Searching for Ronald Fisher (at #Evol2012)

This post is a guest contribution from John Stanton-Geddes, a postdoctoral associate in the Department of Plant Biology at the University of Minnesota. John currently studies the genetic architecture of legume-rhizobium symbiosis in Medicago truncatula, as part of the same lab group as NiB contributor Jeremy Yoder.

If you’d like to write a guest post for Nothing in Biology Makes Sense!, email Jeremy.

Two weeks ago I was fortunate to attend the Evolution Society Conference in Ottawa. I saw many great talks, missed even more great talks and had the opportunity to hobnob with many luminaries of evolutionary biology. One theme that emerged through the meeting was “The genetic basis for [insert trait here]. While this goal of mapping phenotype to genotype has been a primary goal of many evolutionary ecologists since the first QTL mapping studies, it has recently come under strong criticism, notably in a fantastic paper by Matthew Rockman in the journal Evolution last year, but also by Pritchard and Di Rienzo 2010 and in a forthcoming article by Ruth Shaw (full disclosure: Ruth was my PhD advisor) and Mike Travisano. Here’s my take on the current state of Genotype to Phenotype (G-P) research from Evolution 2012, and where I’m excited to see it go.

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#Evol2012: My Final Impressions

Evolution this year was fantastic! So many wonderful talks and posters, THOUSANDS of evolutionary biologists and Ottawa was the perfect venue (in my opinion). To wrap up these four days, I’ve listed below some of my personal highlights (and a few lowlights).

** This video introducing how parasites can affect host behavior, which David Hughes used to introduce the ESEB Symposium (“Influential symbionts: Master manipulators of adaptive host behavior”), was very memorable. The first speaker, Sven Pettersson, had an entertaining anecdote about how babies are parasites and they scream at birth because they’re go from a cozy, warm place to being squeezed through a tube out into a cold foreign place, after which the food tube to their host and only world they’ve ever known is disconnected. This, he said, is our first introduction to anxiety and our microbes may begin to influence us that exact moment.
** The SWEEET symposium featured women with PhDs that now work outside Academia. The talks I attended didn’t apply strictly to women (in a good way) and I found it kind of soothing to hear Lalita Acharya talk about her career with NSERC and Jennifer Carpenter‘s journey to journalism and teaching, because that’s what they wanted to do. The question/answer portion of the symposium held no awkward pauses, as many people had excellent questions. The panelists never regretted getting a PhD before heading out into “the real world” and all believed it had been a major asset in their chosen careers.
** The Jasper Loftus-Hills Young Investigator Awards (sponsored by ASN) was terrific! Rowan Barrett talked about massive field experiments in Sticklebacks and mice; Jen Perry talked about sexual conflict in three (yes, three) insect systems and Liam Revell talked about his latest conquests in R and phytools.
** Lunch was provided the first three days and I thought that was really convenient. It allowed lunch to be a time of chitchat and meetings instead of rushing about trying to make it back to the conference center in time. I hope this continues in the future (even though obtaining pretty good food close to the OCC was relatively easy).
** Peerage of Science intrigues me and anyone who didn’t stop by their booth should consider checking out the webpage (or our previous post on the topic here). Turning peer review into something we choose to do (and get recognized for doing well) instead of something we have to do (and all time spent goes away into anonymity) sounds like a good direction to be heading.
** I am now inclined to join Twitter – the tweets were entertaining and surprisingly useful!
** The Ottawa sound and light show! This was an absolutely amazing presentation on the history of Canada, projected onto Parliament. I’ve never seen anything like it!

** The cost of alcohol, am I right?
** I understand the environmental reasons for no swag, but maybe having a pre-set (or pre-ordered?) number of coffee mugs would have been successful way to balance wastefulness and useful awesomeness (i.e., “I wanted a coffee mug”).

Anyone else have highlights to share? Can’t wait until next year, y’all!

#Evol2012: Puffin poop and predation pressures


A final few propitious presentations from the Evolution meetings in Ottawa:

Kirsten Bowser is running puffin faeces through next-generation sequencing to identify what the adorable seabirds eat—and she’s already found some prey species that wouldn’t be easily identified just by watching what puffins bring back to their nests.

Brian Counterman showed that hybridization between subspecies of the South American butterlfy Heliconius erato with different wing patterns can transfer wing patterning between subspecies—mostly by transferring a single chunk of DNA that doesn’t code for any protein, but performs a regulatory function. What’s more, the same region is being moved between multiple pairs of hybridizing H. erato subspecies.

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#Evol2012: Competitive flowers, bleached lizards, burrowing mice, and robust invaders

Iochroma fuchsioides. Photo via Wikimedia Commons.

It’s already the third day of concurrent sessions a Evolution 2012, and I’m starting to get science overload. And I still have to present my own science tomorrow! But here are some more cool results I saw Sunday and Monday:

Vera Domingues presented a study of beach mice, which have evolved lighter fur after colonizing the sandy dunes of barrier islands off the Gulf Coast. As in many other animal species, a mutation at the pigment-related locus MC1R explains a lot of the color change; Domingues showed that in the population of barrier island mice, every copy of the mutant, “light color” form of MC1R is descended from the same ancestor, and that DNA sequence near the mutation resembles sequence from the ancestral population on the mainland—which suggests that the original mutant predates the move to the barrier islands.

Richard Lankau showed how garlic mustard, an invasive weed in the United States, uses chemical warfare to out-compete native plants. Garlic mustard secretes chemicals into the soil that suppress the growth of other plants, and alters the environment for beneficial mycorrhizal fungi—and plants grown with competitors produce more chemicals. But native plants can adapt; samples of a native competitor collected from sites invaded by garlic mustard were better able to survive near the invader than plants from non-invaded sites, and were less able to benefit from mycorrhizal fungi in soil that hadn’t been exposed to garlic mustard chemistry.

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#Evol2012 Nothing in biology makes sense, except in the light of good models.

Mathematical models are a critical part of evolutionary biology. Sometimes they are used to analyze data, sometimes they are used to make theoretical predictions, but in either case, they represent the purest expression of what biologists suppose about the relationship between the patterns they observe in the natural world and the processes that produce them. As a result, they are often at the core of the most important presentations of research in the scientific literature and at professional conferences. Unfortunately they also tend to be very abstract, and can be a stumbling point in those presentations*.

The conference Evolution 2012 has now been raging for three days, and the air is thick with fascinating models, and also incomprehensible ones, so I wanted to take a moment to highlight a couple of speakers who I felt presented a mathematical model in an exceptionally clear and excellent way.

First, Carl Boettiger, in his half hour talk “Detecting evolutionary regime shifts with comparative phylogenetics.” He spoke about developing a model to analyze trait data in a phylogenetic context to ask whether the evolution of the pharyngeal jaw in Labroid fishes freed them from the suction feeding habits of their ancestors and allowed a burst of morphological and ecological diversification in the group. This question, whether a “key innovation” can release a constraint and result in diversification is a long-standing one in evolution, and no explicit mathematical model capable of being applied to real data had been developed to address it. After explaining this, Boettiger launched into a comprehensive, clear explanation of the derivation of his model, what each of the terms meant and then proceeded to analyze it. Perhaps not surprisingly, he found that the pharyngeal jaw did indeed seem to serve as a key innovation, releasing a constraint and resulting in diversification. (Boettiger’s talk is, amazingly, already on-line if you want to check it out)

The second was Gideon Bradburd. Bradburd gave a 15 minute talk “A Bayesian method for estimating genetic differentiation due to isolation by geographic and ecological distance.” Identifying the factors that cause population divergence is a key task in evolution, ecology and conservation biology. One of the ways to go about doing this is to look for correlations between population genetic divergence and geographical or environmental factors. One of the typical ways that people have gone about doing that is by using a statistical method called a partial mantel test. Unfortunately, the partial Mantel test has some undesirable statistical properties that cause it to be misleading under some circumstances. Enter the new model. In just a few slides, Bradburd clearly explained the data required, the math behind how he models genetic divergence, and how the explanatory variables fit in. He then used the model to ask whether elevation influenced genetic divergence in the wild ancestor of corn, teosinte. He found that the model appeared to perform very well and give strong evidence that elevation was important.

Talks like these make the meetings fun to attend, and represent the kind of clarity I strive for in my own presentations.

*See the much discussed recent paper in PNAS (Fawcett and Higginson 2012), in which it is shown that the density of equations in a scientific publication has a negative impact on its citation rate.

#Evol2012: Inversions and spruces and tethered snails

Some highlights from the first day of concurrent sessions in the Ottawa Convention Centre, on Saturday the 7th:

Mohamed Noor described the importance of chromosomal inversions—literally, chunks of DNA code that have been flipped end-to-end within the chromosome—in reproductive isolation between two species of Drosophila fruit flies. Inversions have the interesting effect of preventing recombination from breaking up groups of genes within the inversion; but some recombination is still possible, if very rare, and it should create predictable patterns of genetic divergence across the inverted region.

Most of the major phenotypic differences between Drosophila pseudoobscura and D. persimilis map to three regions that are inverted in one species relative to the other—Noor presented work from his lab that finds very fine-scale differences in genetic differentiation across the inversions, consistent with predicted variation in recombination. In a much-retweeted line, Noor pointed out that it’s possible to think of species as “groups of alleles in long-term association.” Chromosomal inversions being one way to help maintain those associations, plainly.

Sitka Spruce - Wild-Pacific-Trail-20100606-IMG_1148.jpg

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#Evol2012 Molecular Ecology Symposium: Your overconfidence is your weakness

I arrived in Ottawa a day before the proper start of the Evolution 2012 meetings so as to attend the symposium hosted by the journal Molecular Ecology, which was almost entirely devoted to the joys of genome-scale data collected from wild populations of our favorite species—and what we can and can’t learn from it. This, readers of this blog will recall, is one of the biggest changes in our field in the last few years.

Yes, your NGS-Star has collected six scrillion SNPs—but do you know how to analyze them?

Alex Buerkle kicked things off with the intersting question of how much data, exactly, do we need? It’s easy (given the funding) to obtain a lot of DNA sequence fragments from next-generation sequencing (NGS) methods—but is it better to collect lots of data from a few individuals (and thereby have high confidence in the data) or collect less data from more individuals and accept that there will be some uncertainty in the data for any one individual? Buerkle argued that the second option is preferable; it’s possible to account for uncertainty in your analysis, but if you don’t sample enough individuals, you can miss rare gene variants.

There was a tension between confidence and uncertainty in these great big genetic datasets running through the whole symposium. Buerkle also noted that patterns of differentiation and diversity across the genomes of related species can be very complex—and in the question and answer session, it was pointed out that complexity and noise can be hard to differentiate.

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