Marine ecosystems worldwide are suffering from a loss of biodiversity due to destruction of food chains and habitats. In particular, the effects of commercial fishing on sensitive ecosystems and species has had disastrous effects on marine life in recent years. One way to mitigate for these effects is to create areas which are set aside to protect vulnerable environments and species, or to provide a safe pocket from which fish and larvae can re-seed away from over-exploited seas. These areas are called Marine Protected Areas (MPAs), and play a significant part in global marine conservation strategies, although their effectiveness if often disputed.
MPAs have been shown to be effective in increasing density and biomass of fish, as well as …
February was an unexpectedly busy month for science. A mangy skeleton lying unceremoniously under a concrete parking lot was shown by forensic science to be no lesser a historical figure than the last Plantagenet King of England. To trump Richard III, a once-in-a-century meteor strike in Russia startled stargazers distracted by an asteroid flyby, in a coincidence that I have yet to see a p-value for. But in the genomics world, even stray royals and exploding space rocks cannot compete with the excitement of Florida's annual AGBT conference. In the words of Genome Biology's Editor Clare Garvey: "Rothberg describes a 'future-proof' machine. It's gotta be #agbt13". Yes, machines and the future, that pretty much …
On the list of humanity’s priorities, tissue regeneration finds itself near the very top; together with eternal youth and immortality. And, in legends and myths, both heroes and villains – but most commonly monsters – possess an amazing ability to grow back lost organs and limbs.
Myths can have a grain of truth, though. In 2011, Genome Biology published an article describing the transcriptome of the regenerating head of a planarian flatworm, Schmidtea mediterranea. In early 2012, we published another article seeking to unveil the intricacies of regulatory mechanisms governing flatworm regeneration.
Fortunately, we don’t have to look that far down the evolutionary line to find species capable of tissue regeneration. Much more complex organisms can be found as …
One of the most fascinating leaps in evolution is the transition from unicellular to multicellular organisms. How individual free living cells joined forces to create more complex multicellular organisms is still not well understood. For metazoans, this transition is thought to have occurred through a colonial intermediate that was composed of cells similar to choanoflagellates. In an article published today in Genome Biology, Fairclough et al. use choanoflagellates to gain insight into this evolutionary transition.
Choanoflagellates are free-living unicellular organisms and are the closest living relatives of metazoans. The similarity between these organisms and the proposed ancestor of metazoans has made them attractive to scientists interested in studying this evolutionary shift. Indeed, a previous study of the genome …
Twenty-five years ago today, on the 12th February 1988, a landmark article was published in Science describing a phylogenetic tree of the metazoans, derived from molecular data. The article, by Katherine Field and colleagues (widely referred to as ‘Field et al.’), represented the first use of small subunit ribosomal RNA to establish the metazoan phylogeny. To mark the anniversary of its publication, and coincidentally Darwin’s 204th birthday, a new commentary is published today in EvoDevo evaluating the impacts of this article.
In this commentary, Max Telford (UCL) critically assesses the techniques and methods used by Field et al., and reconstitutes their dataset, to establish a metazoan phylogeny roughly in line with that accepted today. Despite …
During 2013, Plant Methods welcomes submissions to a special thematic series on Next Generation Sequencing (NGS) technologies. The idea for the series arose out of the recent joint GARNet-Genetics Society meeting on “New Technologies to Advance Plant Research” held in November 2012 at Liverpool University.
Speakers at the meeting who will be contributing papers include Klaus Mayer (MIPS), Tom Hardcastle (University of Cambridge), Arthur Korte (Gregor Mendel Institute), Neil Hall (University of Liverpool) and Gordon Simpson (University of Dundee).
The thematic series will cover all aspects of the application of new sequencing technologies to plant research. Potential topics include, but are not limited to, the application of NGS for:
Genome-wide association studies
Fine-mapping of complex loci
De novo and …
As a result of human industrial activities, atmospheric carbon is increasing. This increase has significantly contributed to the climate change that we are experiencing in the world today, and the increasingly worrying predicted changes in climate in the near future. Much scientific research and effort is therefore currently being put into mitigating for these changes in order to ensure environmental stability.
Deforestation has widely been discussed as a major contributor to increasing atmospheric CO2 and subsequently climate change. Most of this discussion revolves around the ability of forests to act as a ‘carbon sink’- storing carbon as vegetative biomass and preventing it from entering the atmosphere. However, the capability of forests to affect their environment is …
Community based conservation (CBC) initiatives seek to unite the aims and purposes of projects working towards economic and ecological goals. They generally aim to promote socio-economic growth through the sustainable use of natural resources which are also of important conservation value. In this way, natural resources can be protected from overuse by an increased community level understanding of the use of resources and their conservation benefits.
CBC often faces harsh criticism on both sides, and its effectiveness has been disputed widely. It is therefore important to evaluate how effective these initiatives are in practice, and to identify how different features in an initiative affect the success both in conservation and economic terms. A new article published in …
So you have just spent the last couple of years on the project: using shiny brandnew machines to sequence the most complex genomes on Earth. You dotted your ‘i’s, crossed the ‘t’s, identified all ‘g’s and ‘c’s. From the (still growing) range of the available assemblers, you picked the one you thought best. And you ended up with the assembly that might be perfect, but might just as well be a disaster waiting to happen.
Both genome assemblies and assemblers can be assessed using a number of different quality metrics. For a long time, N50 was a leading metric used for that purpose but, although N50 scaffold and contig lengths most of the time correlate with assembly quality, the measure …
In 2011 Arumugam et al. described for the first time characteristic patterns of human gut microflora composition, which were seemingly preserved world-wide, across different nations and cultures. These patterns, named enterotypes, were defined by the significantly higher abundance of one of three bacterial genera: Bacteroides (enterotype 1), Prevotella (enterotype 2) and Ruminococcus (enterotype 3).
This simple concept of enterotypes has since divided the microbiome field. Some researchers found themselves influenced by the alluring idea of discrete microflora types, while others dismissed it out of hand as overly simplistic and as blurring what they view as a more accurate, continuous image of our gut flora. It seems, however, that at this stage it is simply a bit too early to …