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 »

When is a gene really an allele?

May 18, 2010

The way some sections of the media use the word “gene” has become a bit of a pet peeve of mine.  Here’s an example from ScienceDaily:

Tibetans Developed Genes to Help Them Adapt to Life at High Elevations

Researchers have long wondered why the people of the Tibetan Highlands can live at elevations that cause some humans to become life-threateningly ill — and a new study answers that mystery, in part, by showing that through thousands of years of natural selection, those hardy inhabitants of south-central Asia evolved 10 unique oxygen-processing genes that help them live in higher climes.

Closer inspection of this research, which was published in Science last week, reveals that Tibetans don’t actually have 10 genes that are missing in the rest of humanity, what they have are different variants of the same genes.  These variants are called alleles, or haplotypes (there is a subtle difference between these two terms which I won’t go into here – but they both basically refer to different forms of the same gene or chromosomal region).  When geneticists refer to genetic variation in a species or population they are referring to the changes in the DNA sequence that results in multiple variant forms (alleles) of any given gene, the stuff that natural selection works on.

This study found that the Tibetan population have DNA changes in 10 genes that appear to be the result of natural selection.  Two of these genes, EGLN1 and PPARA have haplotypes that are significantly associated with the “decreased hemoglobin phenotype”, which is thought to be an adaptation to high altitude living.  These haplotypes appear to be selected for in the Tibetan population.  We all have EGLN1 and PPARA, but the Tibetan populations have unique haplotypes of these genes that help them live in higher climes.

This sort of incorrect usage of the word gene is pervasive in the popular media.  The phrase “the gene for” seems to be everywhere – the gene for breast cancer, the gene for schizophrenia, the gene for diabetes etc etc.  This gives the wrong impression of what these studies actually show, and is just plain incorrect.  What is actually being referred to in these studies is an allele or haplotype of a gene that we all have, and usually it is an allele that is correlated with a slightly higher incidence of the disease, not necessarily one that causes the disease.  Perhaps its time for for biologists to be more clear about what they mean by the word “gene”, and for journalists to incorporate the word “allele” or even just “genetic variant” into their vernacular.

If you want to read more about the Tibetans, the original paper is here, and an excellent summary of it by Razib Khan at Discover Magazine is here.

Mammoth hemoglobin back from the dead

May 5, 2010

While we’re on the subject of extinct species, Prof Kevin Campbell and colleagues in Canada and Australia have reported resurrecting mammoth hemoglobin in a paper out this week in Nature Genetics.  This won’t help at all with cloning a mammoth, but provides a fascinating insight into mammoth physiology and evolution.

Hemoglobin is the protein which transports oxygen in the blood.  It is made up of two subunits, alpha and beta globin, which are coded for by two different genes.  Campbell and colleagues used fairly basic molecular biology techniques to isolate these genes from mammoth remains and express the protein in bacterial cells.  Firstly, they amplified both elephant and mammoth hemoglobin genes using PCR and compared their sequences, finding that mammoth beta-globin protein differs from the elephant protein at three amino acid sites.

Read the rest of this entry »

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 »

The complicated genetics of human eye colour inheritance

February 1, 2010

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. 

Read the rest of this entry »

So what is a gene, exactly?

December 13, 2009

Ever wondered just what a “gene” is, exactly? Well turns out that even geneticists are wondering the same thing these days, as they learn more about the genome and find that the concept of what comprises a gene is becoming more and more vague.

This months BioScience journal has an interesting (open-access) article on how the definition of a gene is changing. 

With the discovery that nearly all of the genome is transcribed, the definition of a “gene” needs another revision.

The article describes how the old definitions based around protein function (genes are units of DNA that code for proteins) have had to be expanded with the discovery that a large portion of the genome is transcribed into RNAs that don’t go on to make proteins, but have an important functional role themselves.

Citation:  Hopkins, K (2009). The Evolving Definition of a Gene. BioScience 59(11):928-931. doi: 10.1525/bio.2009.59.11.3