Category Archives: Conservation

THE PANDA REVEALED

For many people, the giant panda, Ailuropoda melanoleura, is synonymous with conservation. This gentle, bamboo-munching animal is down to around 2,500 individuals, and a combination of small population size and man-made environmental change, means that it is probably doomed to extinction in the wild. All is not gloom, however: the latest issue of Nature [subscription needed to get past abstract] announces the completion of the sequencing of the giant panda genome (or rather, a giant panda genome – the individual in question was a 3-year old female (name unknown). No pandas were hurt in the making of this sequence.

This enormous undertaking, completed by a vast horde of Chinese researchers, reveals a number of fascinating things about the giant panda, and its position on the evolutionary tree. First the scientists investigated which genes are common to three mammals – panda, dog and human. This was a massive computing task – each of the genomes contains around 1.4 gigabases of non-repetitive sequence, or 1,400,000,000 “letters” (A,T,C or G). If each of these DNA molecules was stretched out, it would be about 5 metres long.

It turns out that about 846 megabases (or 3 metres) are common to all three species; of the remainder, more were common to the dog/panda pair than to either the human/panda or human/dog pairs. As you might expect, these shared areas tended to show high levels of synteny – they clump together physically, presumably because they are to do with fundamental biological processes, and have been passed down the eons without much physical or genetic alteration.

The one thing everyone knows about pandas is that they eat bamboo. However, it appears that, strictly speaking, they do not digest it – the genome contains no enzyme-producing genes that could help dissolve the hard plant tissue. That seems to be done by the bacteria that live in the animal’s gut. Unlike the cat – but like the dog and humans – the panda has several T2R genes, which code for the receptor for sweet tastes. On the other hand, the umami taste receptor, which enables animals to taste meat and protein, is not functional. This helps explain why this animal that is classified as a carnivore does not in fact eat meat. It may not even be able to taste it.

One of the most intriguing findings is that, despite the small population size, the panda genome they sequenced is highly heterozygous – each gene is present in two copies, and in this individual the frequency with which those two copies were different (“heterozygous”), was nearly twice that seen in humans. However, the authors note that the individual they studied was a cross between pandas from two regions – it may be that, in each region, pandas tend to have less variability. This would be worrying because it would suggest that in the wild pandas are more inbred, with associated problems for conservation.

Finally, there is the possibility that direct help for panda conservation may come from the identification of what may be a non-functional copy of a hormone involved in stimulating egg production. It is possible that this may explain the notoriously low fecundity of the panda. Or not.

For scientists, probably the most important thing about the panda sequence – and this also explains why it was published in Nature – is the way they went about it. This is an incredibly technical issue, but basically, the authors have shown that it is possible to sequence whole genomes accurately and rapidly (and relatively cheaply) using a new wave of sequencing technology which relies on sequencing lots of small bits of DNA and then assembling them like some massive jigsaw. Unlike previous efforts, the panda sequence was done from scratch, and has been completed. Other mammal sequences (eg the macaque or the cow) were done by less precise methods, with software to work out the gaps.

By sequencing many many small bits of DNA, the Chinese scientists ended up with a coverage that was about eight times as dense as that of previous mammalian sequences. However, the consequence of this approach is that these bits were assembled into chunks (“scaffolds”) that were smaller and more numerous than in previous sequences (there are over 3,800 panda scaffolds as against less than 100 in the dog). This means that some data may be lost when looking for some genes, or looking for large-scale genomic organisation.

Most striking is the cost. A year ago, when the data was acquired, it cost about $900,000, compared to well over $10,000,000 for a genome using classic techniques. 12 months on, prices of sequencers and computers have declined even more, making the possibility of sequencing many more genomes increasingly real.

Ruiqiang Li, et al. (2010) The sequence and de novo assembly of the giant panda genome Nature 463:311-318

5 Comments

Filed under Conservation, Genetics, Mammals

BATS DO BETTER UNDER BRIDGES

In many parts of the world, urban development is providing new roosting sites for bats. Concrete road bridges seem to be a favourite place that bats congregate and rear their young. You might expect that what with toxic fumes, heavy-metal run-off and noise pollution, bats living in these sites would do less well than their relatives living in more traditional sites like caves. That was certainly the prediction of  researchers from Boston and Knoxville, who studied birth size and postnatal growth in Brazilian free-tailed bat pups, and are just about to publish their findings in the Journal of Zoology.

As its name suggests, the Brazilian free-tailed bat (Tadarida brasiliensis) is found throughout much of South America, but its northern range is the southern states of the USA. The study was carried out south-central Texas – the bats migrate north from Mexico each spring, then rear their young. The bats can roost in groups of over a million. Females bear a single pup in May/June; pups can apparently be fed by any lactating female and can fly within 8 weeks. Adults are around 10 cm long and can weigh up to 14g. The bat is called “free-tailed” because it has a tail that projects beyond the hind-most membrane.

tadabras

The Brazilian free-tailed bat, Tadarida brasiliensis (Photo by J. Scott Altenbach, jsa@batphotography.com; Photo Copyright Bat Photography LLC

Around 600,000 bats live under the McNeil Bridge in Williamson County. Every night they come flying out of the bridge to hunt for insects, as seen in this picture:

21-bats

Photo courtesy Karen R. Thompson

To their surprise, the researchers found that pups born under the bridge were heavier and larger at birth, and grew faster, than pups born in a cave. Although a number of factors may have affected the result (in particular, larger females may have been roosting under the bridge, and larger females have larger offspring), they conclude that temperature conditions under the bridge and proximity to foraging areas may account for the apparent success of those bats that took advantage of the man-made structures.

L. C. Allen, C. S. Richardson, G. F. McCracken & T. H. Kunz (2009) Birth size and postnatal growth in cave- and bridge-roosting Brazilian free-tailed bats. Journal of Zoology. (Early View, not yet published).

Abstract available here, subscription needed to read full text.

Leave a comment

Filed under Conservation, Mammals, Uncategorized

WHY MOLECULAR GENETICS IS IMPORTANT

November 2007

Article from earlier in the year using mtDNA to track the number of whales being sold in markets in Korea They discovered that the number actually being consumed was far greater than the number that was officially reported. Uni/Athens needed to see full article.

Leave a comment

Filed under Conservation, Genetics, Mammals

OVERFISHING AND GEOLOGY

November 2007

Two items on this week’s excellent The Material World (Radio 4). Both items look at the past, present and future of their subjects. There’s also a brief reminder of last week’s discussion of bombardier beetles. Click on “listen again”.

Leave a comment

Filed under Audio files, BBC, Conservation

HERO TRIES TO SAVE DOLPHINS

November 2007

This video from Jena Saffery (Final Year): Hayden Panetierre (the cheerleader from Heroes) tries to save some dolphins from Japanese fishermen.

Leave a comment

Filed under Conservation, Mammals

COUNTING TIGERS

November 2007

How do you count tigers? This BBC online article suggests the hard way. What about estimating population size through population genetics? Different level of accuracy, I suppose.

Nature magazine article about attempts to preserve the Siberian tiger (Uni/Athens needed to get past abstract).

Leave a comment

Filed under Conservation, Mammals

FISHERMEN SEE THE LIGHT

November 2007

Without succumbing to national or professional prejudices, I’m sure you’ll agree that the last place you’d expect to hear a call for sustainable fishing would be from a Spanish fishing village. Fishermen from the Gallician village of Lira have realised that there is a future in fishing, as long as the sea is protected from over-exploitation.

Leave a comment

Filed under Conservation