Friday, February 25, 2011
For next week's lab-meeting, we'll become more philosophical and historical, and discuss a book chapter about the history of the Adaptive Landscape metaphor in evolutionary biology. This chapter will be one of approximately 20 chapters in a forthcoming volume at Oxford University Press that I am currently editing together with my colleague Ryan Calsbeek (Dartmouth College, New Hampshire, USA).
This volume is intended to become published in 2012, which marks the 80-year celebration of population geneticist Sewall Wright's famous paper in 1932 where the concept of the Adaptive Landscape was first explicitly presented. Both Ryan and I are looking forward to input on this chapter, and in case you have not received a copy prior to our lab-meeting and wish to participate, send me an e-mail (email@example.com). Time and location for lab-meeting as usual: "Darwin" at 13.30-15.00 on March 2, 2011. Fika volunteers are most welcome!
Monday, February 21, 2011
The topic of this week's announced lab-meeting has been changed, since the manuscripts that were announced were apparently not ready. Instead, we'll discuss two papers that deal with the evolution of premating isolation and species concepts, respectively. Both are published in Evolution, and they can be downloade here and here.
Time and place as usual: "Darwin" at 13.30-15.00 (Wednesday February 23 2011). Tina will bring fika.
Below are the paper titles, the authors and the Abstracts:
Richard M. Merrill, Zachariah Gompert, Lauren M. Dembeck, Marcus R. Kronforst, W. Owen McMillan & Chris D. JigginsPremating behavioral isolation is increasingly recognized as an important part of ecological speciation, where divergent natural selection causes the evolution of reproductive barriers. A number of studies have now demonstrated that traits under divergent natural selection also affect mate preferences. However, studies of single species pairs only capture a snapshot of the speciation process, making it difficult to assess the role of mate preferences throughout the entire process. Heliconius butterflies are well known for their brightly colored mimetic warning patterns, and previous studies have shown that these patterns are also used as mate recognition cues. Here, we present mate preference data for four pairs of sister taxa, representing different stages of divergence, which together allow us to compare diverging mate preferences across the continuum of Heliconius speciation. Using a novel Bayesian approach, our results support a model of ecological speciation in which strong premating isolation arises early, but continues to increase throughout the continuum from polymorphic populations through to “good,” sympatric ecologically divergent species.
New insights in the speciation process and the nature of “species” that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals.
Sunday, February 20, 2011
Any fika volunteer?
Wednesday, February 16, 2011
These days there is a lot of buzz about so-called "Next-generation sequencing" techniques, i. e. the novel molecular methods that allows ecologists and evoutionary biologists to rapidly sequence the entire genomes of their favourite organisms. A lot is promised by enthusiastic proponents, and it is understandable and easy to get carried away and to think that all interesting problems will be solved in the near future. As usual, when it comes to new techniques and fashionable scentific "bandwagons, it is healthy with some sound scepticism and critical attitude. I found an excellent such criticial perspective on the interesting and thoughtful blog "The Molecular Ecologist", which is worth reading. Here are som excerpts, but you should read it in full:
“Developing genomics tools for ecological organisms is desirable because we can study a wider range of phenotypic traits over evolutionary timescales and in more populations than was possible previously. Through this we are likely to gain a more realistic and comparative understanding of how selection works on natural levels of genetic variation, where this genetic variation comes from and how it is maintained.” Stapley et al. 2010 (TREE)
Okay let’s just get this out of the way. We’re way past calling next generation sequencing technologies, “Next Gen.” I mean, really isn’t Next Gen, yesterday’s news? With the advent of the third generation sequencing technologies that can sequence a single-molecule of DNA, we’re out of date in our terms.
The blogger criticizes the often made rather arrogant arguments that next-generation sequencing will solve many of the "mysteries" about the genetics of adaptation that was not possible to study before, while in reality, many workers in the classical model systems knew a lot since before:
In this article, Stapley et al. (2010), suggest that ecologists tend to have a good idea of what traits might be involved in adaptation for their study organism. They also suggest that geneticists know a lot about the genomic architecture of a few classical model organisms but very little about the ecological relevance. This argument is a little bit of a strawman, because it sets up a false opposition between ecology and genetics. In their eyes, the importance of this technology is that it will make it easier to integrate both ecological and genomic data and to develop for ecologically interesting organisms “a range of genomic resources such as whole genome sequences, transcriptome sequences, and genome-wide marker panels can be generated within the scope of a three-year grant.”
When I first read this statement, I thought that the authors had found a practical way to explain the rate at which genomic data can be generated. But then I realized how uncomfortable the phrase, “can be generated within the scope of a three-year grant” made me feel. And while I can’t put my finger on the exact reasons, I think it’s because it underscores the stark reality that research has to operate within the confines of short-term constraints. Clearly the authors mean that this will shorten the timeframe for researchers to start answering the interesting questions on any organism.
Moreover, using next-generation sequencing techniques on "any" randomly chosen organism is unlikely to generate any interesting data per se, if we know little about the ecology and natural history of the organism in question. It will only be interesting if it already is a well-characterized "model organism", in the sense that it has been extensively studied (preferably experimentally and in the field) for many years, and preferably decades. Interesting "questions" do not pop out of the blue and by themselves, but they are only relevant if there is good natural history knowledge about the organism in question. In other words, if you do not have a past research experience of your creature for many years and know "what to do", it will hardly be worth the money and effort to do next-generation sequencing, because you will be flooded with useless genomic information that you will not know what to do with:
However, the link between generating genomic data for interesting ecological organisms and how high-throughput sequencing technology has already reinvigorated current studies of the genetic basis of adaptation is missing something. The tacit implication is that because we can use HTST to create extensive genomic toolkits on non-model organisms, we should be able to gain a stronger understanding of how selection operates on ecologically relevant variation. And thus answer some of the questions that have “puzzled ecological geneticists for decades.”
I don’t disagree that we’ll move science along, but all of the non-model organisms described in the review have had extensive conceptual legwork contributed by many, many scientists over several years. It is because these biological systems are so highly developed conceptually that the power of HTST can be fully realized.
For example in the three-spine stickleback system, it has taken several generations of grad students and postdocs to work out that replicate isolated freshwater stickleback populations were independently derived from their oceanic ancestors, that there is no gene flow between these isolated populations of freshwater habitats, that there is significant variation in behavior, life history, and morphology, that diversification happened very rapidly, and that selection has acted in parallel in these different isolated freshwater habitats evoking similar phenotypic trajectories at local, regional and global scales (the references are too numerous to cite so I’ve included a select few: Orti et al. 1994 Evolution, McKinnon and Rundle 2002 TREE, Hohenlohe et al. 2010 PLoS Genetics).
Lastly, and very importantly, next-generation sequencing techniques can be used in the study of parallell evolution and speciation, but it will not pick up all genes involved in adaptation if there are historical contingencies and if different genotypes contribute to the same phenotype. Here, we'll have to relly on other techniques, such as informed guesses and searching for candidate genes with a priori known function:
In the case of the stickleback system, Baird et al. 2008 and subsequently, Hohenlohe et al. 2010 used Illumina-sequenced RAD tags to gather genome-scale sequence data on natural populations. The data confirmed previous work that freshwater populations were independently derived from the oceanic populations. Furthermore, using high-throughput sequencing technology (RAD-tags), researchers identified 9 genomic regions (3% of the genome) that were differentiated between the two ecotypes (freshwater and oceanic) and thus, putative candidate regions associated with adaptation to freshwater. Some of these genomic regions co-localized with previously identified loci of major effect (e.g. the Ectodysplasin A (Eda) locus). But using this HT sequence data, researchers found several additional regions showing parallel differentiation across independent populations. The power of this much data is that now there is a list of novel candidate regions that may be important in adaptation to freshwater.
Even more interesting is that the data generated from HT sequencing did not find elevated divergence in a region previously identified as underlying a major phenotypic change between the marine and freshwater fish. This pelvic structure, a bony stomach with spines, is present in the marine fish but reduced in the freshwater. The region responsible is a cis-acting tissue-specific enhancer located in the Pituitary homeobox transcription factor 1 gene (Pitx1) found at the telomeric end of linkage group seven (Chan et al. 2008 Science) . So why did high-throughput sequencing data, which provided 45,000 SNPs to the researchers not detect this locus? Hohenlohe et al. (2010) suggest that multiple alleles were selected in different freshwater populations leading to a soft sweep pattern. If, as Hohenlohe et al. suggest, that the soft sweep pattern is true, then using only high-throughput sequencing data to detect regions of adaptive significance could potentially lead to a bias against detecting this form of selection.
High-throughput sequencing technologies do allow each lab to cheaply and in a relatively quick timeframe generate a specific type of genomic data that can inform our understanding of how ecology impacts the genomic architecture of an organism. But it does not mean that within the scope of a three-year grant we will generate anything remotely resembling a detailed picture of the genetics of adaptation. This rich picture will be formed after several decades of hair-pulling by grad students, postdocs and their supervisors all of whom will toil away testing, challenging and advancing our understanding of adaptation.
So what should we conclude then? Next-generation sequencing is dead, long live phenomics", perhaps? Only time will tell. There is clearly a reaction and a movement away from the naive reductionist world-view created by genomics, and increasing awareness that the phenotype should be put back in to the centre of evolutionary biology. My educated guess is that this trend will continue and grow in the near future, as many are gathering messy and large data-sets from next-generation sequencing, and will struggle to get any meaningful results from these data. What we can conclude already now, I think, is that (as usual) new techniques promise more than they can deliver, and we will never find the "silver bullet" method that explains everything. As usual, it is the ecological and evolutionary questions that must be at the centre of attention of any investigation. A dose of healthy scepticism is, however, usually very helpful. And do not forget to read the classics and learn your natural history. That will help a lot, also in the future.
Thursday, February 10, 2011
Hej guys, in conjunction with the lab-meeting next wednesday, which unfortunately will be my last before a long time (I am moving to Oslo to work with Glenn-peter Saetre and Thomas Hansen for the next two years, for those of you who don`t know yet), I was thinking that if you guys are free, we could go eat something and drink a few beers the same evening.
I was thinking we could meet at Botulfs at around 18 and then we'll see. I ll buy the first round, so come on time ;) and I will also bring fika for the usual meeting. I hope you guys can make it. Cheers
Next week's lab meeting will get philosophical - we will discuss the concept of free will!
Free will used to be a theological and a metaphysical concept, and philosphers have long pondered its implications for society. Natural scientists, in contrast, have often shied away from discussing the concept of free will because of its metaphysical history (dualism of body and soul) or have argued in favor of deterministic brains and our actions being direct consequences of gene–environment interactions.
In his recent paper "Towards a scientific concept of free will as a biological trait: spontaneous actions and decision-making in invertebrates" (Proc. R. Soc. Lond. B. vol. 278 no. 1707, pp. 930-939) Björn Brembs takes another viewpoint and argues that free will is a biological trait and not a metaphysical concept, based mainly on neurobiological findings in insects.
"Until the advent of modern neuroscience, free will used to be a theological and a metaphysical concept, debated with little reference to brain function. Today, with ever increasing understanding of neurons, circuits and cognition, this concept has become outdated and any metaphysical account of free will is rightfully rejected. The consequence is not, however, that we become mindless automata responding predictably to external stimuli. On the contrary, accumulating evidence also from brains much smaller than ours points towards a general organization of brain function that incorporates flexible decisionmaking on the basis of complex computations negotiating internal and external processing. The adaptive value of such an organization consists of being unpredictable for competitors, prey or predators, as well as being able to explore the hidden resource deterministic automats would never find. At the same time, this organization allows all animals to respond efficiently with tried-and-tested behaviours to predictable and reliable stimuli. As has been the case so many times in the history of neuroscience, invertebrate model systems are spearheading these research efforts. This comparatively recent evidence indicates that one common ability of most if not all brains is to choose among different behavioural options even in the absence of differences in the environment and perform genuinely novel acts. Therefore, it seems a reasonable effort for any neurobiologist to join and support a rather illustrious list of scholars who are trying to wrestle the term 'free will' from its metaphysical ancestry. The goal is to arrive at a scientific concept of free will, starting from these recently discovered processes with a strong emphasis on the neurobiological mechanisms underlying them."
The paper can be downloaded (open-access) from the publisher's website using the following link:
If you have trouble downloading the pdf, drop me a line and I can send you a copy of the paper. It makes interesting reading and should provide enough ideas for a lively discussion (for example, are we really free to decide if we join the lab meetings? Or are we forced by Erik's deterministic decision and our body's craving for fika?)
Lund University, Sweden
Sunday, February 6, 2011
Picture sources from Wikipedia.
This week's lab-meeting will take place at 13.30 on Wednesday February 9 in "Darwin", in accordance with our new schedule. We will discuss a very interesting article from Naomi Pierce's laboratory, which deals with biogeography and multiple "waves" of colonization of Polyommatus blues (butterflies belonging to the family Lycaenidae), as they crossed the Bering's Strait in North America. This beatiful paper integrates ancestral state reconstructions of an ecological important trait (thermal tolerance), biogeography, phylogeny and is of also of litterary interest, as the authors confirm a hypothesis by amateur lepidopterist and famous russian author Nabokov.
Vladimir Nabokov worked at the museum in Harvard (where Naomi Pierce is active today), during the middle part of the last century. Nabokov is mainly known as an important figure in litterature for his famous but controversial erotic novel "Lolita", about the sexual attraction a middle-age man felt towards a young 12-year old girl. Then and now quite a forbidden topic. But Nabokov was also an excellent amateur entomologist and systematist, whose expertise in butterflies exceeded many professional systematists.
Nabokovs biogeographical hypothesis about multiple waves of colonization of bluets to the New World was based on considerations of genital morphology, but has now proven to be largely correct and validated by molecular data. An excellent example how natural history, systematics and museum expertise can be predictive sciences and complement molecular systematics, rather than being replaced by it. I think our former postdoc and beloved co-worker Shawn Kuchta will love this paper. There is an interesting popular essay in New York Times as well, which might be of interest and worth reading prior to the lab-meeting. You can find that excellent essay by Carl Zimmer here. A blog post on the interesting phylogenetic blog "Dechronization" also comments on Zimmer's paper.
Below is the Abstract to the original article in Proc. R. Soc. Lond. B. that we will discuss on Wednesday. It is an "Open Acess"-article, so just follow the link to the abstract and then you should be able to download it.
Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World
- Roger Vila1,2,
- Charles D. Bell3,
- Richard Macniven1,4,
- Benjamin Goldman-Huertas1,5,
- Richard H. Ree6,
- Charles R. Marshall1,7,
- Zsolt Bálint8,
- Kurt Johnson9,
- Dubi Benyamini10 and
- Naomi E. Pierce1,*
- 1Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- 2ICREA and Institute of Evolutionary Biology (CSIC-UPF), Passeig Marítim de la Barceloneta 37–49, Barcelona 08003, Spain
- 3Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
- 4Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA
- 5Department of Ecology and Evolution, The University of Arizona, 424 Biosciences West, Tucson, AZ 85721, USA
- 6Department of Botany, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
- 7University of California Museum of Paleontology, and Department of Integrative Biology, University of California, Berkeley, 1101 Valley Life Sciences Building, Berkeley, CA 02138, USA
- 8Department of Zoology, Hungarian Natural History Museum H-1088, Budapest, Baross utca 13, Hungary
- 9Florida State Collection of Arthropods/McGuire Center, University of Florida Cultural Plaza, Hull Road, Gainesville, FL 32611, USA
- 1091 Levona Street, Bet Arye, 71947, Israel