Cheetah genetic diversity revisited

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.

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

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.

Update on 10,000 genomes and tasmanian devils

A while back I wrote about the Genome 10K project, an ambitious initiative from a consortium of mostly US-based researchers to sequence 10,000 vertebrate genomes.  Recently BGI (formerly known as the Beijing Genomics Institute)  embarked on a similar project, aiming to sequence 1000 plant and animal genomes to create a library of digital life, and in May they announced that they would sequence the first 100 vertebrate genomes for the Genome 10K project.   BGI have invested $100m into the digital library project, enabling them to fully fund some genome projects, and partially fund others.

The 100 species to be included in the Genome 10K project are being chosen on the basis of their biology, diversity, specimen availability, and the existence of a scientific community with expertise in the species.  And if your favourite genome is not on their current to-do list, don’t despair, as BGI are calling for proposals for other genomes to sequence.

Last week I went along to a seminar by representatives from BGI at Victoria University.  I was kind of blown away by their the sheer size and scale of their operation – they have a workforce of about 3000 people and billions of dollars in facilities all dedicated to pumping out and assembling DNA sequence, and really seem to be taking over the world when it comes to genomics.

But one genome that BGI hasn’t been sequencing is the tasmanian devil.  Its been a big month for tassie devil news:  first from the fight against devil facial tumour disease,  the news that Cedric, an animal with a putative “resistant” genotype, had died of the disease; and secondly the announcement that the tasmanian devil genome has been sequenced.  The genome was sequenced by the Wellcome Trust Sanger Institute in the UK.  They have  sequenced the genome of a healthy tasmanian devil plus two independent tumour samples, in the hope that they will be able to pinpoint mutations that will improve understanding of the disease and how it spreads.

Chemical attraction? (re-post)

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”.

Human handedness – inherited or developed?

This post is a little off the topic of what I normally write about, but its something I’ve been wondering about lately as the little munchkin grows up. She’s 6 months old now and is starting to use her hands a lot, going through that grabby stage where anything within arms length is grabbed and shoved in the mouth.  I’ve noticed that more often than not she’s using her left hand for this exploring.  It’s her left hand that grabs her left foot, and her left hand that grabs the spoon during my attempts to introduce her to the wonderful world of solid food.

Does this mean she’s going to be left-handed?  Coming from an extended family of determinedly right-handed people this comes as a bit of a surprise, and makes me wonder if there is an inherited component to handedness, or if there is some trigger during development that makes babies favour one hand over the other.

Beating the creationists at their own game?

The presence of “gaps” in the fossil record is one of the main arguments creationists use against evolution. The transition from Coelurosaurian dinosaurs to birds is one such purported gap that creationists like to harp on about.  Evolutionary biologists would argue that Archeopteryx fills this gap quite nicely, but this is disputed by creationists, who argue that Archaeopteryx is a true bird and not a transitional form.

A recent study by Phil Senter of Fayetteville State University in North Carolina, published in Journal of Evolutionary Biology, takes another look at the evolution of Coelurosauria but with a twist.  Senter takes on the creationists on their own terms, using a statistical method developed by creationists to visualise morphological gaps in the fossil record, to show that actually, there aren’t any morphological gaps in the fossil record between basal birds (including Archeopteryx) and a range of non-avian dinosaurs.  These findings will come as no great surprise to evolutionary biologists who have long accepted that birds evolved from dinosaurs and that Archaeopteryx has both bird-like and dinosaur-like features.   However, Senter’s rational for doing this study was that if you can demonstrate evolutionary relatedness between species under creationist’s criteria, then they will be obliged to accept the results.

So now you know…

This from Stuff.co.nz:

British scientists believe they have cracked the answer to the age-old question of which came first, the chicken or the egg?

Researchers have found that a protein called ovocleidin (OC-17) is crucial in the formulation of eggshells, and it is produced in the pregnant hen’s ovaries, the Daily Express reports.

Therefore, the answer to the conundrum must be that the chicken came first.

Using a high-tech computer to look at the molecular structure of a shell, the team of scientists from the Universities of Sheffield and Warwick found that OC-17 acts as a catalyst, kick-starting the conversion of calcium carbonate in the chicken’s body into calcite crystals.

They make up the hard shell that houses the yolk and its protective fluids while the chick develops.

“It had long been suspected that the egg came first but now we have the scientific proof that shows that in fact the chicken came first,” said Dr Colin Freeman, from Sheffield University.

“The protein had been identified before and it was linked to egg formation but by examining it closely we have been able to see how it controls the process.”

But the researchers have not yet got an answer to how the protein-producing chicken existed in the first place.

I may have more to say about this later…  I don’t quite see how this is “proof” that the chicken came first.

Update:  Here’s PZ Myer’s take on this.  In a nutshell:

You simply can’t make the conclusion the reporter was making here. The species ancestral to Gallus gallus laid eggs, the last common ancestor of all birds laid eggs, the reptiles that preceded the birds laid eggs…the appearance of egg laying was not coincident with the evolution of ovocleidin. The first chicken that acquired the protein we call ovocleidin now by mutation of a prior protein also hatched from an egg.

Tuatara holds clues to human evolution

A 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

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.    

The complicated genetics of human eye colour inheritance

I’ll be taking a break from blogging over the next month as the “egg” (or is that the chicken?) will be hatching.  As you do, when about to have a baby, I’ve been thinking a bit about inheritance lately – what colour eyes or hair will my baby have, how tall, who will he/she take after? The questions are endless really (and no we DONT know the sex!). 

Being a geneticist, I figured the answers to at least some of these questions must be relatively well worked out.  Eye colour for starters – we all know brown eyes are dominant to blue, right?  And if you google “eye colour inheritance” you can find any number of “eye colour calculators” that will work out the likely eye colour of your offspring.  I tried to use one of these and immediately ran into a problem – even the most sophisticated one I could find only allowed brown, blue or green as eye colours.  Well, my eyes are hazel (grey/green with a brown ring around the pupil).  Does this count as green? And my partners eyes are not exactly blue or green, they are kind of greyish-greenish-blueish with a tendency to change colour depending on his clothes and the light.  So having fallen at the first hurdle, I began to suspect that eye colour might be a whole lot more complicated than what you learn at school.