HOW WE GOT WHERE WE ARE

An excellent resource in the latest issue of Current Biology – seven reviews on the global genetic history of Homo sapiens, all available FREE. Not all the articles are easy going for the non-specialist, and lay readers might wish to focus on the introductory and concluding paragraphs, but this must surely be the most authoritative publicly available resource on the topic.

The issue opens with a guest editorial by archaeologist Colin Renfrew, summarising the “new synthesis” of genetic, linguistic and archaeological studies that are used to understand the history of our species. Genetics has shown clearly that we did indeed come “out of Africa”, around 70,000 years ago:

A study of 121 ethnically diverse African populations indicated the presence of 14 genetically distinct ancestral population clusters in Africa. Anatomically modern humans evolved in Africa around 200,000 yeas ago, migrated to Eurasia within the last 40000–80000 years and then migrated to the Americas within the last 15000–30000 years. The geographic expansion from Africa is thought to have been accompanied by a population bottleneck and a concomitant loss of genetic diversity. The migration of populations across the globe occurred in many small steps, with each migration event involving a sampling of variation from the previous population. In this figure, decreasing intensity of color represents the concomitant loss of genetic diversity as populations migrated in an eastward direction from Africa. Solid horizontal lines indicate gene-flow between ancestral human populations and the dashed horizontal line indicates recent gene-flow between Asian and Australian/Melanesian populations. (Taken from Current Biology)

Genetics can also show us how we colonised Europe:

This schematic map depicts major migratory events thought to have affected the gene pool of modern Europeans. Black arrows indicate the first settlement by modern humans around 45 thousand years ago (kya). At the end of the last ice age, around 10–15 kya, Europe was re-populated from glacial refugia (red arrows). Around 8–10 kya, Neolithic farmers came to Europe from Anatolia and the Fertile Crescent (green arrows). (Figure by Alessandro Achilli and Antonio Torroni.) Taken from Current Biology.

However, for the moment genetics is less able to resolve issues to do with the last 15-10,000 years, once we had become sedentary. For example, Renfrew writes:

“From a linguistic point of view, it is widely supposed that Proto-Indo-European or early Indo-European language, which is ancestral to Vedic Sanskrit and to most of the languages of North India and Pakistan (but not the Dravidian languages of the south), must have come to the sub-continent during the second millennium BC, presumably associated with some incoming population. But, even leaving linguistic issues aside, molecular genetic indicators for these migrations have not been very clearly identified”

To understand our more recent past, we not only need more data – for example from ancient DNA extracted from bones – we also need to develop new computational tools to be able to model the effects of migration and other changes on genetic and linguistic diversity in human populations. And above all we need to be able to confront these hypotheses with more reliable and unambiguous archaeological data. But for anyone interested in the history of our species, these are exciting times.

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

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.

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…

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.

FLAME-HAIRED NEANDERTHALS

October 2007

Did Neanderthals have red hair? Some recent evidence to be published in Science points that way (you or your institution will need a subscription to get past the abstract).

BBC summary.

MYSTERIOUS ULTRA-CONSERVED DNA

September 2007

There are huge tracts (some up to 730 bp long) of the *non-coding* mammalian genome that are ultra-conserved over 80 million years, without a single base-pair change. We share these sequences with rats, cats and apes. When these were discovered in 2004, people assumed they must play a role in regulating some important developmental genes. Now someone has made a knock-out mouse that lacks this sequence and – of course! – it is perfectly viable. There are no phenotypic differences at all… Weird or what?

News and views from PLoS Biology; original article (both open access).

HOW HOX MADE FISH FINGERS

May 2007

Remember all that stuff about Hox genes in the first year? Well it IS important! A study from Chicago shows that a primitive fish, Polyodon, shows expression of Hox and Sonic hedegog (one of my favourite gene names) in a pattern similar to that seen in tetrapods. The authors interpret this in terms of the gradual evolution of legs, over a 20 million year timescale.

Nature article (subscription needed to get past abstract), BBC article, an article by me about gene names.

MEASURING MINKE MORTALITY

May 2007

Molecular ecological techniques for estimating the number of Minke whales “accidentally” caught that end up on Japanese dining tables. A magazine article from Nature (subscription needed to get past abstract).

ONE GENE DOES IT ALL?

March 2007

Open Access article in PLoS Biology on the role of the vitellogenin gene on social organisation in honey bees, using RNAi to demonstrate its function at different stages