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 »

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 »

Update on 10,000 genomes and tasmanian devils

September 27, 2010

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)

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 »

Human handedness – inherited or developed?

August 3, 2010

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. Read the rest of this entry »

Beating the creationists at their own game?

July 21, 2010 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.

Read the rest of this entry »

So now you know…

July 15, 2010

This from

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.