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 »

Origins of the tree of life (re-post)

August 27, 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 post is from August 2009.

Darwin is usually credited with being the first person to describe relationships among species as a tree.  I’ll admit I always thought this was the case, until this week when some discussion on an evolution email list I subscribe to enlightened me.

Darwin used this tree figure in The Origin of Species to illustrate his idea of “descent with modification”, with the branches representing the diversity of species all interconnected back through time.

Darwin’s tree of life – the only figure in The Origin of Species.

However, some 50 years earlier, in fact in the year of Darwin’s birth 1809, Jean-Baptiste Lamarck used a tree of sorts to depict evolution in his book Philosophie Zoologique.  Lamarck is best known for wrongly believing that evolution happened by the inheritance of acquired characteristics, but he should be given credit for being the first scientist to develop a theory of evolution – unfortunately he just had the mechanism wrong.

But ideas about trees were around even before Lamarck’s time.  Perhaps the earliest description of a tree of life comes from Russian naturalist Peter Simon Pallas, in 1766:

But the system of organic bodies is best of all represented by an image of a tree which immediately from the root would lead forth out of the most simple plants and animals a double, variously contiguous animal and vegetable trunk; the first of which would proceed from mollusks to fishes, with a large side branch of insects sent out between these, hence to amphibians and at the farthest tip it would sustain the quadrupeds, but below the quadrupeds it would put forth birds as an equally large side branch.

The earliest published tree diagram likely comes from 1801, when French botanist Augustin Augier published his Arbre Botanique, a detailed tree diagram complete with leaves that depicted his view of the relationships between members of the plant kingdom.

Arbre Botanique

Of course the theory of evolution has advanced somewhat since Darwin’s time and we now know that the idea of a tree of life is a little too simplistic.  As explained in a recent article in New Scientist (which was published with the outrageously inflammatory cover “Darwin was wrong” that no doubt excited a few creationists), some species relationships, particularly of the earliest organisms, are better described by a network rather than a tree, which acknowledges that hybridisation and horizontal gene transfer play a big role in evolution.

If you want to read more on the history of the tree of life, have a look at this article by David Archibald from San Diego State University.

3D animation for teaching ecology and evolution

July 29, 2010

The Plant Ecology and Evolution group at the University of Vigo in Spain has been making 3D animation videos about their research, which are free to download for teaching purposes.

Here’s a sample of their work, showing how lizards disperse seeds

A full list of their videos is available on their website.

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 »

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

An interview with Rebecca Cann of Mitochondrial Eve fame

June 1, 2010

In 1987, Rebecca Cann, Mark Stoneking and the late Allan Wilson published a paper in Nature showing that all human females can trace their lineage back to a single maternal ancestor (“mitochondrial Eve“) located in Africa.  In Plos Genetics this week there is an interesting interview with Rebecca Cann, where she talks about her own history and the research behind the mitochondrial Eve hypothesis.

In unearthing the genetic history of human populations, the recent pace of discovery has been so rapid that we can lose sight of the impact made by a single paper. In a 1987 Nature article, Rebecca Cann and her co-workers, Mark Stoneking and the late Allan Wilson, painstakingly analyzed mitochondrial DNA purified from placentas that had been collected from women of many different ancestral origins. By comparing the mitochondrial DNA variants to each other, the authors produced a phylogenetic tree that showed how human mitochondria are all related to each other and, by implication, how all living females, through whom mitochondria are transmitted, are descended from a single maternal ancestor. Not only that, they localized the root of the tree in Africa. The report left a wake, still rippling today, that stimulated not just geneticists and paleo-anthropologists, but the layperson as well, especially as the ancestor was quickly dubbed “Mitochondrial Eve.”

For the full interview, see Gitschier J (2010) All About Mitochondrial Eve: An Interview with Rebecca Cann. PLoS Genet 6(5): e1000959. doi:10.1371/journal.pgen.1000959