the sequences could shed light on the mechanism of endocrine-disrupting chemicals such as polychlorinated biphenyls (PCBs) - colloquially known as "gender-benders" - which impact many animals, but amphibians in particular because of their skin's high permeability.

"Understanding the effects of these hormone disruptors will help us preserve frog diversity and, since these chemicals also affect humans, could have a positive effect on human health," he said.

Frogs much like humans, genetically speaking

At least 1,700 genes in African clawed frog genome are similar to humans 

African clawed frogs have more in common with humans than you might think, according to their newly sequenced genome, which shows a surprising number of commonalities with the human genome.

The frog in question is a slimy, rotund type scientifically named Xenopus tropicalis. This is the first time an amphibian genome has been sequenced, and scientists say it represents a big hop forward in understanding not just frogs but Earth's whole tree of life.

"A lot of furry animals have been sequenced, but far fewer other vertebrates," said study co-leader Richard Harland, a biologist at the University of California, Berkeley. "Having a complete catalog of the genes in Xenopus, along with those of humans, rats, mice and chickens, will help us reassemble the full complement of ancestral vertebrate genes." 

Currently, more than 175 organisms have had their genetic information nearly completely sequenced. That's just a drop in the bucket of the world's plethora of life.

In fact, many of Earth's creatures are more similar to each other, genetically speaking, than you might guess just by looking at them. When scientists compared regions around specific genes in the frog genome to those same regions in chicken and human genomes, they found some amazing similarities, indicating a high level of conservation of organization, or structure, on the chromosomes (packets of DNA in cells).

"When you look at segments of the Xenopus genome, you literally are looking at structures that are 360 million years old and were part of the genome of the last common ancestor of all birds, frogs, dinosaurs and mammals that ever roamed the Earth," said study leader Uffe Hellsten of the Department of Energy's Joint Genome Institute in Walnut Creek, Calif. "Chromosome archaeology helps [us] to understand the history of evolution, showing us how the genetic material has rearranged itself to create the present-day mammalian genome and present-day amphibian genome."

At least 1,700 genes in the African clawed frog genome are very similar to genes in humans that are associated with specific diseases, such as cancer, asthma, and heart disease. So finding these connections means that experiments on the frogs could help doctors learn more about how to treat those conditions in people.

The frogs' similarity to humans has come in handy before.

In the early 20th century biologists discovered that these frogs were unusually sensitive to human chorionic gonadotropin, a hormone produced by pregnant women. The frogs gained popularity as a low-cost pregnancy test in the 1940s and 1950s. Doctors would inject a frog with a woman's urine, and if she was pregnant, the frog would ovulate and produce eggs in 8 to 10 hours.

 

Close encounters with Japan's 'living fossil'

It soon becomes clear that the giant salamander has hit Claude Gascon's enthusiasm button smack on the nose.

"This is a dinosaur, this is amazing," he enthuses.

"We're talking about salamanders that usually fit in the palm of your hand. This one will chop your hand off."

As a leader of Conservation International's (CI) scientific programmes, and co-chair of the Amphibian Specialist Group with the International Union for the Conservation of Nature (IUCN), Dr Gascon has seen a fair few frogs and salamanders in his life; but little, he says, to compare with this.

Fortunately for all of our digits, this particular giant salamander is in no position to chop off anything, trapped in a tank in the visitors' centre in Maniwa City, about 800km west of Tokyo.

But impressive it certainly is: about 1.7m (5ft 6in) long, covered in a leathery skin that speaks of many decades passed, with a massive gnarled head covered in tubercles whose presumed sensitivity to motion probably helped it catch fish by the thousand over its lifetime.

If local legend is to be believed, though, this specimen is a mere tadpole compared with the biggest ever seen around Maniwa.

A 17th Century tale, related to us by cultural heritage officer Takashi Sakata, tells of a salamander (or hanzaki, in local parlance) 10m long that marauded its way across the countryside chomping cows and horses in its tracks.

The hanzaki shrine is an attempt to make up for a mythical killing

A local hero was found, one Mitsui Hikoshiro, who allowed the hanzaki to swallow him whole along with his trusty sword - which implement he then used, in the best heroic tradition, to rend the beast from stem to stern.

It proved not to be such a good move, however.

Crops failed, people started dying in mysterious ways - including Mr Hikoshiro himself.

Pretty soon the villagers drew the obvious conclusion that the salamander's spirit was wreaking revenge from beyond the grave, and must be placated. That is why Maniwa City boasts a shrine to the hanzaki.

The story illustrates the cultural importance that this remarkable creature has in some parts of Japan.

Its scientific importance, meanwhile, lies in two main areas: its "living fossil" identity, and its apparently peaceful co-existence with the chytrid fungus that has devastated so many other amphibian species from Australia to the Andes.

Close family

"The skeleton of this species is almost identical to that of the fossil from 30 million years ago," recounts Takeyoshi Tochimoto, director of the Hanzaki Institute near Hyogo.

"Therefore it's called the 'living fossil'."

The hanzaki (Andrias japonicus) only has two close living relatives: the Chinese giant salamander (A. davidianus), which is close enough in size and shape and habits that the two can easily cross-breed, and the much smaller hellbender (Cryptobranchus alleganiensis) of the south-eastern US.

Creatures rather like these were certainly around when dinosaurs dominated life on land, and fossils of the family have been found much further afield than their current tight distribution - in northern Europe, certainly, where scientists presumed the the lineages had gone extinct until tales of the strange Oriental forms made their way back to the scientific burghers of Vienna and Leiden a couple of centuries ago.

"They are thought to be extremely primitive species, partly due to the fact that they are the only salamanders that have external fertilisation," says Don Church, a salamander specialist with CI.

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Scientists at the Hanzaki Insitute filmed a fight between two of the giant beasts

The fertilisation ritual must be quite some sight.

Into a riverbank den that is usually occupied by the dominant male (the "den-master") swim several females, and also a few other males.

The den-master and the females release everything they have got, turning incessantly to stir the eggs and spermatozoa round in a roiling mass.

Maybe the lesser males sneak in a package or two as well; their function in the ménage-a-many is not completely clear.

When the waters still, everyone but the den-master leaves; and he alone guards the nest and its juvenile brood.

It is not an ideal method of reproduction.

Research shows that genetic diversity among the hanzaki is smaller than it might be, partly as a result of the repeated polygamy, which in turn leaves them more prone to damage through environmental change.

But for the moment, it seems to work.

Outside the breeding season, the salamander's life appears to consist of remaining as inconspicuous as possible in the river (whether hiding in leaves, as the small ones do, or under the riverbanks like their larger fellows) and snapping whatever comes within reach, their usual meandering torpor transformed in an instant as the smell of a fish brushes by.

The adults' jaws are not to be treated lightly.

Among Dr Tochimoto's extensive collection of photos is one of bloodied human hands; and as he warns: "you may be attacked and injured; please be careful".

The giant Maniwa hanzaki brought gasps from experienced amphibian-watchers

When the chytrid fungus was identified just over a decade ago, indications were that Japan would be an unlikely place to look for its origins.

With the discovery of chytrid on museum specimens of the African clawed frog (Xenopus laevis), an out-of-Africa migration spurred by human transportation of amphibians once seemed the simple likelihood.

But just last year, a team of researchers led by Koichi Goka from Japan's National Institute for Environmental Studies published research showing that certain strains of chytrid were present on Japanese giant salamanders, and only on Japanese giant salamanders, including museum specimens from a century or so back; and that the relationship seemed benign.

AMPHIBIANS: A QUICK GUIDE First true amphibians evolved about 250m years ago There are three orders: frogs (including toads), salamanders (including newts) and caecilians, which are limbless Adapted to many different aquatic and terrestrial habitats Present today on every continent except Antarctica Many undergo metamorphosis, from larvae to adults

The hanzaki-loving strains of chytrid appear to differ from those that are proving so virulent to amphibians now.

Unravelling all that, says Don Church, might tell us something about the origins and spread of chytrid - and there is so much diversity among Japanese chytrid strains that the country is now being touted as a possible origin, as diversity often implies a long evolutionary timeframe.

More importantly, the discovery might also provide options for treating the infection.

"In the case of the North American salamanders, what was found was that they have bacteria living on their skin that produce peptides that are lethal to the amphibian chytrid fungus," says Dr Church.

"And those bacteria might be able to be transplanted to other species that can't fight off the fungus."

This is a line of research that is very much in play in laboratories around the world.

It appears likely now that studies of the Japanese giant salamander can expand the number of chytrid-fighting bacteria known to science, and so extend the options for developing treatments for an infection that currently cannot be controlled in the wild.

But that can only come to pass if the giant salamanders endure; something that is not guaranteed, with the challenges they face in modern Japan including, perhaps, new strains of chytrid itself.

There is as yet no modern hero able to still the pace of habitat loss or prevent invasion from rival species.