Cheetah genetic diversity revisited

February 4, 2011

Another chapter has been added to the story of genetic variation in the cheetah, with a paper out in next month’s Molecular Biology and Evolution journal giving a detailed description of variation at key immune genes in the species.  I first became familiar with the cheetah story as a PhD student when I was studying genetic diversity in the black robin.  At the time the cheetah was something of a poster child for the perils of low genetic variation, but this most recent paper suggests that their immune system is not as genetically invariant as first thought, and they may not be so vulnerable to disease after all. Read the rest of this entry »

A simple change determines male vs female organ development in flowers

October 30, 2010 Gene duplication is a  major source of genomic novelty for evolution to work on.  When genes duplicate, the extra copy of the gene is often redundant – it might degrade and become a pseudogene or take on a completely new function.  Alternatively, the function of the original gene might become partitioned between the two duplicates in a process known as subfunctionalization.  An excellent example of this has recently been reported in the genes that control male and female organ development in the flower, and it’s (almost) all down to a single amino acid change between the duplicate genes.

Development of male and female reproductive organs in flowers is controlled largely by a group of genes called MADS-box transcription factors. Different versions of these transcription factors (known as A, B or C function genes) are expressed in different parts of the developing flower, acting either alone or together to produce sepals, petals, stamens (male) or carpels (female)*.

Much of what we know about flower development comes from studies on two “model” plants – Arabidopsis (rockcress) and Antirrhinum (snapdragon).  In these species, and in many other flowering plants, the MADs-box C-function gene that controls the production of carpels vs stamens has duplicated. In Arabidopsis, one of the copies (called AG) makes both male and female organs, but the other copy has taken on the completely new function of making seed pods shatter (and is appropriately called SHATTERPROOF).  However, in Antirrhinum both copies still play a role in sex organ development: one copy (called FAR) makes only male parts, while the other copy (PLE) makes mainly female parts but also has a small role in making male parts.

Thus in Antirrhinum, the function of the original gene (making both male and female parts) has almost been split between the two duplicate copies.  In a study published online in PNAS last week, researchers at the University of Leeds, led by Professor Brendan Davies,  found a surprisingly simple difference in the two copies has led to their profoundly different roles. Read the rest of this entry »

Tuatara tuesday – how cold is too cold for a tuatara?

October 5, 2010 Tuatara like it cold.  Unusually so, for a reptile.  While reptiles in most other countries are happiest with temperatures over 25 degrees celcius, here in New Zealand our reptiles prefer much lower temperatures.  Alison Cree’s group at the University of Otago has been investigating exactly which temperatures tuatara prefer, with a view to determining whether new populations of tuatara could be established in the southern South Island.

Read the rest of this entry »

Chemical attraction? (re-post)

August 12, 2010

The chicken or egg blog family is on holiday in Germany during August, so I probably won’t have a chance to write any new posts.  To keep you all entertained, I’ll be re-posting some of my earlier (pre-Sciblogs) articles.  This one is the very first post I wrote for this blog, from March 2009.

Research published in last month’s Chemistry and Biodiversity journal heralded the discovery of a new compound “tuataric acid”. Yes, isolated from our very own tuatara.

Stefan Schulz and his colleagues at University of Braunschweig, and collaborator Paul Weldon at the Smithsonian Institution, have analysed the constituents of the cloacal secretions in tuatara and found an unexpectedly diverse array of compounds. As tuatara have no external sexual organs, the cloaca is the “one stop shop” opening at their posterior end, with prominent skin glands on either side of the opening that secrete a greasy white substance. When the tuatara secretions were analysed, Schulz and colleagues found over 150 different types of glyceride-based molecules, including one never-before seen compound, which they dubbed “tuataric acid”.
Read the rest of this entry »

Tuatara holds clues to human evolution

June 16, 2010

ResearchBlogging.orgA while ago I wrote about the value of genome sequences, not just for helping us understand the biology of a particular organism, but also for enabling large-scale comparisons across species that can help spot patterns in genome evolution which wouldn’t otherwise be apparent.  A recent paper in Journal of Heredity by Craig Lowe, David Haussler and colleagues at the University of California provides an excellent example of this in action, using sequences from the tuatara genome to identify the evolutionary origin of parts of the human genome.

Lowe and colleagues were looking for functional elements (like parts of genes and their regulatory regions) in the human genome that originated from retrotransposon insertions.  Retrotransposons are mobile bits of DNA that have a tendency to make copies of themselves and insert themselves in various different places in the genome.  They contain everything needed for this copying, plus often include functional modules like exons of genes, or transcription factor binding sites.  These functional modules may be co-opted for a new function in the new site, a process known as exaptation.  Once a retrotransposon is inserted in a new location it is often inactivated, and then begins to accumulate mutations which render it unrecognisable as a retrotransposon. This makes it difficult to identify exaptation events in any given genome and hence trace the origin of many of the functional elements of that genome.  However, by comparing the genomes of many different species in different lineages it may be possible to identify ancestral versions of these elements, and so trace their evolutionary history.

Lowe and colleagues found a previously unknown retrotransposon in the small part of the tuatara genome that has been sequenced.  This retrotransposon is of a type known as a LINE – Long Interpersed Nucleotide Element – and was named EDGR-LINE  (endangered-LINE).  A search of human genome against this sequence found 18 elements that are likely to be the result of insertion of this retrotransposon into the genome at some point in evolutionary time.  Seventeen of these elements are gene regulatory regions and one is an exon of a gene called ASXL3.  ASXL3 is important for regulation of other genes during development and the additional exon co-opted from EDGR-LINE appears to help control its expression.

These 18 exaptation events likely occurred early in mammalian evolution, but the retrotransposon itself has long since been inactivated in humans so all traces of it have been lost.  The functional elements it contained are able to be identified because they are under strong purifying selection (i.e. have not accumulated many mutations), so can still be aligned with the tuatara sequence.  Its only through this comparison that it is possible to know that these 18 elements originated from the same retrotransposon.

EDGR-LINE was also found in the lizard, frog, and coelecanth, but no traces of it remain in mammals, crocodylia and birds.  EDGR-LINE appears to be more slowly evolving in tuatara than in lizards, so is closest to the mammalian ancestral version of EDGR-LINE and hence more informative for identifying elements in the human genome. In fact, 10 of the 18 elements could only be identified by comparison with tuatara and not with these other species.

Evolution of the EDGR-LINE in vertebrates. The EDGR-LINE appears to have been introduced in the common ancestor of tetrapods and lobe-finned fish, and lineages where the LINE was active are shown with green. The LINE is not noticeable in mammals, crocodylia, aves, or testudines, so it has already been inactivated at least twice in evolution.

This is not the only example of genomic information from a rare species shedding light on the evolutionary history of human genome.  The genome of the threatened desert tortoise Gopherus agassizii also harbours an ancient LINE that has enabled functional elements of the human genome to be identified.  Lowe and colleagues speculate that this may be due to the very nature of endangered species, and ran simulations to show that theoretically, mobile elements like LINEs are active for longer and evolve more slowly in small populations.   This effect comes about because of the relationship between population size and selection – selection is more efficient in large populations so is more likely to remove genetic variants which are mildly harmful (or deleterious) to the organism, and to fix mutations which are beneficial.  The smaller the population, the more likely it is that deleterious genetic variants will become fixed in that population and beneficial mutations will be removed.  Insertion of mobile elements into new places in the genome is almost always deleterious, as it messes with existing genes and their regulatory regions.  Thus small populations will be more likely to accumulate additional copies of the mobile elements, and less likely to accumulate mutations which would remove or inactivate them.  I should point out here that tuatara are not actually classified as endangered (as the paper claims), but they have had a historically low population size, with probably a severe population bottleneck during the oligocene inundation of the New Zealand land mass.  In addition, we now know that even large tuatara populations can have a small effective population size, as few individuals actually contribute to mating at any one time.

Lowe and colleagues point out that without the tuatara, we would not have been able to identify these particular functional elements in the human genome, and that we never know what additional information about human evolution we might glean from threatened species in the future.  This underscores the importance of projects like the Genome10K initiative to sequence 10,000 vertebrate genomes.  Of course I would add that we should preserve these species for their intrinsic worth not just because of what they can tell us about human evolution, but this paper does highlight the unexpected ways that genomic data from diverse species can help us understand evolution.

Lowe, C., Bejerano, G., Salama, S., & Haussler, D. (2010). Endangered Species Hold Clues to Human Evolution Journal of Heredity DOI: 10.1093/jhered/esq016

Tasmanian devil facial tumour disease: too good a match for the immune system

April 13, 2010
A central premise in conservation genetics is that high genetic diversity is good for a species’ continued survival, and low genetic diversity is bad. This seems intuitively obvious (after all, we all know that you shouldn’t marry your cousin) but actually finding examples in nature where we can say for sure that low genetic diversity has contributed to a population’s demise is difficult.   

However, the recent decline of tasmanian devil populations due to disease provides an excellent example of the perils of low genetic diversity.  Wild devil populations in eastern Tasmania have been decimated in recent years by devil facial tumour disease (DFTD).  This nasty disease is a transmissible cancer spread by biting, and causes large tumours to form around the mouth, interferring with feeding and eventually causing death.  Kathy Belov’s group at the University of Sydney has been studying the genetic basis of DFTD susceptibility in devils and has found that a lack of variation in immune system genes is responsible for the spread of the cancer in some populations.     Read the rest of this entry »

How hard can a tuatara bite?

January 6, 2010

ResearchBlogging.orgAs a geneticist, I’m only rarely let out of the lab to chase after my study animal, the tuatara.  I count these occasions as a gift, where I get to feel like a “real” biologist and learn to talk knowledgably about the ecology and habits of tuatara (which, lets face it, are generally of more interest to the lay person than their genes).  I also count myself lucky that I’ve never been bitten by a tuatara – although I have helped extract other people’s fingers from the mouths of tuatara and can confirm that it is an eye-watering experience.

We now know exactly how hard a tuatara can bite, thanks to a recent study published in the Journal of the Royal Society of New ZealandMarc Jones (University College London) and Kristopher Lappin (California State Polytechnic University) have measured bite force in adult tuatara and found that a male tuatara could produce a bite force of up to 238 Newtons.  Jones and Lappin measured bite force using a custom-designed isometric force transducer.  They report that the tuatara needed little encouragement to bite onto the leather-covered bite plates, and that “once biting commenced the tuatara would maintain its grip with considerable reluctance to release”.  Something that will come as no surprise to those who have been on the receiving end of a tuatara bite! Read the rest of this entry »