Wednesday, February 22, 2012

Phylogenetic Tree Challenge in Encyclopedia Of Life

 The Encyclopedia of Life initiative aims at providing an open, digital resource providing comprehensive information about the diversity of life. It has recently opened a call for teams that can provide a phylogeny-aware organization of as many scientific names as possible. This text is from the call:

A prize is offered to the individual or team that can provide a very large, phylogenetically-organized set(s) of scientific names suitable for ingestion into the Encyclopedia of Life as an alternate browsing hierarchy.  

[...]


Among other factors, the total number of uniquely named nodes, node/leaf ratios and tree height may be used to compare entries so contestants should consider how they wish to trade off strict consensus versus other methods of reflecting the state of phylogenetic knowledge.
Problems to solve include 1) how to assign labels to unnamed nodes, 2) how to fill in gaps so that the set of taxa included is as comprehensive as possible, even if trees are not fully resolved or all taxa have not been analyzed, 3) how to handle competing hypotheses, 4) how to update the hierarchy at least annually.  
The winning submission must be available to EOL and others under an acceptable CC license if it is under copyright.  The tree need not be previously published in peer-reviewed form.
 
 and more information is available here.

  

Wednesday, February 8, 2012

Getting more complex and gaining.... nothing

 The origin of complexity is a highly debated issue in biology. For instance, many functions in the cell are carried out by intricate macro-molecular complexes formed of a multitude of subunits. When tracing the evolution of such complexes, as we did with mitochondrial Complex I, one often finds that the number of subunits have increased through time. However, the addition of subunits not always seems to correlate with the acquisition of novel functions, which would provide a selective advantage for the increase in complexity.  Can we think of a mechanism promoting a trend for increasing complexity in the absence of a selective advantage provided by a novel function?.

 A recent paper by Finnigan and colleagues show a plausible mechanism and present evidence that this may have been responsible for the acquisition of a novel subunit in fungal vacuolar ATPases (depicted below).

 This molecular machines that pump protons across membranes have a membrane ring (in green in the figure) formed by 6 units. In vertebrates two different subunits (originated from the duplication of an ancestral gene) form the 6-units ring in a 1:5, stoichiometry. In fungi a more recent duplication brought about one more subunit type so that the ring is formed by the products of three different genes in a 1:1:4 organization. Using ancestral sequence resurrection (I love that name!), a technique that consists of reconstructing most likely ancestral sequences and then synthesizing them in the lab, they show that a single mutation acquired early in each paralogue, was sufficient for making the two of them indispensable. Thus, such model could explain a trend to increase complexity in multi-paralogue complexes (those comprised by some subunits derived from duplicated genes) without a requirement for an initial selective advantage.  

 In a way, I see this model as a special type of sub-functionalization. That is, the two new paralogues would in sum make the same function that was performed by the ancestral gene. In the absence of more examples we do not know how widespread is this mechanism, but the fact that it does require few likely events and that it actually constitutes a "ratchet" (as noted by W Ford Doolittle), that is once you gain that complexity you don't go back, one would expect to have occurred in several of many multi-paralogue complexes, at least in some lineages. 

 Perhaps this could explain an intersting finding we did some years ago when looking at the evolution of the mitochondrial electron transport chain in fungi (mostly formed by multi-protein complexes): the amount of duplications in members of this complexes was of the same level as other proteins. This is in contrast to the gene-dosage effect hypothesis that states that complexes would tend to duplicate only when the stochiometry is conserved (that is in when the whole complex duplicates, e.g in whole genome duplications). 

 Finally, another remark that I always do when seeing ancestral sequence resurrection working is that the fact that ancestral reconstructions display the expected biochemical activities (e.g by complementing extant sequences) is an indication that the models of evolution we use are not that wrong after all.







 

Sunday, January 29, 2012

Interview with Nick Lane

As I reported in an earlier post, I had the opportunity to meet Nick Lane during the Spanish Evolutionary Society meeting. We had a very interesting discussion over a couple of beers around mitochondrial endosymbiosis and the origin of eukaryotes. Some days after the meeiing, Andrés Moya, the President of the society, suggested to me to interview him for the Society's  Bulletin eVolución.  You can find this interview translated to Spanish in the current issue of eVolution 7(1), however I think the interview might be of interest for a broader audience and thus I paste here the original, English version. 


TG- After your recent visit to Spain as an invited speaker to the III SESBE congress (Madrid, November 2011), what is your opinion about the field of Evolutionary Biology in Spain?
 
NL- Well, I thoroughly enjoyed the few talks I attended, but my Spanish is poor and I could hardly judge many of them; and unfortunately I missed much of the conference. But I liked the great range of themes that were being discussed. And in general I am impressed with a lot of evolutionary research going on in Spain. There is a tendency to consider comparative physiology in evolution more than there is in England, for example, and I find that a very insightful approach. One thing that has struck me over the years is that Spanish researchers are not cited as frequently as they ought to be. This does not reflect the quality of the research, but rather the US-dominated English-language citation bias.

TG- Your career has been quite unconventional. Can you summarize for our readers which have been the major steps in your career path?
 
NL- It sure has! I had a medical research background, and my PhD was on mitochondrial function and oxygen free radicals in transplanted organs. But I was getting nowhere with that, and couldn’t see a way of getting from there into what was really an interest for me: evolutionary biology. So I took to writing instead, for several independent agencies doing medical education for pharmaceutical companies. That was an eye opener, and I learnt to write clearly and quickly, but it was also a frustration. After quite a lot of hard work I finally got a contract to write Oxygen, which was initially conceived as a book about free radicals, mitochondria and medicine, but ended up reflecting my interests in evolutionary biology to a much greater extent. That was the beginning of a decade spent writing books on evolutionary biochemistry, drawing heavily on my background in bioenergetics but ranging widely over any material that interested me. It was fantastic fun but no way to make a living. And ultimately frustrating too, in that in writing on that scope, you can’t help but come up with new ideas, essentially a broad synthesis with gaps, that you sketch in with speculations, which can be reframed as testable hypotheses. That’s what drew me back into research – the frustrated desire to test some of these hypotheses.

3) Thus, you have been active as a science writer, a researcher, and now you seem to combine both aspects. Do these two tasks reinforce or rather interfere with each other?
 
Both. I think I’ve benefited tremendously as a researcher from the decade I spent thinking and writing. I now have a coherent set of hypotheses that are testable in one way or another – experimentally or by some kind of mathematical modeling, or just by empirical analysis of existing data. So I’m drawing heavily on this ‘credit’ now. At the same time it is hard to think synthetically or to write books while in research, there are so many demands on time. So on a daily basis, writing and research interfere with each other, but I think if you are able to focus on one or the other for periods then they can, and should, reinforce each other. The trick is to balance each so that they reinforce each other over time. I’m not sure I’ve mastered that trick yet, but it is my long term goal: for me, it is the best way to understand the most interesting evolutionary questions, and that is what I want to do.

4) In your view, where lies the main responsibility of communicating science to the general society (e.g scientists, funding agencies, scientific societies etc, science journalists)?
 
Good question. There is certainly a responsibility, but being responsible counts for nothing if nobody listens to what you have to say: as a writer, you must be interesting to be noticed at all. And society is rarely interested in responsible but boring views. So there is a balance that you have to wrestle with every sentence, between interest and accuracy. That’s another reason I’m happy to be back in research: to write accurately (in precise scientific language) is at least as much pleasure for me as to write interestingly. Frankly it is the questions themselves that interest me. I think that the real challenge in writing for the public is to find ways of phrasing questions in an interesting way, which draws attention to the problem, without sacrificing the accuracy. That is the ideal: responsible (boring) and interesting at the same time.

With respect to which group has the responsability, I don't think that one group alone can be considered responsible communicating science to general society. Each group can address different needs, and each has its own responsibility. Scientists are responsible for sculpting new ideas, for conveying the excitement and intellectual thrust of science. The best ideas in science are still driven by individuals with passion, insight and ingenuity, and there is nobody better to convey this intensity to the general reader, although it is rare. Journalists are responsible for balanced reporting, explaining ideas clearly and intelligibly, providing context for the reader, ideally some commentary from other scientists. It is unusual for journalists to drive the scientific agenda, but serious journalists have a broader perspective and can sometimes see things that scientists can't.

Scientific societies can provide very helpful consensus statements on difficult issues, from global warming to the effectiveness of chemotherapy. It's not really for them to give a sense of the cut and thrust of science, more the strength of the conclusions that emerge from the uncertainty.

Finally, funding agencies. In my view, funding agencies have a duty to explain to the public and to politicians that research is open-ended and unpredictable. Research that appears to have little immediate societal impact can have immense and unimagined benefits in the future. Most major scientific breakthroughs, with the greatest economic benefits, came from unexpected quarters, and could not have been anticipated by either the scientists themselves or the funders. This perspective is being lost in a political drive to justify spending by societal impact. As with so much, short-term political cycles are trumping long term good sense. It is up to funding agencies to explain why research should be funded on its own merits, without constant recourse to some hoped-for and probably illusory impact.      

 TG- In one of you articles, to commemorate the 150 anniversary of “The Origin of species”, you discuss about what Darwin would love to know about the origin of the eye if he were still alive. Darwin is granted for being the first who used a “tree of life” to describe the evolutionary relationships of species and their shared ancestry. What do you think he would love to now in this respect if he were still alive?
 
NL- Well I think he’d love what’s going on in microbial genomics. The picture that has emerged over the last couple of decades of lateral gene transfer and endosymbiosis in microbes is radically different to the idea of gene sequence divergence between populations. Having said that, I see all this as a juxtaposition to standard Neodarwinian population genetics. He would have loved that too, although it is old hat to us now; but given that Darwin knew nothing about genes, he would have been thrilled by the Neodarwinian synthesis, and what amounted to a genetic basis for a tree of life. All of this means that variation is more complex than any of us imagined; and in this sense, Darwin’s coyness on the mechanisms of variation was well placed: it really is wild and fascinating.

  TG- In one of your last books, you mention 10 major transitions in the evolution of life on earth. Which one of them is, according to you, the most enigmatic or difficult to explain?
 
NL- Consciousness, without a doubt. Frequently the origin of life and consciousness are put forward as the twin pinnacles, the two big unanswered questions in biology. I think we’re actually quite close to understanding the origin of life in conceptual terms, but I personally can’t understand consciousness well at all. I read a lot on the subject and came to the conclusion that nobody really does. We still can’t answer the simple question: how does the depolarization of a neuron give rise to a feeling or sensation of anything at all? They are two different languages, and we don’t seem to have any kind of Rosetta stone at the moment.

  TG- Some of these transitions seem to have happened only once in the history of life. If they were so advantageous why they have been restricted to a single lineage?
 
NL- I think each transition has to be taken on its own terms. These are tremendously difficult questions and you will find diametrically opposed answers to each question from very insightful researchers. The answers reflect temperament more than anything else. Christian de Duve actually wrote a book called ‘Singularities’, and my reading of that is that there isn’t a single answer that would apply to the origin of life, the origin of photosynthesis, the origin of the eukaryotic cell, the origin of animals, and the origin of consciousness. Obviously for some reason, each was improbable or it would have happened more than once (like eyes), but the reasons for improbability differ and are very dependent on context. In the case of eukaryotes, I would say their unique origin was based on an improbable endosymbiosis between prokaryotes, followed by a problematic reconciliation of selfish interests between two entities that had to live in intimate union. There were no advantages at all until they had come out of that tight bottleneck; on the contrary, all the advantages were with the bacteria that just kept on doing their bacterial thing. From that point of view, the difficult question is why did it happen at all?

  TG- Some of your research interests concern very ancient events (e.g. the origin of eukaryotes, of life itself). This is a field in which different hypotheses are difficult to prove right or wrong given the difficulty of direct experimentation. What are the criteria used by scientists in your area to reach a consensus over which is the support for the different  scenarios?
 
NL- There is a consensus on quite a lot: cell structure, behavior (phagocytosis or sex) genome sequences (albeit with disputes over methodology), the existence of introns in certain positions and so on. Where consensus breaks down is when different methods give different answers. That happens all the time. I’m actually focusing a lot of my attention now on the origin of life itself, because this seems to me to be more experimentally tractable: we can ask specific experimental questions that involve chemistry and thermodynamics, which are much more reliable than biology and genes, so although the event was the most ancient of all, it is not necessarily the most inaccessible. I think we’re making progress on many questions, but in the case of the origin of eukaryotes a lot of the evidence is oblique and disputable. The reasoning is often equivalent to historical reconstruction in that you need to weigh the evidence: there’s no doubt that it happened, and there’s plenty of evidence, it’s just that some of it is unreliable and some is irrelevant, so there’s plenty of scope for argument still.

  TG- In this respect. What is the impact on your field of the ever-growing number of genome sequencing projects?. What are the species or environments you would like to be sampled in order to help answering important questions in the origin and evolution of complex life.
 
NL- Genome sequences have made a tremendous difference, the only trouble being that they tend to reflect pathogens or industrially interesting bugs, rather than those most relevant to, say, the origin of eukaryotes. I would love to see more genomes from anoxic or anaerobic deep ocean environments, or the deep hot biosphere. I’m especially interested in two questions: the variation in eukaryotic genomes, and the variation in mitochondrial genomes. There is a brilliant and bold hypothesis that the origin of the eukaryotic cell was an endosymbiosis between two prokaryotes, an archaeon host cell and an alpha-proteobacterium (or somesuch). The prediction is that all eukaryotes should have mitochondria or organelles derived from them like hydrogenosomes or mitosomes; and that in terms of mitochondrial genomes we should find more overlap between bacterial metabolic capacity and metabolically versatile mitochondria. This is a wonderful prediction because it is so easy to falsify, and yet all the genome sequencing so far has failed to disprove it. The places most likely to disprove – or prove – it are precisely those anaerobic environments that have been undersampled so far.

TG- Carbon has always been considered a hallmark of life on earth, but life (elsewhere) based on other molecules (e.g Silicium) has been speculated. You seem to favor the idea that oxygen was the molecule that enabled the appearance of complex life on earth, could you speculate on the theoretical possibility of other molecules playing a similar role in other forms of life.
 
NL- I think it is most likely that life elsewhere would be constrained by much the same issues that constrain life here. I doubt very much that there will be silicon based life forms. There are two important properties of carbon: it is much better than silicon at organic chemistry; but equally important, it is available in the form of a gaseous oxide, a Lego brick if you will. There are no gaseous silicon oxides, only sand, which is vast and unwieldy in comparison. You can’t build a house on sand and you can’t build an organism from sand. My feeling is that not only is carbon especially useful, it is also more abundant than silicon. Likewise, water is more abundant than methane and a much better solvent (you can’t dissolve carbon chains of more than about 5 carbon atoms in methane). And so on. On the basis of usefulness and abundance, I would argue that life would mostly be carbon based. I would go further to argue that it is likely to require proton gradients over membranes for thermodynamic reasons. When I say that oxygen is necessary for complex life, I mean large active animals. I doubt that anything else could do the job: nothing else could accumulate to the appropriate level in an atmosphere and at the same time be sufficiently reactive to provide the power needed. So I’d say that in terms of their broad biochemistry, alien life won’t be all that different. In terms of morphology or the specifics of their biochemistry, they could be very different, of course.

  TG- Are you already working on your next book?, can you advance something on what is it about?
 
NL- I’m not writing yet, but I do have a contract… and it will be about everything I have talked about here. The origin of complex life, and why it was a unique event here on Earth.

Tuesday, January 24, 2012

RECOMB 2012 (Barcelona): one week left for early registration

 As I reported in an earlier post, RECOMB 2012 will be held in Barcelona and CRG's Bioinformatics and Genomics program is part of the local organizing committee.
 This post is a reminder that the deadline for early registration with a reduced rate is approaching and will expire 31st of January. More information here.

 See you there!

Friday, January 13, 2012

SMBE 2012 early registration deadline and symposium on orthology

 For those who don't know, the deadline for abstract to the next Society for Molecular Biology and Evolution meeting (Dublin 23-26 June) is approaching. I am co-organizing a workshop on orthology/paralogy and function in collaboration with Marc Robinson-Rechavi, Matthew Hahn, and Iddo Friedberg. Find below an invitation to submit to SMBE2012 and more info on this workshop.

 Hope we can meet in Dublin. 




Dear colleague,

We invite you to submit an abstract to the symposium "The complex relationship between orthology, paralogy, and function" to take place at the meeting of the Society for Molecular Biology and Evolution in Dublin (23rd-26th June, 2012).

The deadline to submit an abstract is the 27th of January 2012, for more details please visit:

http://www.smbe2012.org/scientific-content/call-for-abstracts.html


Symposium "The complex relationship between orthology, paralogy, and function"

Orthology and paralogy have been central concepts in molecular evolution since the distinction was first proposed by Fitch in 1970. A long standing interpretation of this distinction has been that orthologs would be more similar in function than paralogs. Until recently, this interpretation was rarely tested, and in fact rarely explicitly articulated in a testable manner. Yet it has been widely used, from undergraduate teaching, to the practical application of orthology searches for genome annotation. There has been a recent increase of research, seeking to define and test this "ortholog conjecture". Notably, a recent paper (Nehrt et al. 2011, PloS Comput. Biol.) has reported a higher functional similarity of paralogs than of orthologs. This paper has generated much attention and debate, while at the same time recent work on orthologs has shown the vitality and importance of this field to a broad range of applications and questions. Our symposium will feature speakers addressing the fundamental relationships between molecular evolution and biological function, focusing especially on the role of orthology and paralogy in modulating such relationships.

Confirmed speakers: Eugene V. Koonin, Jianzhi Zhang

If you have any question regarding this symposium please do not hesitate to contact us:

Toni Gabaldon , Matthew Hahn , Iddo Friedberg, Marc Robinson-Rechavi

Tuesday, January 10, 2012

Diversity arises whenever, wherever, and at whatever rate is advantageous

 This is the conclusion from a recent paper from the group of Mark Pagel, in which they analyzed a dataset of body sizes of 3,185 extant mammals in a phylogenetic context.

  They modeled the evolution of body sizes across the  phylogeny using a Bayesian approach that allows evolutionary rates to vary at every branch. 

This provided them with an idea of where burst of evolution (big shifts in sizes) had occurred. The main idea was to contrast a long-held hypothesis that the early radiation of mammals was accompanied by increased rates of body-size variation (i.e burst in species diversity coincided with burst in body-size). This was explained by the idea that mammals expanded into a largely-unoccupied niche which provided opportunities for diversification. When the niche was filled up, diversification and evolutionary rates decreased. 

  Results from this team are in stark contrast with such view, since they see bursts at many different places of the phylogeny, which are uncoupled with the early radiation of mammals. 

 Reading this paper was very useful to me since, I was by then preparing the evaluation of a PhD thesis by Victor soria-Carrasco (see some related paper here) on, precisely mammalian, diversification. In the thesis they found that most mammalian orders showed a decline in the rate of diversification (in terms of forming of new species), which may seem compatible with the idea of a niche being filled-up. This highlights the importance of properly delimiting what evolutionary rates we refer to (sequence variation, variation in some morphological character, speciation rate...), since we may reach apparently different conclusions. Complicating the issue further, one does not know whether niche limitation may select for or against diversification. 
 In any case it is comforting to see that the increasing amount of genetic, phylogenetic, and other type of data, as well as sophisticated models, enable us to explore such interesting issues at the edge between evolution, phylogenetics and ecology. I was really impressed by the works mentioned. 

Saturday, December 10, 2011

Sequencing species.... by the thousands

 When I was giving my first steps in the field of comparative genomics, there was not much to think about when deciding which genomic datasets to use: one would just take them all. With only a few dozens of genomes, mostly of bacteria, one could have everything at hand, in the local disk, just need to update every couple of months by adding one or two more...

 These times have definitely passed, and now the flow of newly sequenced genomes is... well, overwhelming (see figure below, taken from Genomes Online). This is both a blessing and a curse for us doing comparative genomics, since we have an unprecedented amount of data which enables more resolution, but we are increasingly facing novel technical and analyitical challenges.


 Just to give a taste of this avalanche of genomes from different species (projects for sequencing genomes for a given species, such as the 1000 genomes is another story) that is coming, I here list some of the projects I am aware of that aim at sequencing thousands of genomes from a given taxonomic group.

As expected, in this kind of projects it is way more easy to come up with a bold number, than to actually define the list of species that are actually going to be sequenced. At least this is what I can tell from my involvement in the i5K initiative, in which prioritisation of species to be sequenced is not simple, since usually one wants to weigh in different criteria (phylogenetic relevance, biological, economical, and clinical importance, etc).   

 I'm sure I missed some, and, in addition, there is a growing flow of genomes that are sequenced by independent groups, including my modest own group. One common weakness of this large, and small-scale initiatives is that they sometimes come with the cost for covering the genome sequencing but do not account for the necessary bioinformatics analyses to actually make sense of the data. With the sequencing costs dropping and the potential analyses becoming more complex, the actual costs of sequencing projects will more and more be on the side of the analysis beyond the assembly and annotation phases. As a result, many bioinformatics groups are streching their resources to contribute to genomics projects without getting any specific funding.

In my opinion the planning of a sequencing project should account for all the downstream phases with their associated costs. With such an approach we may end up having a handful of genomes less, but we will definitely learn more from them.