Category Archives: Mammals

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

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Filed under Conservation, Genetics, Mammals

HOW THE CAT GOT ITS COAT

Mammalian coat colour remains a mystery. Although we know a lot about the patterns involved, and can guess about some of their adaptive advantages, their genetic bases are largely unknown. Using a mixture of classic pedigree studies and molecular genetics, a new paper in Genetics (abstract only unless you have a subscription) has examined the genetic bases of stripes and spots in the domestic cat.

Source: Genetics.

Previous attempts to unravel the genetics of coat colour in domestic cats had come up with the following hypothesis, based on tracking coat patterns down the generations. The character(s) producing the classic tabby (like my cat Pepper) – D in the figure above – is/are recessive to all other forms (the is/are ambiguity is because we have (or had) no idea about the number of genes involved). The dominant form is the unmarked (Abyssinian) form (A), which is dominant over the spotted coat (B), which in turn is dominant over the striped coat (like my cat Ollie – C).

To see how many genes are actually involved in determining cat coat patterns,  the researchers, led by Eduardo Eizirik, now at the Pontifíca Uniservidade Católica de Rio Grande do Sul (Porto Alegre, Brazil), set up a series of mating crosses. The figure below shows the way they studied the basis of the spotted and “ticked” (Abyssinian) variants. They crossed homozygous individuals (aa or AA, respectively), then “backcrossed” their heterozygous offspring (Aa – called the F1 generation), to each of the parental types (only aa in this example) and tried to make sense of what happened in the third generation (or backcross – this is the bottom line on the figure). This is essentially the same procedure used by Gregor Mendel with his peas, over 150 years ago, which led to the foundation of genetics.

Source: Genetics

The figure below shows what happened when they tried to work out what genes are controlling the “spotted” coat variant, by crossing it to the tabby version (top line). The offspring (F1) showed a range from stripes to spots to tabby blotches (not shown). The backcross animals sometimes showed complete stripes, including the “mackerel” variant (bottom left).

Source: Genetics

They then used “microsatellite” genetic markers – small sequences of DNA that can be used to track and identify regions of the genome that may be responsible for the character under study. They were able to identify at least three different genes responsible for coat patterns – Tabby, which has two alleles or versions (one producing the mackerel pattern, the other the blotched); Ticked, which has an Abyssinian and a non-Absyssinian version, and one or more genes that alter the mackerel stripes and may also produce the blotched pattern. Furthermore, Ticked can alter the way Tabby is expressed.

In other words, it’s complicated. Which is hardly surprising, in a way – if it was straightforward, cat breeders would have figured it out long ago. What this study has shown is that there are genes involved in coding colour and pattern, that they are not necessarily the same, and that they affect the way each others’ expression. Exactly how this happens – or indeed, what these genes actually do – is unknown. They have yet to be identified at the molecular level.

Intriguingly, some of these genes may have equivalents in other animals, and may help in precisely identifying the genes involved in cat coat colour. For example, a human gene that may be similar to Tabby may be involved in the rare Hermansky-Pudlak syndrome type 2, where patients have reduced skin pigmentation.

Once the genes involved in determining coat colour and pattern in cats have been identified, we will be able to have a stab at understanding how they do what they do what they do. It will also give us the opportunity to study these genes in the 37 felid species that are still roaming the planet. In turn, that may help us understand apparently simpler patterns, such as those seen in tapirs, raccoons and badgers. Of course, just because different species have similar patterns, that doesn’t mean that they will necessarily use the same genes to produce them. Natural selection “cares” about the phenotype, not the genes that underlie that phenotype. There is more than one way to skin a cat.

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THE LEOPARD AND THE MOUSE

These photos were taken early in summer 2009 by photography student Casey Gutteridge at the Santago Rare Leopard Project in Hertfordshire, England. The leopard – a female called Sheena – discovered a visitor in her enclosure:

Intrigued by the mouse, the cat sniffed the visitor:

The mouse didn’t seem too concerned and carried on eating:

Although we generally think of mice as granivores, many rodents will eat virtually anything (plastic, candle wax etc), and are quite happy to eat meat, although not necessarily under the gaze of a leopard…

h/t: Cathy McCrohan and Jo Butler

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Filed under Images, Mammals, Uncategorized, Zoos

A PREDICTION ABOUT THE PINE MARTEN GENOME

The European pine marten (Martes martes) is a mustelid – part of the weasel family. There is also a North American relative (Martes americana). They mainly nocturnal and pretty hard to spot. Here’s a rather nice picture of a pine marten, from DJS photography (note its right ear, presumably nibbled in a fight):

On the last episode of Autumnwatch on the BBC last night, Chris Packham claimed that pine martens are very partial to a jam sandwich, and this does indeed seem to be the case (Mr Google has 272 hits with those two phrases – 273 now this page has been posted).

Although primarily carnivorous, they will also eat berries, honey and other sweet stuff. Hence the jam sandwiches. Cats, on the other hand, do not eat jam sandwiches or honey. And cats cannot taste sugar, for the simple reason that their genome does not possess the relevant T1R2 receptor which, together with the T1R3 receptor (which they do have), enables mammals to detect sugar.

So I predict that when the pine marten genome is eventually sequenced, we will find, nestled in its chromosomes, the T1R2 receptor…

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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.

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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.

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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.

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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).

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ALL THAT FROM A TOOTH

November 2007

A tooth found in India suggests that ungulates – hoofed mammals – existed in India before the end of the Cretaceous (ie before the end of the dinosaurs), while the sub-continent was charging across the Indian Ocean towards its current destination. They may even have originated in India. This tooth was found in the lava of the Deccan Traps (this will mean something to those who were paying attention in The Evolution of Animals).

Article from Science (subscription needed to get past abstract).

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FAINTING GOATS

November 2007

This video from Natalie Beresford (First Year). This is actually quite a serious question – these goats have a mutation in a muscle protein that makes them fall down. What human diseases might be related to this? What natural behaviours in other animals look like this?

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Filed under Diseases, Mammals, Videos