New project: Surveying LGBTQ folks working in science

Rainbow leds Photo by Julio Martinez.

I’m pleased and excited to announce that a project I’ve been working on for the last few months is finally ready to launch: A new, nationwide survey of queer folks working in science, technology, engineering, and mathematics.

You may recall that back when I hosted the first Pride Month edition of the Diversity in Science Carnival, one of the recurring themes was that, although we know lesbians, gay men, and bisexual and trans* folks work in STEM fields, our presence isn’t very visible. A few months ago, I started poking around the peer-reviewed literature, looking for studies of LGBT folks in science. I didn’t find much. Studies of LGBT folks in academia either focus primarily on undergraduate students, or consider faculty and staff across all academic disciplines as a group, or they consider very small, localized samples. And careers in STEM extend well beyond the campuses of research universities—what about folks outside the ivory tower?

I brought this up with my friend Allison Mattheis, who just happens to be the perfect person to talk to about this kind of thing: she’s just finished a Ph.D. in Organizational Leadership, Policy, and Development, and who is starting a faculty position in the College of Education at California State University Los Angeles this fall. Together we decided that, yes, there’s a real gap in the existing literature—and we want to close that gap.

So, in our not-very-considerable spare time, Alli and I have been putting together the first stage of a study to answer the questions we have about queer folks in STEM: who we are, what we study, and how our identities have shaped our interest in science and our experiences of working in research. That first stage is an online survey, which we’re hoping to distribute as widely as possible using a strategy called (heh) “snowball sampling”—asking folks who take the survey to pass it on to their friends and colleagues.

As of today, that survey is live and accepting responses at a dedicated website, QueerSTEM.org. If you’re lesbian, gay, bisexual, or trans*, have at least a Bachelor’s or technical degree, and are currently working in a STEM field in any capacity—from grad school to tenure-track faculty to corporate R&D to government employees to teachers—then we want to hear from you. Go take the survey, and then help us spread the word by sharing the short-link http://bit.ly/queerSTEM on Facebook and Google Plus, tweeting it (with the hashtag #QueerSTEM, if you please), or e-mailing it to folks who should contribute.

The plan is to leave the survey open for sampling until we’re satisified that we’ve collected a large, thorough sample of queer folks working in STEM in the U.S. I’ll share prelminary results as they become available—both here and on the blog at QueerSTEM.org—and, with any luck, we’ll ultimately publish what we find in an appropriate scholarly journal. We’re very excited to see the picture of sexual diversity in scientific careers that emerges from this work.◼

Nothing in Biology Makes Sense: Making sense of gene tree conflict across an entire genome

The only illustration in The Origin of Species. Image via Wikimedia Commons.

This week at Nothing in Biology Makes Sense, I discuss my latest research paper, which has just been published online ahead of print in Systematic Biology. In it, my coauthors and I use a genome-wide data set to reconstruct relationships among a couple dozen species in the genus Medicago—a data set that proved to be kind of a challenge.

Using that data, we identified some 87,000 individual DNA bases that varied among the sampled species—single-nucleotide polymorphisms, or SNPs. That’s not a lot in terms of actual sequence data—but considering that every one of those 87,000 SNPs is a variable character, and that most of them were probably spread far enough across the genome to have independent evolutionary histories, it contains many more independent “gene trees” than most DNA data sets used to estimate phylogenies.

To learn how we tackled all those gene trees, and what we found when we did, go read the whole thing.◼

Sequencing: The Next Generation

Wasn't expecting this on my evening jog. Sighted in the woods near Northgate Park, Durham. For real. Photo by jby.

I’m spending the next two weeks in Durham, North Carolina, for the NESCent workshop on next-generation sequencing. Which is to say, a workshop about collecting great big genetic datasets, and what you can do with them once you have them. I’ll be stretching my programming skills to the maximum, and hopefully getting a head start on some ideas I’ve had for good old Medicago truncatula.

If time permits, I may take a page from Carl Boettinger’s literally open lab notebook and post some notes and thoughts here as the workshop progresses, but it’s looking likely to be a full two weeks, and time may very well not permit. ◼

What’s in that dissertation, anyway?

About to take the plunge. Photo by jby.

So, what with getting my sparrows in a row for my dissertation defense on Friday, I haven’t written any new science post for this week. But! As it happens, I have written about most of the component chapters of my dissertation—so in lieu of something new this week, why not check out those posts?

  • The first chapter of my dissertation is a literature review about the phenomenon ecologists call ecological opportunity, and how it may or may not explain big, rapid evolutionary changes. I’ve also written about this topic for the Scientific American guest blog.
  • The second chapter uses phylogenetic methods to reconstruct what yucca moths were like before they were yucca moths.
  • The third chapter presents a mathematical model of coevolution between two species, and determines what kind of interactions—predation, parasitism, mutualism, competition—can cause those species to evolve greater diversity.
  • The fourth chapter is the latest work on my lab’s big study of Joshua trees and their pollinators. The material I’m including in this chapter hasn’t been reviewed and published yet, but you can read the most recent Joshua tree post to learn what we know so far, and what kinds of questions we still want to answer.

Regular posting resumes next week, provided that I pass my defense and the celebrating afterward doesn’t interfere with my blogging capacity.

Coevolutionary constraints may divide Joshua trees

ResearchBlogging.orgScientists love it when the real world validates our more theoretical predictions. It helps, of course, if those predictions are rooted in the real world to begin with. This is more or less what happened in my own research, with results reported in two just-published scientific papers. In the first, which I discussed last week, my coauthor and I showed that some kinds of species interactions can reduce the diversity of the interacting species [PDF]. Today, I’m turning to the second, in which my coauthors and I found exactly this predicted pattern in one such species interaction, the pollination mutualism between Joshua tree and yucca moths.

The new paper, published this month in the Journal of Evolutionary Biology, examines the phenotypic variation of two forms of Joshua tree and the two different moth species that pollinate it. The data show that although the Joshua trees pollinated by different moths are very different from each other, those pollinated by the same moth species are extremely similar [PDF].

Two forms of Joshua tree pollinated by different moth species, seen here side by side, don’t vary much among themselves. Photo by jby.

This is a nice confirmation of the theory paper because it strongly suggests that coevolution between mutualists like Joshua tree and its pollinators works the way the theoretical model assumes it does, with natural selection favoring individuals who best match their partners in the other species.

We already have good direct evidence that selection favors yucca moths who closely match the local Joshua tree population. Joshua tree’s pollinators are entirely dependent on the plant as a food source—they don’t eat nectar or pollen like many other pollinators, but Joshua tree seeds. Female moths lay eggs in Joshua tree flowers, then deliberately pollinate them using pollen carried in unique, specialized mouthparts. When the fertilized flowers develop into fruit, the moth eggs hatch, and the emerging larvae eat some of the seeds inside the fruit.


Scaled comparison of pollinator moth body sizes and Joshua tree pistils. To lay eggs in a flower, moths must drill from near the top of the pistil to the positions marked by dotted lines. Illustration from Smith et al.(2009), fig 1.

If the pollinating moths do too much damage to the flower in the course of laying their eggs, the flower dies off—which helps keep the moths from over-exploiting the relationship by laying lots of eggs or delivering too little pollen. This also means that moths with over-long ovipositors, the appendages used to drill into the flower to lay eggs, may do more damage than necessary and risk killing the flowers they pollinate. As it happens, the two types of Joshua tree have differently-shaped flowers, and the two pollinator species differ in their ovipositor lengths—and moths with overlong ovipositors can’t successfully raise larvae on small-flowered Joshua trees.

The new analysis compares moths’ ovipositor lengths and measurements of Joshua tree flowers from across the entire Mojave Desert, where both are found. The two moth species differ significantly, and so do trees from populations pollinated by different moths species—as we’ve previously found. But because the dataset is more detailed than before, we could also look at how variation is distributed within the two types of Joshua tree and the two pollinator species.

The answer almost feels disappointing: within tree types or pollinator species there just isn’t much variation. In fact, the variation we can detect seems to be random—just statistical noise. That may mean our measurement methods are too imprecise to detect fine-scale patterns in Joshua tree and yucca moth populations. But it’s also what we would expect if Joshua tree and its pollinators were under strong selection to match each other. Natural selection against less-well-matched moths and trees should eliminate heritable variation in moth ovipositor length and Joshua tree flower shape from natural populations. This would leave only non-heritable variation due to causes like developmental errors and environmental effects, which are random with respect to the local plant or pollinator population.

This is the pattern predicted by the mathematical model of coevolution I’ve just published with Scott Nuismer: when coevolution favors closer matching, it should act to reduce variation within the interacting species. The connection was striking enough that we decided to discuss the theory result in a press release about the new Joshua tree study. Coevolutionary constraint might seem to reduce the chances for speciation in interactions like those between Joshua tree and its pollinators. However, constraint might also act to reinforce isolation created by other means; we already have good reason to think that it helps prevent the yucca moths from cross-pollinating the two forms of Joshua tree.

References

Godsoe, W., Yoder, J.B., Smith, C.I, Drummond, C., & Pellmyr, O. (2010). Absence of population-level phenotype matching in an obligate pollination mutualism Journal of Evolutionary Biology, 23 (12), 2739-46 DOI: 10.1111/j.1420-9101.2010.02120.x

Yoder, J.B., & Nuismer, S. (2010). When does coevolution promote diversification? The American Naturalist, 176 (6), 802-817 DOI: 10.1086/657048

Not all species interactions are (co)evolved equal

This post was chosen as an Editor's Selection for ResearchBlogging.orgBiologists have long thought that coevolutionary interactions between species help to generate greater biological diversity. This idea goes all the way back to The Origin of Species, in which Darwin proposed that natural selection generated by competition for resources helped cause species to diverge over time:

Natural selection, also, leads to divergence of character; for more living beings can be supported on the same area the more they diverge in structure, habits, and constitution, of which we see proof by looking at the inhabitants of any small spot or at naturalised productions.
—Darwin (1859), page 128.

In the twentieth century, this idea was extended into suggestions that coevolution between plants and herbivores or flowers and pollinators helped to generate the tremendous diversity of flowering plants we see today. In general, biologists have found that strong coevolutionary interactions are indeed associated with greater diversity.

Yet although there is a well-established association between coevolution and evolutionary diversification, correlation isn’t causation. Furthermore, every species may coevolve with many others, and diversification that seems to be driven by one type of interaction might actually be better explained by another. It has even been suggested that coevolution rarely causes speciation at all.

Species interact in a lot of different ways, as antagonists, competitors, and mutualists. Do all these interactions shape diversity the same way? Photos by jby.

One step toward determining how often coevolution promotes diversification would be to identify what kinds of coevolutionary interaction are more likely to generate diversity. This is precisely the goal of a paper I’ve just published with Scott Nuismer in this month’s issue of The American Naturalist. In it, we present a single mathematical model that compares a wide range of species interactions to see how they shape diversification, and that model shows that coevolution doesn’t always promote diversity [PDF].

The model

The model considers two coevolving species that interact in many discrete populations linked by migration. The environment varies from population to population, and each population is finite, and so may be affected by genetic drift. The simulated critters reproduced in randomly-drawn pairs, with each pairing producing a single offspring whose trait value was the average of its parents’, plus a small random effect to simulate mutation. These conditions mean that the two species would become more diverse even without coevolution—genetic drift and variable natural selection from the environment would both tend to increase diversity. Scott and I were interested in how coevolution changed this “baseline” diversification rate.

To do determine that, we allowed the two species to interact in a variety of different ways that mimic different kinds of real-world coevolutionary interactions. We then tracked the evolution of a single trait in each species that was necessary to the coevolutionary interaction, like a plant’s anti-herbivore defenses, or a parasite’s ability to infect its host, to see whether the trait became more diverse than expected without coevolution. By running these scenarios as computer simulations for hundreds of replicates, we could see what each kind of interaction did on average—a distribution of possible diversification. I’ll discuss the specific results for three types of interactions.

Escalation

Escalation, or “arms race” dynamics, is what many people first think of when they think of evolution. In escalation interactions, each species benefits from having a trait that beats out the other species—plants that produce lots of defensive toxins, for instance, or prey with stronger shells to resist predators’ jaws. Our simulations found that such interactions don’t increase diversity in the two interacting species, as you can see from the graphic below.

When coevolution is mediated by “arms race” escalation, it results in about the same diversity that would evolve without coevolution. Image adapted from Yoder and Nusimer (2010).

The graphic shows two histograms, one overlaid on top of the other. The lower, green histogram shows the distribution of trait diversity, or phenotypic variance, values at the end of each of one thousand replicate simulations of escalation coevolution. The translucent white histogram shows the distribution of phenotypic variance values at the end of each of one thousand replicate simulations without any coevolution—and it almost exactly overlaps the green histogram. This means that escalation interactions do not tend to lead to greater diversity of the interacting trait. This occurred even though the species’ traits “escalated,” getting bigger over time—because phenotypes increased in every population, this arms race didn’t result in more diversity among the populations.

Competition

Now consider competition over resources, as Darwin originally discussed. In this kind of species interaction, natural selection favors competitors that are less similar to each other—not necessarily bigger or smaller, just different. This kind of coevolution is thought to have contributed to the diversification of many different groups of organisms, including anole lizards on Caribbean islands. And in this case, our model found that coevolution boosted diversity quite a bit.

Competition causes many simulations to evolve greater diversity than they would without coevolution. Image adapted from Yoder and Nusimer (2010).

Many individual simulations ended up with more diversity than was seen in any of the simulations without coevolution—that long tail of orange sticking out from behind the white baseline distribution is a signal of greater diversification.

Mutualism

And what about mutualism, in which two interacting species benefit from being better matched to each other? This is the sort of coevolutionary selection apparently arising from the interaction of Joshua tree and its pollinators, which seem to be diverging in tandem. But when Scott and I simulated such an interaction, we found that it usually decreased diversity.

Mutualistic matching leads to less diversity than would otherwise evolve. Image adapted from Yoder and Nusimer (2010).

As you can see, the dark blue distribution of results is substantially narrower than the white baseline distribution, meaning that most simulations of mutualistic coevolution resulted in less phenotypic variance than would evolve in the absence of coevolution. It so happens that the latest analysis of Joshua trees and their pollinators [PDF] actually seems to confirm this prediction, but I’ll discuss that result at a later date.

Coevolutionary selection isn’t the whole story

In some respects these are surprising results—Scott and I found that some kinds of coevolutionary interaction that have been widely associated with greater diversity may actually have no effect on diversification, or act to reduce it. However, there are some caveats to consider in understanding our model. Specifically, we didn’t simulate the actual formation of new species—just the evolution of diversity within species. It’s possible that coevolutionary selection that acts to reduce diversity within species could actually make them more likely to form new species when some other force, like the creation of a geographic barrier, splits the species. I particularly think this is what’s happened in the case of Joshua tree.

In fact, species interactions might often create new species indirectly in this fashion. For instance, plants with seeds evolved to be dispersed by ants seem to form new species more rapidly; but that’s because ants are lousy seed dispersers, not because they create natural selection that directly forms new ant-dispersed plant species. Hopefully, this new model will help to differentiate these direct and indirect effects of coevolution on biological diversity.

References

Darwin, C. (1859). On the Origin of Species. London: John Murray. Full text on Google Books.

Godsoe, W., Yoder, J.B., Smith, C.I, Drummond, C., & Pellmyr, O. (2010). Absence of population-level phenotype matching in an obligate pollination mutualism J. Evol. Biology, 23 (12), 2739-46 DOI: 10.1111/j.1420-9101.2010.02120.x

Yoder, J., & Nuismer, S. (2010). When does coevolution promote diversification? The American Naturalist, 176 (6), 802-17 DOI: 10.1086/657048

Before they were yucca moths

This post was chosen as an Editor's Selection for ResearchBlogging.orgYuccas and yucca moths have one of the most peculiar pollination relationships known to science. The moths are the only pollinators of yuccas, carrying pollen from flower to flower in specialized mouthparts and actively tamping it into the tip of the pistil. Before she pollinates, though, each moth lays eggs in the flower—the developing yucca seeds will be the only thing her offspring eat. How does such a specialized, co-adapted interaction evolve in the first place? My coauthors and I attempted to answer this question in a paper just published in the Biological Journal of the Linnean Society, by reconstructing the ecology of yucca moths before they were yucca moths [PDF].

Continue reading

Interview at Coyote Crossing

Nature writer and photographer Chris Clarke is a great fan of yuccas and yucca moths—he’s working on a book about Joshua trees right now—and so he asked me to answer a few questions about the latest research on the evolutionary history of yucca moths, which was just published in the Biological Journal of the Linnean Society. Check out Clarke’s discussion of the mutualism, and our e-mailed interview, on his blog Coyote Crossing. Look for a post about the paper, with some basic explanation of the methods used in it, right here at D&T next Tuesday.

Ladybird beetle on a Joshua tree leaf. Photo by jby.

When ecological opportunity knocks, does adaptive radiation answer?

ResearchBlogging.orgOne of the most basic questions in evolutionary ecology is, “why are there more kinds of this kind of critter than that kind of critter?” As in, why are there more than twenty thousand species of orchids, but only one species of ginkgo? Why are there hundreds of thousands of species of beetles, but only four species of horseshoe crab? In a literature review just released online—and my first publication as lead author!—my coauthors and I assess the support for one hypothesis: that species multiply because of ecological opportunity.

Biologists interested in the origins of species diversity frequently focus on the phenomenon of adaptive radiation, the process by which a single species rapidly gives rise to many new species, each with different traits adapted to different lifestyles. Darwin’s finches, with their beaks shaped to suit to different foods [$a], are a classic case; the Anolis lizards of the Caribbean, which have repeatedly evolved into a handful of “ecomorphs” with different body sizes and shapes adapted to different perching locations [PDF], are another.

Why are there so many [insert taxon here]? Photos by Bill & Mark Bell (1 & 2), fturmog (3 & 4).

The two most influential theories of adaptive radiation—by G.G. Simpson and Dolph Schluter—have suggested that it results when a species encounters ecological opportunity. Ecological opportunity might be a newly-evolved trait, or a new habitat, or the extinction of a species’ competitors or predators. For instance, a butterfly might evolve a way to overcome the chemical defenses of an abundant plant species, or a plant introduced by humans to a new habitat might find that local pathogens aren’t as deadly to it as the ones in its native range. Ecological opportunities have the effect of granting access to new resources. We have pretty good evidence that this can allow individual populations to increase in number, and even evolve greater diversity—but is that enough to spur the rapid speciation that forms adaptive radiation?

Ecological opportunity ? adaptive radiation

We’re pretty sure about steps 1 and 3. We’re still trying to figure out step 2.

Readers in certain demographic groups may think this sounds like an underpants gnome problem. But it isn’t, exactly. The gnomes’ business model can’t get to from step 1 (collect underpants) to step 3 (profit) because they don’t have a step 2. Evolutionary ecologists, on the other hand, already have their step 3 in the phenomenon of adaptive radiation. Ecological opportunity looks like a good prospect for step 1 precisely because it suggests some plausible options for step 2.

When a population encounters ecological opportunity, the new habitat, new trait, or extinction of antagonists provides access to new resources, and relaxes natural selection on the population. This leads to three phenomena usually grouped together under the term ecological release

  • The population experiences density compensation—more individuals can live in a particular area, creating stronger competition within the population.
  • Because of this stronger competition within the population, or because there isn’t much competition from other species, members of the population venture into new habitats, or use new food resources.
  • The population becomes more diverse, either because of the relaxed selection, or because of competition-driven selection for using new habitat and new resources.

One or more of these three aspects of ecological release turn up whenever populations find new food resources, or escape predators and/or competitors. Density compensation has been widely observed in populations colonizing new habitats, especially islands; and experiments with sticklebacks and fruit flies [$a] suggest that the stronger competition resulting from density compensation can spur the population to become more diverse in its use of resources. Bacterial populations can even evolve different specialized forms—adaptive radiations in microcosm—when introduced to new food resources.

Anoles show signs of density compensation on Caribbean islands—is that the reason behind their diversification? (Pictured: Anolis oculatus.) Photo via WikiMedia Commons

But where’s the speciation?

However, the evolution of bigger, more diverse populations is not the same thing as the evolution of new species—and that’s what adaptive radiation is really all about. These changes resulting from ecological opportunity might directly promote speciation if stronger competition leads to disruptive natural selection. Similarly, the competition-driven incentive to colonize new habitats or exploit new food sources could expose some parts of the population to different forms of natural selection, eventually causing them to evolve into specialists on the new resources. Finally, even if speciation only happens when natural barriers cut off migration, maybe larger, more variable populations provide more diversity for vicariance events to divvy up.

This is all pretty speculative, though. We still don’t know how often—or how rarely—divergent natural selection contributes to making new species. One way to deal with this is to approach the question from the other direction: look backward at the history of existing species, rather than following what happens to populations immediately after ecological release.

A backward-looking approach might use statistical analyses of the evolutionary relationships between living things to identify points in time when species formed unusually fast, and try to identify the cause. Some of my coauthors from the review paper recently published an analysis of the evolutionary tree connecting all vertebrates, and found that speciation rates increased around the origins of the largest group of birds, a large portion of the lizards and snakes, and non-marsupial mammals, among others.

This is very much a starting point, but maybe by complementing similar studies with research on populations currently evolving in response to ecological opportunity, biologists can work our way closer to understanding the origins of the endless and beautiful forms of life on Earth.

References

Alfaro, M., Santini, F., Brock, C., Alamillo, H., Dornburg, A., Rabosky, D., Carnevale, G., & Harmon, L. (2009). Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Nat. Acad. Sci. USA, 106 (32), 13410-4 DOI: 10.1073/pnas.0811087106

Bolnick, D. (2001). Intraspecific competition favours niche width expansion in Drosophila melanogaster. Nature, 410 (6827), 463-6 DOI: 10.1038/35068555

Blumenthal, D., Mitchell, C., Pysek, P., & Jarosik, V. (2009). Synergy between pathogen release and resource availability in plant invasion. Proc. Nat. Acad. Sci. USA, 106 (19), 7899-904 DOI: 10.1073/pnas.0812607106

Grant, B., & Grant, P. (1989). Natural selection in a population of Darwin’s finches. The American Naturalist, 133 (3), 377-93 DOI: 10.1086/284924

Kassen, R. (2009). Toward a general theory of adaptive radiation: Insights from microbial experimental evolution. Annals New York Acad. Sci., 1168 (1), 3-22 DOI: 10.1111/j.1749-6632.2009.04574.x

Losos, J. (1990). Ecomorphology, performance capability, and scaling of West Indian Anolis lizards: An evolutionary analysis. Ecological Monographs, 60 (3), 369-88 DOI: 10.2307/1943062

Schluter, D. 2000. The Ecology of Adaptive Radiation. Oxford University Press. Google Books.

Simpson, G.G. 1949. Tempo and Mode in Evolution. Columbia University Press. Google Books

Svanbäck, R., & Bolnick, D. (2007). Intraspecific competition drives increased resource use diversity within a natural population. Proc. Royal Soc. B, 274 (1611), 839-44 DOI: 10.1098/rspb.2006.0198

Wheat, C., Vogel, H., Wittstock, U., Braby, M., Underwood, D., & Mitchell-Olds, T. (2007). The genetic basis of a plant insect coevolutionary key innovation. Proc. Nat. Acad. Sci. USA, 104 (51), 20427-31 DOI: 10.1073/pnas.0706229104

Yoder, J.B., Des Roches, S., Eastman, J.M., Gentry, L., Godsoe, W.K.W., Hagey, T., Jochimsen, D., Oswald, B.P., Robertson, J., Sarver, B.A.J., Schenk, J.J., Spear, S.F., & Harmon, L.J. (2010). Ecological opportunity and the origin of adaptive radiations. Journal of Evolutionary Biology DOI: 10.1111/j.1420-9101.2010.02029.x

While I was out

Things that happened while I was in the middle of the Nevada desert harassing Joshua trees:


Yeah, it was worth it. Photo by jby.