Science Secretary & NIE?

President-elect Obama released his appointees for top science advising jobs. They include names that may be familiar to our blog readers: Jane Lubchenco (NOAA), Harold Varmus and Eric Lander (PCAST),  and John Holdren (Chief Advisor, OSTP). In case you missed it, the Secretary of Energy nominee, announced last week, is Steven Chu. Generally speaking this is great.

A basic understanding of science is increasingly necessary as a basis for informed decisions on a range of economic and environmental issues. Yet there are only four scientists in the House (Boyda D-KS, Ehlers R-MI, Foster D-IL, Holt, Jr. D-NJ, and McNerney D-CA, all physical sciences/math) and zero in the Senate (see here)! The situation in the current Executive Branch could barely be worse (sub-zero?), and the Supreme Court is clearly devoid of scientists. How is this possible in a country that appears preoccupied with science-related problems, like global warming, and is in stiff need of science breakthroughs to fuel another dot-com-like boom? Obama should be urged to push for establishment of a cabinet-level position for Holdren (Science Secretary). 

And in the micro-funding world of ecology and evolution, it may be time to revive our prescient colleagues' (including Hank Howe and Steve Hubbell) idea for the formation of the National Institutes for the Environment, and give it another push in the now-friendlier Congress and White House.

Cost Unrelated to Quality Among Evolution Journals

I just received the latest institutional subscription fees from our librarian. He's expecting a lower budget for next year and looking to drop journals that are no longer relevant to our needs. When I noticed we were paying 20 times more for the Biological Journal of the Linnean Society ($4,950 from Wiley-Blackwell) than for Systematic Biology ($248 from Oxford Press) I thought it might be fun to plot the cost of 21 journals related to evolutionary biology against their impact factor. Turns out there's virtually no association between the importance of a journal and its cost (see simple linear regression in figure).

It doesn't take a genius to see that blood-sucking corporate publishers are taking advantage of us. Although this point has been made many times before (see also Jonathan Eisen's blog where academic publishing and open access journals are regular topics of conversation), I want my fellow phylogeneticists to know that we're being screwed particularly by Wiley-Blackwell, publisher of the three most expensive journals in our field (Molecular Ecology, $8,967, IF=5.169; Journal of Biogeography, $5,826, IF=3.539; Biological Journal of the Linnean Society, $4950.01, IF=2.368). In spite of their middling impact factors, all three of these journals are ridiculously expensive (see the "Wiley-Blackwell Zone" in the figure). Don't get me wrong, I like the science in these journals and have published in two of the three, but is it really worth it at those prices?

I know we're all under pressure to publish in places that get us attention (and hopefully tenure), but there's no time like the present economic crisis to start factoring a journal's fees into our decisions about where to submit. Perhaps you'll also think about the cost of these journals the next time you volunteer your time as a reviewer for a corporate publishing entity.

Bad News for Academic Job Hunters

Citing a financial challenge that is without historical precedent (including the Great Depression), Harvard University has announced some sobering cost saving measures. In a Dec. 15th e-mail, the Dean of the Faculty of Arts and Sciences notes that all "originally authorized tenure-track and tenured searches have been reviewed and most have been postponed until a point in time when our financial situation has improved." You know things are bad when an institution that had 34 billion dollars in the bank just a year ago is canceling job searches. They're expecting a 30% reduction in their endowment and a $100+ million dollar budget gap. Here at the University of Rochester we're moving forward with one scheduled search for a cell/developmental/molecular biologist, but I've heard searches in other Departments have been canceled...

My New Favorite Plant

Botanists everywhere rejoice! Along the lines of the leafy sea dragon, we now have another plant-like animal to admire, the sea slug Elysia chlorotica.

It seems that this sea slug, which feeds on filamentous algae (Vaucheria sp.), intracellularly sequesters algal chloroplasts. Simple enough, right? No. The algae are secondary photosynthesizers, ancient heterotrophs whose ancestors acquired that ability from other algae. Their chloroplasts only encode a small fraction of genes required for their function, while the rest are ordinarily encoded by the nuclear genome. So, how does the sea slug maintain functioning chloroplasts without the supporting cast of nuclear genes? Horizontal gene transfer.

The authors find that at least one gene (psbO)  is encoded by the sea slug's own nuclear genome. It is nearly identical to the algal gene. This strongly argues for the horizontal transfer of photosynthetic ability from prey to predator. Amazing! 

[Rumpho et al. 2008. Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. PNAS 105:17867–17871.]

"Museomics" May Make Mammoths

For the first time, the "complete" genome of an extinct species has been generated. This week, the wooly mammoth, Mammuthus primigenius, had its DNA decoded by a team of researchers, with the results published in Nature. "Complete" was in quotes back there because without a modern species, like the African elephant's genome to compare it to, generated from intact chromosomes, the team can't be totally sure that they have the whole thing. Nonetheless, it's very exciting that a combination of some hair from the long-dead beast and next-generation sequencing technologies (oh, and $10 million) may one day allow a mammoth to walk the Earth again. It's also created the next in line of "-omics" - "Museomics" where natural history specimens, ancient DNA technology and pyrosequencing combine.

The World Like You've Never Seen It Before: Worldmapper

A colleague just sent me a link to this cool website that has a slew of world maps with countries drawn in proportion to various categories. A few of these are biological and pretty cool. The one shown here is a map of species at risk.

A Tangled Bank of Genes - and Methods

The identification of orthologous genes is a fundamental process in many fields of biology. For systematists, sequencing and analyzing orthologs is critical for accurately recovering the right phylogenetic tree. Molecular biologists hoping to understand protein function and evolution similarly need to be looking at orthologs. The trouble is that gene duplication and differentiation is rampant in genomes and many, many genes exist as members of gene families. Start looking at more than one species and now speciation and the genetic processes and consequences of that will make things even messier still. In the most recent Trends in Genetics, Kuzniar et al. present an ambitious review of what I can only hope are all of the currently available methods for identifying orthologous genes. No fewer than 25 different methods, algorithms, and/or programs (that collectively created a jumble that made me feel a lot like I'd fallen into a bowl of Alphabits) are listed along with their pros and cons. These programs are grouped into tree-based methods, graph-based methods and hybrid methods that use a little of both. The authors attempt to give a few simple examples of how different methods can produce different conclusions and also show how hybrid proteins can really mess with the various algorithms. Fortunately, they do a nice job creating a decision tree at the end of the paper that is based on just 3 simple questions to help one choose what ortholog detection method is right for the job at hand. Still, reading the paper made me wonder why so, so many of these programs are out there - why hasn't natural selection pared a few of these out?

Kuzniar, A., R.C.H.J. van Ham, S. Pongor, and J.A.M. Leunissen. 2008. The quest for orthologs: finding the corresponding genes across genomes. Trends in Genetics 24:539-551.

Now There's a Country that Appreciates Science!

Dan Rabosky just sent me this scan of England's ten pound note, expressing the hope that the United States might someday be so bold. Although such an appreciation for science may seem a long way off in a country where 55 million people just voted for a politician who believes humans walked with dinosaurs, there is already talk about undoing some of the anti-scientific legislation enacted over the past eight years. Obamanos!

The Latest Word on Metazoan Phylogenetics

The architect of the latest Metazoan phylogeny - Casey Dunn - was in Rochester this week talking about everything from siphonophore development to basal metazoan relations. Fans of his recent Nature paper on metazoan phylogenetics will be delighted to learn that Casey and his colleagues are dramatically expanding their EST data set. In addition to adding data from a few new taxa, the number of genes has increased by an order of magnitude to around 1,500. Their preliminary matrix is around 20% complete and they're now very actively re-evaluating the patterns recovered by the previously published dataset.

Although preliminary results largely agree with the previously published phylogeny, there is one interesting new pattern: acoel worms+xenoturbella as the basal bilaterians. Along with other organisms lacking a true coelem, acoel worms were traditionally united with platyhelminthes and placed at the base of the metazoan tree. Although rapid rates of evolution and long-branch attraction complicated molecular phylogenetic analyses these acoelemate forms, a string of studies -- including Dunn et al.'s previous analysis -- rejected the basal position of the platyhelminthes and acoels and suggested instead that they form a clade nested within the lophotrochozoa. Nevertheless, the phylogenetic distinctness of acoels and platyhelminthes, and a return of the acoels to the base of bilaterians recovered by the new dataset and preliminary analsyes, is not entirely unexpected; indeed, this conclusion brings the Dunn et al. tree in line with the conclusions of a carefully implemented 18S study. Xenoturbella (see image above), which has long been one of the greatest phylogenetic mysteries in the tree of life, is another story. As recently as the late 1990s, it was hypothesized that these almond-looking creatures were protostomes allied with molluscs. Although this story fell apart rather dramatically, I'm not aware of previous studies that have united these creatures with the aceols at the base of the bilaterians.

In addition to addressing specific phylogenetic hypotheses -- which, in Dunn's own words basically amounts to figuring out how all the various types of worms are related -- his group is also devoting attention to general systematic issues related to data-sampling and analysis efficiency. He makes a convincing case for the idea that a revolution in analytical techniques will be needed as we enter an era during which computational capabilities will be more limiting than data availability. Exciting times. If you want to get involved, you should drop Casey a line, I know he's looking for bright students and post-docs to populate his new lab.

Snake Versus Frog

The amazing photo at top is one of the winners in the BBC's annual Wildlife Photographer of the Year competition. Photographer David Maitland sat for three hours watching a frog battle for its life against the snake that was trying to eat it. Unfortunately, we don't know how things ended because the frog and snake were still locked in this position when he bailed. Although my photo is an embarrassment relative to Maitland's, I captured a similar moment a few years back when I saw a Hispaniolan vine snake (Uromacer) trying to eat a tree frog (Osteopilus) in the Dominican Republic. In this battle the frog managed to escape, due in part to flipping his legs over the snakes head and shoving off from the palm leaf as the snake tried to pull it in the other direction.

Economic post-Darwinism?

Stanley, Gould, & Co. have earned a popular blog endorsement. A recent article about the proposed GM-Chrysler megamerger in the Daily Kos puts itself squarely into the species selection corner. It argues that species selection for body size in dinosaurs can be instructive in consideration of state-aided large corporate mergers. While clearly meant for a layperson, it is surprisingly lucid and on the mark.

The units and levels of selection, as well as the emergent properties within and among state-aided corporations remain unclear, however.

Christopher Hitchens: Defender of Fruitflies

Palin is an easy target for the man who took down Mother Teresa.Update: Dan Warren pointed us to this watercolor by Zina Saunders that sums up Palin's attitude toward fruitfly research.

Update: Jerry Coyne has join the fray.

Rapid Diversification - In Journals

A while back, I was asked to join an editorial board for a new open-access journal called "Theoretical Biology Insights," published by Libertas Academica. I think open access is great, and I am familiar with another LA journal, Evolutionary Bioinformatics, that has published some good things. I responded enthusiastically, and was added to the slate. I haven't yet been involved with the journal in any other way, but it is really just starting out.

Perusing the first two papers of this journal, I couldn't help but notice that one of them seems to be about how the complete state of all human brains might somehow be encoded in the Earth's magnetic field. (image 'borrowed' from here). Now, I may be misinterpreting this paper - in fact, I probably am. But the correct interpretation of this paper has to be equally strange, even if strange in a different way. Here, I must confess that I'm not a (psychologist? physicist? geoneurobiologist?)... well I don't feel really qualified to judge this paper.

The point of this post is mainly to wonder what everyone thinks the role of journals like this one or others from LA will be. There are also the many new OA journals from Bentham Science Publishers (you might have gotten an email or two from them), one of which is about evolution. These may be a different type of thing from the LA journals, but I'm finding it difficult or impossible to really predict where all of this is going.

To me, perhaps the new journal with the best potential is PLoS ONE, which takes papers and then hopes that peer review will be a continuing process; anyone can comment on the papers on the website. However, in my experience (n=1), people don't comment.

I'd love to hear anyone's thoughts on this topic, especially people who have experience with these new journals. Send your electromagnetic waves my way.

Persinger, M. A. 2008. On the possible representation of the electromagnetic equivalents of all human memory within the Earth's magnetic field: implications for theoretical biology. Theoretical Biology Insights 1:3-11.

The Hassles of High Throughput Sequencing #1

As my lab strives to adopt increasingly high throughput molecular practices, we've hit a few bumps along the way. One involves the first step in the process of obtaining DNA sequence data: extraction. As a molecular biologist, I've grown up in the era of kits: I've always done genomic extractions by pulling a Qiagen/Promega/Viogene kit off the shelf, dropping a chunk of tissue into a tube and following instructions. This simple and convenient approach, however, is challenged by the needs of the very high throughput facility we're working with. They're asking for genomic DNA with a 260/280 ratio (a measure of a sample's quality that reflects the ratio of DNA to undesirable proteins) between 1.8 and 2.0. Essentially, they're asking for genomic DNA that is completely free of protein contaminants. Unfortunately, kits that rely on a silica filters tend to give us ratios in the 1.2-1.3 range. After a week of experimentation, we've been able to get samples with ratios in the 1.6-1.7 range, but only via phenol-chloroform extraction. Although I've spent my career avoiding a method that has always been described as "unpleasant", several gel-based methods make the phenol-chloroform process relatively painless (check out Phase Lock Gel from Eppendorf [apparently discontinued] and MaXtract from Qiagen). I'm sure we're not the first to encounter this problem, but hopefully this post will help others avoid the trouble of extracting dozens of samples only to be told later that the resulting samples weren't good enough!

R Tip: Labeling Trees w/ Posterior Probability and Bootstrap Support

What's the worst part about making figures for phylogeny papers? When I sat down yesterday to make some new figures I realized that my answer was the same as it was ten years ago: adding support values to each node by hand using programs like Adobe Illustrator. I decided I was never going to go through this archaic error-prone process again. In sharing my solution here, I hope that none of you will either! The text below is an annottated R script that does most of the hard work for you (you'll still have to tweak a few things in Illustrator). Of course, you'll need to get familiar with basic R functions for phylogentics before attempting to use these scripts. The best way to do this is to pick up a copy of Paradis' nice little introductory text^{abe/half/amzn/bn}. Don't be lazy and tell yourself you can label your nodes by hand quicker than you could learn R. This might be true if you only had to label one tree, but what are you going to do for your next paper, or when the reviewers advise you to re-run your analyses? If you know how to use the scripts below you'll just be able to plug any tree in and have your labeled tree almost instantly!

#Fist we need to open some necessary libraries
library(ape)
library(geiger)
#The getAllSubTrees function below is a necessary subfunction that atomizes a tree into each individual subclade and was provided compliments of Luke Harmon.
getAllSubtrees<-function(phy, minSize=2) {
res<-list()
count=1
ntip<-length(phy$tip.label)
for(i in 1:phy$Nnode) {
l<-node.leaves(phy, ntip+i)
bt<-match(phy$tip.label, l)
if(sum(is.na(bt))==0) {
st<-phy
} else st<-drop.tip(phy, phy$tip.label[is.na(bt)])
if(length(st$tip.label)>=minSize) {
res[[count]]<-st
count<-count+1
}}res}

#The plotBayesBoot function below plots both posterior probability and bootstrap values on each node of the consensus tree obtained from your Bayesian analysis. Bootstrap values will appear in bold text immediately below and to the left of the node they support, whereas Bayesian posterior probabilies will appear in regular face above and to the left of the node.

plotBayesBoot <- function(bayesTree,bootTree) {
getAllSubtrees(bayesTree)->bayesSub
getAllSubtrees(bootTree)->bootSub
bootList<-matrix("<50",nnode(bayestree),1)
#The commands below compare all the subclades in the Bayes tree to all the subclades in the bootstrap tree, and vice versa, and identifies all those clades that are identical.
for(i in 1:Nnode(bayesTree)) {
for(j in 1:Nnode(bootTree)) {
match(bayesSub[[i]]$tip.label[order(bayesSub[[i]]$tip.label)], bootSub[[j]]$tip.label[order(bootSub[[j]]$tip.label)])->shared
match(bootSub[[j]]$tip.label[order(bootSub[[j]]$tip.label)], bayesSub[[i]]$tip.label[order(bayesSub[[i]]$tip.label)])->shared2
if(sum(is.na(c(shared,shared2)))==0) {
bootTree$node.label[j]->bootList[i]
}}}
plot(bayesTree, cex=1, lwd=0.5) #Plots your Bayesian consensus tree
nodelabels(bayesTree$node.label, adj=c(1.2, -0.3), frame="n", cex=1, font=1) #Adds posterior probability values to the tree. Change the 'cex' value to make the fond smaller or larger. A value of 1 will give you a readable result in the R quartz window, but a value closer to 0.25 might be better for publication)
nodelabels(bootList, adj=c(1.4, 1.3), frame="n", cex=1, font=2) #Adds bootstrap values.
}

#Now you're ready to read your trees in and make your figure!
read.nexus("yourBayesTree.con")->bayesTree #Reads in the .con file that results from analyses in MrBayes.
bayesTree[[1]]->bayesTree #Extracts one of the two trees in the .con file.
read.nexus("yourBootTree.nex")->bootTree #Reads in the consensus tree from a bootstrap analysis in PAUP.
plotBayesBoot(bayesTree, bootTree)

Nothing To Do With Phylogenetics...

but it's Friday, and this is my new car.

Penalized Likelihood for Trees

The parsimony versus likelihood debate seems to have cooled off considerably in recent years. Still, we don't know how complex of a model is appropriate for building trees from DNA sequence data. This is expressed, for example, by the question of how many separate partitions should be used for a particular data set. Basically, we create models with widely varying numbers of parameters, and it is not always obvious when to stop doing this to avoid overparameterization.

One solution to this problem is a method called penalized likelihood. In PL, parameters are allowed to vary in the model, but there is a penalty for dramatic changes in parameter values. For example, one might want to vary the rate of evolution across a phylogenetic tree, but give a penalty when parameter values change a lot between adjacent branches. This is the basic idea of PL in the r8s program.

Kim and Sanderson have now implemented this approach as a way to build phylogenetic trees. This could be very useful; as the authors mention, various other phylogenetic reconstruction methods can be viewed as special cases of penalized likelihood, which can thus cover ground in the spaces between existing methods. This seems promising to me, I'm excited to try it on my own data.

The picture, brought to my attention by Brian O'Meara, is from Sanderson's lab page. I think I need that for my own lab.

The $3-million "Overhead" Projector

While occupants of the White House clearly have indirect effects on nearly every aspect of our lives, at least two phrases or topics mentioned in last night's presidential debate directly concern science. 

Senator McCain repeated his charge that Senator Obama engaged in wasteful pork barrell politics when he sponsored a request for three million dollars for "an overhead projector at a planetarium in Chicago, Illinois." This is deeply misleading. The projector in question is Zeiss Mark VI (similar to photo shown at above-left). As PolitiFact put it:

McCain refers to the item as an "overhead projector," conjuring images of those little projectors on carts in public school libraries all over America, but calling this piece of equipment an overhead projector is like calling the space shuttle a bottle rocket. 

In addition, the Adler Planetarium has published this press release to explain its involvement in this funding request. The Planetarium uses the projector to show the position and glow of thousands of stars in the sky to its visitors, including joint programs with the Chicago Public Schools. In other words, the funding for what is perhaps the most inspiring human experience, that of considering the imponderable size of the universe, was turned into a political weapon. Boo.

Disclosure: I will openly admit that my lip quivered with delight when Senator Obama mentioned "basic science research." I bet he meant population genetic and phylogenetically-informed analyses of plant mating system evolution.

New Journal - Mitochondrial DNA

There's a new journal by Informa Press called "Mitochondrial DNA". From the announcement by the editor-in-chief, Rob Desalle, the list of topics that this journal hopes to cover is as follows:
* mapping, sequencing, and analysis of mitochondrial DNA and RNA
* descriptive studies of DNA sequences from whole mitochondrial genomes
* population genetics, medical genetics, phylogenetics and human evolution that use mitochondrial DNA as a source of evidence for studies
* population genetics and systematics theory that specifically address the use of mitochondrial DNA sequences
* utility of mitochondrial DNA information in medical studies and in human evolutionary biology
* DNA barcoding studies using both empirical approaches and theory-based critiques
Plus, timely reviews on subjects relevant to mitochondrial genomics, genetics and medicine and a regular feature each issue called “mito-communications” that highlight and summarize published research or conference summaries that are relevant to the subject of mitochondrial genomics and genetics.

To access journal information and to submit a manuscript please go to the following URLs.
SUBMISSIONS: http://mc.manuscriptcentral.com/gdna

INFORMATION: http://www.informaworld.com/MitochondrialDNA

Why Do People Believe Weird Things?

I'm not really sure if this is a recent phenomenon or not, but there is a super-abundance of people out there who believe in "weird things" - or, things that are directly contradicted by scientific information. Painting with a broad brush, I would include things like creationism, but also anti-vaccination, psychic detectives, Sept. 11 conspiracy theories, alien abductions, etc. I'm sure you can think of your own examples (it's worth clicking on that one). One interesting thing about these types of beliefs is that they cut across the "divide" between conservatives and liberals; there are examples on both sides of the aisle. Given this, I've been thinking about what people with beliefs like this have in common. It seems to me that some of these ways of thinking might be on the rise across all of our society, and could potentially explain the rise of such distinctly different phenomena as the Discovery Institute and the crusade against vaccinating children.

I think that many people who believe things like this share the following beliefs:

1. Anecdotal information, especially when it's personal, is more convincing than statistical analyses. For example, there are a few strange artifacts that some creationists believe are fatal to the theory of evolution; similarly, there are some emotional case-stories about kids with autism that can sway people to forgo shots.

Why is this misleading? Because human brains are trained to see patterns where there is none, anecdotal information can be misleading. Broad statistical methods are designed explicitly to address these sorts of issues.

2. It is possible that powerful groups in society are secretly operating vast conspiracies against the people. Creationists believe that biologists are actively collaborating to prevent their false believe in evolution from being exposed; anti-vaccine advocates believe that the entire medical (or, perhaps, pharmaceutical) industry is conspiring against them.

Why is this misleading? Although our government is not exactly "open source," it is impossible to coordinate conspiracies as vast as the ones required to support some of these theories. In particular, science is very competitive, and scientists are skeptical of other scientists' work. I can't even imagine how someone would get all of us to agree to mislead about data. Also, bureaucracies are incompetent.

3. Sharing radical ideas provides a deep connection with people, even over the internet. I am sometimes struck by the reasonably cohesive nature of these sets of people. The best example of this is moderated internet forums or blogs where large sets of people, all in agreement with each other, can discuss the issues without dissent. If you are a creationist, you might feel an instant connection when, say, you sit near another creationist on an airplane. By contrast, it is entirely unremarkable to meet someone else who accepts the evolutionary worldview.

Why is this misleading? This is a trickier one, because it has more to do with human society than any particular worldview. However, I can speak from personal experience. Some people think that people's political views are a good predictor of whether or not they will make good friends; I have found this not to be the case. Hanging out with people who disagree with you can be much more interesting, and I think personalities cannot be pigeonholed like that.

The really surprising thing, to me, is that I understand why these ways of viewing the world are appealing. As a parent, I rely to a great extent on anecdotal information about how to handle certain situations with the boys. I think the current administration is operating, for the most part, under a cloud of secrecy. And I like radical ideas, and feel bonded to others who can think "outside the box." But together, these things are a potent cocktail for misunderstanding.

To me, this is relevant to my teaching. Perhaps science classes can help students reconcile their framework for the world with scientific information, so that they aren't taken advantage of by these sorts of, to me, counterproductive movements. There are strong arguments against all three of these viewpoints when it comes to complex issues; anecdotal information is deceptive, bureaucratic organizations are too incompetent to really succeed in fooling everyone, and radical ideas don't really lead to lasting relationships. Perhaps we should think about how to get this sort of information across.

One reason why I wanted to post this is that I think the common way of interpreting creationists as "nutcases" or "religious fanatics" is not really a proper explanation (the cartoon here illustrates this way of thinking). In fact, the belief that people who disagree with you are less intelligent and morally inferior in some way is a common thread that is lurking behind many issues in society today - in fact, perhaps both Bush and Bin Laden share that way of thinking. But that seems like another post. Here, my goal is to point out that there are real reasons why people hold the beliefs that they do. If you want to really affect these people - or even coexist with them - then you have to get to the core of the issue.

Two more malaria parasite genomes

In this week's Nature, the complete genome sequences of two additional species of malaria parasites, Plasmodium vivax and Plasmodium knowlesi are reported. These two species both are capable of infecting humans - in fact, P. vivax is probably the most common malaria parasite in people, though does not share the high mortality rate of its cousin, Plasmodium falciparum, whose genome was published in 2002. P. knowlesi has recently gained more interest in the biomedical community as this parasite that was thought to use macaques as its hosts was found to infect humans at a much higher rate than ever thought. These two genomes will mark a significant stride forward toward being able to do real comparative biology of these parasites and to use key differences in the life cycle and other biological factors toward perhaps finding new drug and/or vaccine therapies. The P. knowlesi genome was completed largely by a team from Sanger and congrats to my my friend, Jane Carlton, formerly of TIGR and now on the faculty of the NYU School of Medicine and her team for their huge accomplishment on the P. vivax genome (and thanks for the acknowledgment in the paper -- I did the phylogeny for Jane that's in the supplemental methods.)

Evolutionary Applications: A New Journal Worth a Look

There is a new journal, Evolutionary Applications, that everyone should check out. I know there's a glut of journals out there, so sometimes new ones can get lost in the shuffle. But I think the first three issues of this journal (available online free in 2008) speak for themselves. First of all, there are papers from many outstanding scientists that have already been published. Second, I think this journal covers a subject that is of critical importance. Evolutionary applications in medicine, for example, will likely form a cornerstone of many advances in health care over the coming years. Showing that our work has practical importance to society may also help in the discussion about the role of evolution in education. So, check it out!

What Do Sarah Palin & Ricky Gervais Have in Common?

Shortly after Sarah Palin delivered her rousing speech at the Republican National Convention, I received a gloating e-mail from my Republican father about his party's "home run." Although I responded with concern that her religious zealotry committed her to the denial of established scientific facts, he suggested that this concern was premature. It was true that she advocated creationism in previous campaigns, but I had to admit the possibility that that she had changed her mind since. I decided to withhold further slander until she made her latest views clear. Well, here they are.

Her "teach the controversy" perspective suggests that, at best, she views the first few pages of the Old Testament as an equally meaningful perspective on life as decades of intense study by thousands of other evolutionary biologists. We all know, however, that her true ignorance runs much deeper: "teach the controversy" is merely cover for those who view evolution as a hoax and Genesis' account as literal truth. Now that her zealotry has been confirmed, I hope she'll consider following Ricky Gervais example by expressing her views more directly.

PS - It gets better! The LA Times ran a story a few days ago which quotes Palin saying "dinosaurs and humans walked the Earth at the same time." Note to Gwen Ifill: Please ask the candidates about dinosaurs at the debate tonight. Don't give Palin a chance to spin her "teach the controversy" BS by asking a general question about evolution, just come right out and ask about the dinosaurs!

Comic Relief For Academics In These Economic Times

Job Hunters, Don't Overlook This Opportunity!

Job hunting can be a fickle, frustrating process. Thankfully the good people at the Institute for Creation Research offer an excruciatingly detailed account of the requirements for their open Assistant Professor position. On top of the basic degree requirements, applicants must also agree with the ICR doctrinal statements and tenets. I love that they have a such a direct mechanism for preventing anyone from doing actual science at the ICR. Even more than this list, I love the header photo on their 'science' page, which shows a girl staring into some green water through an Erlenmeyer flask. Recalling the famous Peanut Butter principle, I can't help but imagine a room full of young scholars staring at such flasks to prove that evolution doesn't happen.

Is Local Adaptative Variation Tied to Mate Choice?

With the growing popularity of ecological speciation, instances of local adaptation have taken on added significance. In addition to being powerful examples of natural selection in action, local adaptation is now recognized as a potential starting point for the process of speciation. In order to invoke speciation or incipient speciation, however, it's necessary to show that some degree of reproductive isolation exists among local variants. Although this hypothesis is often tested indirectly with molecular markers, relatively few authors have succeeded in conducting direct behavioral assays of reproductive isolation in nature.

In the latest issue of Journal of Herpetology, Erica Bree Rosenblum uses a series of relatively simple behavioral experiments to examine reproductive isolation between the light and dark color morphs of the Lesser Earless Lizard (Holbrookia maculata). These forms evolved over the last 6,000 years to match substrate variation in the southwestern United States. While she found that light individuals are more likely to court other light individuals, this decision does not appear to be the result of body coloration: similar results were obtained even when light individuals were painted to resemble dark individuals. She suggests that behavioral signals or other aspects of the animal's coloration that are not obviously associated with crypsis (e.g., throat coloration) may be the mechanisms driving mate choice in Holbrookia.

The conclusion that the trait involved in adaptive divergence for improved crypsis is decoupled from the trait(s) involved in mate choice is surprising because it requires a more complicated model of speciation than when the same trait is filling both roles. Specifically, successful speciation under this scenario requires linkage between two traits that likely have distinct genetic foundations. Because the evolution of such linkage has always been viewed as one of the main impediments to ecological speciation it's going to be interesting to see how this story plays out, and how general this pattern is among other putative examples of ecological speciation.

What the Hell is Niche Conservatism?

Niche conservatism is all the rage; virtually unheard of at the turn of the Millenium, 2008 has already seen nearly 30 papers on the subject. The only problem? Nobody seems to agree on what it is!

In a recent exchange in Ecological Letters, Jonathan Losos and John Wiens try to cut through the confusion. Let's begin with Losos' definition of niche conservatism as a pattern that "results when closely related species are more ecologically similar that [sic] would be expected based on their phylogenetic relationships" (emphasis mine). In advocating this definition, Losos argues strongly against the view that niche conservatism is a synonym for phylogenetic signal (i.e., the tendency for related species to be more similar than species drawn at random from a phylogeny). To make this equation, he argues, would defy the original meaning of the term niche conservatism and expands its scope so broadly as to render it meaningless. As Losos notes, some degree of ecological similarity is expected among closely related species even under the simplest models of evolution (e.g., Brownian motion resulting from shifting selective pressures or drift). Niche conservatism, meanwhile, results when species are more similar than expected under this simple model due to constraint by natural (stabilizing) selection, gene flow, pleiotropy or the absence of variation. Although Wiens agrees on this point, many recent studies claiming to support niche conservation involve nothing more than simple tests of phylogenetic signal. In Losos' view, these studies provide evidence that is necessary, but not sufficient, for the identification of niche conservation.

Although I've previously confounded niche conservatism and phylogenetic signal in my own work, I've come around to the view shared by Wiens and Losos. Another influential voice in the field -- Michael Donoghue (2008) -- seems to straddle the fence when he says "strictly speaking, it is not necessary to link PNC with the view that there are constraints on niche evolution, [but] I believe that it is the relative difficulty of making major ecological shifts that explains [patterns of niche conservation]." What do you all think?

If people are into this topic, perhaps we can try to tackle Losos and Wiens arguments about how and when niche conservatism should be studied, and whether it represents a pattern, a process, or both...

Literature Cited:
Losos, J. B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters 11:995-1003.

Wiens, J. J. 2008. Commentary on Losos (2008): Niche Conservatism Déjá Vu. Ecology Letters 11:1004-1005.

Losos, J. B. 2008. Rejoinder to Wiens (2008): Phylogenetic niche conservatism, its occurrence and importance. Ecology Letters 11:1005-1007.

Donoghue, M. J. 2008. A phylogenetic perspective on the distribution of plant diversity. PNAS 105:11549-11555.

Ray-finned fish phylogeny: Going nuclear!

The most recent issue of Systematic Biology has a great new phylogenetic analysis of actinopterygian fishes that uses 10 nuclear genes. Chenhong Li, Guoqing Lu, and Guillermo Orti present an excellent study of ray-finned (actinopterygian) fish phylogeny. The trees generated in this study reflect some very interesting hypotheses of actinopt relationships hypothesized by pre-cladistic evolutionary biologists and ichthyologists. Li et al. present a cutting edge analysis of a very impressive dataset, and offer a new strategy to consider when partitioning data for maximum likelihood or Bayesian phylogenetic analyses.

Spore

Our own Tom Near was prominently featured in a New York Times article. And not just peripherally mentioned, mind you--he was called "a heavy-duty gamer." Holy crap! The article is about Spore, a recently released game from Will Wright (of SimCity and The Sims fame). It's a sketch-simulation of life from the origin on. According to some of the nerdbags quoted in the article,  the game may get the tempo and mode of evolution wrong. 

Here's my favorite excerpt from the beginning of the piece:

By night, Dr. Near, an assistant professor at Yale, is a heavy-duty gamer, steering tanks or playing football on his computer. This afternoon his two lives have come together.

The Fisher Archive

A couple of years ago, while following up on my reading of Provine's book about Sewall Wright, I stumbled upon the University of Adelaide's Ronald A. Fisher Digital Archive. [Fisher and Wright tangled over the problem of maintenance of polymorphism at the self-incompatibility locus in plants.] I not only found what I was looking for--Fisher's unpublished manuscript on self-incompatibility--but also a trove of other manuscripts, documents, and letters.

By the way, Fisher's Erdös number is 2. I wonder if some crafty programmer-biologist out there would mind writing a Lande distance, or something similar.

These Lizards are Making Me Look Bad

Ok, I try to get up every morning and do a bit of a work out...but sure, sometimes I spend the half hour sipping coffee on the couch instead - and then I feel a little guilty. Now I've got lizards to make me feel even worse! A new study by Terry Ord, a postdoc in the Losos lab at Harvard shows that four species of Anolis lizards on Jamaica do their characteristic push-ups and dewlapping displays at dawn and/or at dusk. This is the first time that such a "silent dawn chorus" has been demonstrated - but shows similarities to birds and other acoustic animals who broadcast their presence in their territories. This strategy is thought to be more efficient at maintaining stable territories and communities by advertising a male's ability to defend its territory -without having to actually go through the hassle (and energy expense and danger) of doing so. Doing it at dawn and dusk sort of "bookends" this information - in the a.m. it establishes which territories are occupied and in the evening, it advertises, "Hey, I'm still here - no snake or bird - or biologist! - got me today. Going to bed - see you in the morning."

Ugh - these things are exercising twice a day! I promise to get up early tomorrow and do some push-ups of my own...and I'm leaving the shades up so the neighbors can make no mistake that this is my apartment.

Popular press picked this up, too.

Dawkins' Hate Mail

This short video of Richard Dawkins doesn't exactly conjure up anything related to phylogenetics, but I couldn't resist it.

(originally courtesy of boingboing, latest version from bligbi)

Bioinformatics Pays - Literally

Congratulations to Vince Smith of the National History Museum in London, the talented biodiversity bioinformatician with "Cybertaxonomist" on his business cards. Vince is the 2008 winner of the Ebbe Nielsen Prize, an award given by GBIF to "a researcher who is combining biosystematics and biodiversity informatics research in an exciting and novel way." And, it's not just a plaque and a handshake - the prize carries with it a cheque in the amount of 30,000 euros (which seems like something like 2 million U.S. dollars to those of us traveling abroad and dealing with the current exchange rates). Vince will use this money to help continue the work on his Scratchpads project, but I bet just a wee bit might go for a celebratory beer. Guess I can forgive him for swapping around his seminar date at the AMNH because of having to go to Tanzania to collect his prize as long as he buys a round for me when he does come to town.

A Teacher on the Front Line (NYT)

A splendid New York Times article is making the evolution blog rounds. While we chose to not concentrate on the complex political issues surrounding the education curriculum, this piece is simply too good and inspiring to miss.

Amy Harmon describes a day in the life of David Campbell, a Jacksonville area biology teacher, who puts us to shame with his commitment to Florida's schools and reason. While this is no doubt a reality for many teachers, I find it difficult to fathom calmly teaching evolution in my classroom as my colleague undermines me next door. 

And if you get to reading, you'll find to this passage, pure gold:

When he was 5, Mr. Campbell’s aunt took him on a trip from his home in Connecticut to the American Museum of Natural History in New York City. At the end of the day, she had to pry him away from the Tyrannosaurus rex.

Hot Off the Press: Evolution 62(8)

Although the article layout still looks like a 13-year-old kid spilled a bag of bad ideas onto a page, a new issue of Evolution arrived in the mail. (Take a look at that crisp and readable 1980s article design.) At least the contents seem unaffected by style.

Liu et al. augment the approach initially outlined most recently in Edwards et al. (2007) and Liu and Pearl (2007; see previous post), and hinted elsewhere, for estimating species trees with multiple-allele sequence data. Brandley et al. argue that reconstructions of ancestral states alone can reveal important insights into the evolutionary history of morphological changes--their number and directionality, for example. Although, they employ a nifty model, it is likely that ignoring some well known violations of the models of character evolution yield spurious results (in this and hundreds of other studies). In other words, I don't buy the regain of limbs in squamates. Still, the regression analyses of traits associated with lizard- or snake-like body form make for nice lecture material. I wonder if they could post the data and code for R instruction? (they did!) Hansen et al. expand the earlier models of quantitative character evolution by giving consideration to the shifts in trait optima, in addition to character state shifts themselves. Strasburg and Rieseberg, and Currat et al. examine the magnitude of introgression in an empirical multi-gene study of sunflowers and in simulations of invading/local populations, respectively. Finally, Rabosky and Lovette develop a method for estimating speciation and extinction rates that vary continuously through time, and find that the common slow-down in species accumulations are driven by lower speciation, not higher extinction rates.

Dominican Transportation

In our efforts to sample anoles from across the Dominican Republic we've been doing lots of driving. While on the road we've been constantly entertained by the things Dominicans manage to move around on motorcycles. The photos above are only a small sampling of what we've seen: eggs, cases of beer, a steel gate, and five (!) people. Believe it or not, this was the first of three five-tops we've seen. Remarkabely, that's not even the record -- a few years ago I spotted seven-top that included three adults and four children.

Maldito Fowleri

The rarest anole in the Dominican Republic has been spotted once more! Anolis fowleri is a montane species found only in the Dominican Republic's Cordillera Central that has been seen alive by less than twenty naturalists. The last sighting was six years ago when Steve Poe, Paul Hime and I found three animals south of Constanza. I've tried to find it a few times since, most recently in 2006 with a group that included the Dominican naturalist and photographer Eladio Fernandez, who was left cursing "maldito fowleri" when our efforts failed. A few nights ago, Luke Mahler of Harvard University snagged another animal from the type locality. Seen in these pictures is Luke with his prize, as well as our new friend Miguel Landestoy with the same animal. Miguel is the first Dominican of his generation to see this species and will hopefully be posting some beautiful photos on his Flickr pages soon. Almost nothing is known of fowleri's ecology or life history, a deficiency that Luke hopes to remedy by spending a few weeks on the hunt this summer.

Goin' Parasite Hunting, Back in Two Weeks

On Monday, I will board a plane to Santo Domingo and hook up with Rich and crew who are down there hunting all kinds of anoles. My new graduate student, Bryan Falk, is there with them now and our goal on this trip (besides convincing Rich that field work can indeed involve fun things, too), is to sample three main types of parasites from the anoles. We'll be taking blood samples, like I always do, to extend our work on malaria parasites. Last time we were down there, I found 4 species in the Dominican anoles - one (shown in photo in a lizard erythrocyte) was originally described as a subspecies of P. fairchildi, a species originally described from Costa Rica, but our genetic data show that this relationship is not valid. We'll also be collecting a pinworm, Parapharyngodon cubensis and mites, to see if these parasites mirror the differentiation, be it at the population or the species level, of their hosts. If all goes well, we'll be back on the 24th of this month. Have a good couple of weeks, everyone!

A great day for us all

There have been a number of monumental moments in the history of Evolutionary Biology: Darwin's publication of the Origin, the modern synthesis, the invention and development of cladistic methods... and now, we are all about to witness the next milestone. In the August 2008 issue of Systematic Biology, Bond and Stockman have published a paper describing a method for the mathematical delimitation of cohesion species.  Although this is interesting in itself, the truly monumental part of the paper is the name they have chosen for this new species: Aptostichus stephencolberti. That's right, Americans, the species has been named after the great Patriot himself. I'm hopeful that this is the first of many contributions that Mr. Colbert will make to our field.

Update: better video

There's also some other great stuff coming online as the issue is being assembled.  To me, Lemmon and Lemmon's approach to quantitative biogeography on a continuous landscape is really exciting; we've needed a method like this for some time, especially given recent criticism of nested clade analysis. There's also a dull paper in there about day geckos that you might want to check out.

Passive voice was used

Recently, many manuscripts from graduate students were read, and comments made by me. It was noticed that students choose to use passive voice for much of their papers (especially descriptions of sequencing and tree building). Some speculations were proposed as to why the students were doing this. It was concluded that they are trying to sound more "science-y," but that it was not really working very well. 

Please, stop!  You're all slowly killing me with these sentences. 

Goin' Lizard Hunting, Back in September

This might be my last post for a while: tomorrow I'm off for six weeks of lizard hunting on Hispaniola, four in the Dominican Republic and two in Haiti.

Our first stop will be the Recodo Road, a locality made famous by the studies of the late Harvard Professor and and godfather of Anolis lizard biology Ernest Williams. Our first step will be to see how far up the road we can go; as Williams noted "there are no problems other than two fords, the first possible in a rented car, the second not so." In spite of this challenge, anole populations along the Recodo road have a history of yielding insight into the role of the dewlap in anole communication and speciation.

It was along the Recodo road that Williams and his students discovered some unusual trunk-ground anoles that could only be distinguished from the widespread Anolis cybotes by their striking purple and red dewlaps. They turned out to be a distinct new species - Anolis marcanoi - and one of the first whose validity was confirmed via molecular genetic analyses. Later, an experimental behavioral study - which remains one a few of its kind - suggested an important role for dewlap divergence in dictating the nature of interspecific interactions between A. cybotes and A. marcanoi, and marked a career beginning for the man who has assumed the anole throne at Harvard.

We'll be looking at an even more interesting species complex of trunk anoles that also attracted the attention of Williams and his students (see attached figure from the 1977 Anolis newsletter). Unfortunately, the main architect of this work - Preston Webster - died tragically before completing his thesis. Although incomplete, his work marked the high point of the Williams lab's foray into molecular analyses of species and speciation. Webster's preliminary field and allozymic studies were published posthumously in the third Anolis newsletter and got far enough to reveal evidence for two intriguing patterns: habitat-mediated dewlap divergence (a key to ecological speciation) and reproductive character displacement (perhaps driven by selection against hybridization events that were shown to produce sterile male offspring). Although these observations prompted Williams himself to suggest that there "are obviously several problems here crying for solution", they have remained unexplained for more than three decades.

It never hurts to go into a field trip with the blessings of the godfather...

Phylota: My Mind is Blown

In the June issue of Systematic Biology, Sanderson et al. report the availability of the PhyLoTA browser. If you haven't checked this out yet, do - it can be a real boon to phylogenetic analyses in the age of Bioinformatics. For clades in the Tree of Life, PhyLoTA identifies clusters, which are sets of sequences for the same gene across sets of taxa. For example, here are some clusters for the geckos. You can see the big hitters in there: c-mos, 12s, 16s, cytochrome b. There are also a few decent data sets for other genes as well. You can then download preliminary alignments for the clusters for your phylogenetic analyses.

If you've every tried to do this sort of thing directly in GenBank, the value of this will be immediately apparent. This is particularly useful if you, like me, suck at sequencing.

As a side note, I talked to a colleague who got harassed at the Ichs and Herps meeting for... gasp... downloading sequences from GenBank and using them without asking the author's permission! Good lord, what is the world coming to? I'm surprised to hear of such active resistance to public availability of information.

UPDATE: Further discussion of the final paragraph at <bbgm>.

Highlights (or Lack Thereof) from Ichthyology & Herpetology 2008

I'm just back from the Ichs and Herps meetings in Montreal. Overall, the meetings were a bit of a let-down. They suffered in particular by comparison to the Evolution meetings just a few weeks previously. At Evolution, I saw lots of phylogenies reconstructed with 10-20 nuclear loci as well as a range of exciting new phylogenetic and comparative methods. At Ichs and Herps, phylogenies from mitochondrial DNA plus 0-5 nuclear loci were the norm and hardly anybody was doing innovative or novel analyses.

The coolest science talk I saw was Todd Castoe's talk about mtDNA evolution in snakes. Apparently, the remarkably rapid rate of mtDNA evolution in snakes is due primarily to non-synonymous substitutions in cytochrome oxidase (a transmembrane protein complex that is esstential for cellular respiration). In their recent PLoS One paper, Todd and his colleagues reasonably suggested that this is due to the radical shift in niche and diet that accompanied snake evolution, and their tendency to endure long fasts punctuated by the occasional very large meal in particular.

Structurama: Revisiting models for the inference of population structure

We've previously highlighted updates of Structure, commonly used for inferring population structure, and Distruct, the sister package used for pretty result plotting . Specifically, Structure uses a fixed number of populations (K) to assign posterior probabilities of assigning individuals to populations. It's worth pointing out that Huelsenbeck and Andolfatto (2007) have implemented a nice modification (originally suggested by Pella and Masuda 2006), which can consider K as a random variable that follows a Dirichlet process prior. In other words, it's no longer necessarily fixed to some arbitrary value. The Dirichlet process is nicely explained in the

Structurama manual.

In another homage to a previous post, it's also worth highlighting that it is remarkably easy to use R to manipulate the resulting plots (results are arrayed in columns) and create output very similar to that obtained in Distruct.

R Tip: Indicating Tree Support

I can't take any more of the tiny, unreadable posterior probability and bootstrap support values that I've been seeing on phylogenetic trees at the Ichs and Herps Meeting. Wouldn't it be easier to to put some easy-to-read symbols on the nodes instead of text in 4 point font? I understand why people haven't done this in the past -- it would have required individually replacing text with symbol at each node. Thanks to R, however, this tedious process is no longer necessary. Below are some simple instructions for doing this with posterior probability values included in the '.con' trees that are output from MrBayes using the sumt command (see further details in Paradis' book on R for phylogenetics). If you've never used R for phylogenetics before, you might also want to start at the new R-phylo Wiki.

#First, load the required library.
library(ape)
#Next, get your consensus tree from MrBayes into R.
read.nexus("your_file.con") -> your_tree
#Then, simplify matters by using only the tree with PP values.
your_tree[[1]] -> your_tree
#Tell R to save the resulting tree file in PDF format.
pdf(file="labeled_tree.pdf")
#Generate the vector required to store values for background colors for symbols.
p <- character(length(your_tree$node.label))
#The following three lines define your labeling scheme. p[your_tree$node.label >= 0.95] <- "black"
p[your_tree$node.label < 0.95 & your_tree$node.label >= 0.75] <- "gray"
p[your_tree$node.label < 0.75] <- "white"
#Almost done, you're ready to plot your tree
plot(your_tree)
#Now label your tree:'pch' tells R to use filled circles, 'cex' defines the size of the circles, and 'bg' tells it the name of the vector including the fill colors.
nodelabels(pch=21, cex = .75, bg = p)
#Finally, turn off the PDF writing
dev.off()