Holidays 2013: Research Update

Tags

evolution, figshare, open access, open access journal, PeerJ, PLoS Biology, research, science, sexual selection

Merry Christmas, it’s time for an update on my research. My first project on age-dependent sexual signals, long nicknamed Project Zero during the four years (!) I’ve been working on it has been published by PeerJ. Not only published, but featured on the homepage and the blog. There’s an interview there where you can read all about it, so I will skip the details here. This journal is open access, so you can read the article for free. You can also download the simulation code and all the data for the figures at figshare.

My next research project has been submitted to Ecology and Evolution, another open access journal, published by Wiley. I have already put the manuscript on ArXiv, so go read it!  I also presented this at the Evolution conference over the summer.  The scenario I describe in this paper is that when females have preferences for older males, as they would for an age-dependent trait, they will inevitably encounter deleterious mutations. Since mutations pile up in the male germ line with age, more attractive, older males may not necessarily yield more fit offspring.  If the female preference is directly costly, then natural selection may eliminate the preference.  What I found instead is that germ line mutation actually supplies the necessary genetic variation for selection to act, in other words, it reinforces sexual selection and further facilitates evolution of extravagance.

I’m still working through the math on a third paper.  The subject here is the evolution of female choosiness as a function of age.  Some studies show that females are more choosy when they are older, while others show that females are more choosy when they are young.  There are arguments on both sides suggesting how selection produces these patterns.  We just had a lab meeting where my colleagues helped me to clarify how to build the model.  My hope is to have this one ready for publication sometime in the early spring.

Another paper with my name on it was published in May, although it has been on the web and finished for so long that I didn’t notice its publication in PLoS Biology, the flagship open access biology journal. This article was a collaboration with people I mainly met on Twitter. We wrote an opinion piece on how biologists of all disciplines, but especially in ecology and evolution, could embrace putting their work online at preprint servers like ArXiv, Figshare, PeerJ Preprints, and F1000Research. This practice is common in mathematics and physics, and although it’s gaining popularity in biology, most biologists I know recoil in disgust at the thought of putting their work online before it’s peer-reviewed. Well, actually these days the younger scientists respond with interest rather than recoil in shock.

The funny thing about peer review is that it takes a really long time to get stuff published.  By “published” I mean “done with.”  I have been working on the first project above for over four years if you count the time I spent programming the multilocus genetics library.  I have submitted it to four journals, and it was outright rejected from the first three for various reasons, most of them not scientific.  What I don’t like is that I would like to spend time working on newer things.  I’m simply interested in new things now.  This reminds me of the situation in Pink Floyd’s 1980s and 1990s tours, where some fans wanted them to play their classics, and they wanted to play their new music (some of which they actually put a lot of effort into writing, and thought was better music, but what do they know?). However, I am grateful for all the chances I’ve had to revise that paper, since my understanding of science and how to do it are totally different four years later.  Even in the weeks since I submitted the paper to PeerJ and got the (very helpful!) reviews back, I have found better ways to express the ideas in the paper and improve the writing.  It’s a double-edged sword, and I’m not quite ready to do away with it.

The other drawback is not getting the research into a place where people can see it.  I’ve been showing that model to people for all but six months of the time I’ve been working on it, and it has taken another three years to get one step closer to publication.  That’s why we have arXiv and figshare.  People can see it pre-peer-review and get ideas from it.  They can even cite it.

Related articles

• Figshare for sharing academic papers with their datasets (jilltxt.net)
• A book chapter I can’t share with you but some figures that i can, thanks to Figshare (biogeopen.wordpress.com)
• New Preprint Server Aims to Be Biologists’ Answer to Physicists’ arXiv (news.sciencemag.org)

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Sexual selection with age-dependent mutation

Tags

evolution, Genetic variation, mutation, research

I recently got the opportunity to give a talk at both UNC and Eastern Carolina University on my current research project. The talk is available over at figshare if you’d like to scrutinize the details. I’ll give you some of the background here since the talks have no narration.

For starters I’m interested in males that provide only potential genetic benefits to their offspring; I’m also looking at the model where females are assessing male genetic quality based on a male morphological trait (such as an ornament, weapon or body size). This means that females expect to have offspring that are both more sexy and who survive better when she mates with a highly ornamented male, rather than a less well-ornamented male. The problem in this setting is the “lek paradox,” where eventually a female will do just as good to mate randomly as she would to be choosy, since there will be no genetic variation in ornamentation or condition. Usually in models we use mutation to maintain genetic variation for condition; I think I’ve found that being more specific about the type of mutation gives us a good theory that will resolve the lek paradox (yet again!).

The bighorn sheep is Alberta’s provincial animal (Photo credit: Wikipedia)

My question specifically deals with the scenario where males all start out with the same trait value and then grow that trait throughout their lives (I call this an age-dependent trait). Females can’t tell who is in good condition when looking just at young males. Several models have shown that age-dependent traits are a good strategy for males with relatively good health. They will have more matings over their lifetimes if they ramp up their signaling over their lifetimes. One particular model showed that if males are in good health, they should delay as long as possible, so as not to incur the wrath of natural selection, until they have had lots of opportunities to mate. Lower condition males should adopt a “hope I die before I get old” strategy and be as sexy as possible, as soon as possible.

The problem with these models is that they assume the full range of strategic variation is present in a particular population. They don’t represent changes over time; they just say what the best strategies are. I showed in a previous model that in a population-genetic simulation an age-dependent trait that starts out small will lead to the evolution of preferences and age-dependent traits. This makes sense from a dynamical point of view because selection is weaker at older ages: since older-aged males are only a small fraction of the population, any genetic variation in those males will not contribute much to the whole pot of variation. Selection can’t do much with genetic variation in older males, hence they are relatively free to be as extravagant as they want.

But what if old, sexy males are carrying mutations in their sperm that females cannot detect? I assumed that males will contribute harmful (deleterious) mutations to their offspring at a rate that is basically their age times a per-age mutation rate. I also assumed that the trait increases linearly. This is not realistic, as a lot of traits grow up to a point and then stop or even decline in old age. However, it gets the point across that young males are similarly sized and old males vary in their traits depending on their condition.

The results I have as of yet show that this process actually ensures continued genetic variation in the overall condition trait. The equilibrium female preference hovers above the equilibrium trait size, ensuring that females will always be going for the older, sexier males that carry mutations in their sperm. Mate choice therefore reinforces the process that keeps genetic variation in the population. I hope this result holds up under further mathematical scrutiny, because it’s a nice surprise.

I have a few snags to work out before I write this up; the feedback I got from the talks was invaluable. A few people had really great ideas, like a female strategy to screen sperm for deleterious mutations, and a research strategy to scan sperm samples for such mutations. Although my first reaction was “that’s going to be a lot of work!” my host chimed in that someone actually is doing this already. Wow!

Related articles

• Two studies reveal genetic variation driving human evolution (medicalxpress.com)
• New technique can sequence entire genome from single cell (nextbigfuture.com)

Student-Centered Teaching

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Education, Philosophy, research

I recently prepared an essay on my philosophy of teaching. Part of my rationale for starting this blog was to explain to friends and family members how I do my research. Teaching is really the core of what I do, however, so I should also spend some time talking about teaching. I prepared the essay for two reasons: firstly, I think it’s important for students and other teachers to know where I’m coming from, and what they can learn about concepts in education. The other main reason was to have some kind of a record for myself of all the research I’ve done on the topic, and also construct a set of working hypotheses to guide my teaching work.

The philosophy has three main hypotheses: (1) children are born motivated, i.e. motivation is not something that teachers have to put into them; (2) students can, and should be encouraged to self-assess, i.e. to find their own answers; and (3) research and teaching are essentially the same activity, not things to divide up a scientist’s schedule. The corollary to all these is that the teacher’s main jobs are (a) to set up the right environment for learning and (b) remove obstacles for learning.

Motivation is probably the most important aspect. Motivation is a matter that I often find troubling to talk about with my fellow educators: I’m simply surprised how often I find that scientists think that their own topics are so boring that they need to get students interested. The students are interested already! For one reason or another, they want to learn. Many of them just love learning.

Self-assessment is easy to implement, encourages students by making assessment part of the discovery process, and offers genuine, highly informational feedback. The main way I do this is by never answering a question directly: I tell students to test their own logic, do their own research and figure out if their particular guess is “right.” This gives them more information, is more fun, and incorporates more learning than simply checking “right” or “wrong” and giving them a grade.

Research and teaching are bound together like painting and seeing. I find this to be a necessity: I just can’t teach something unless I apply the same learning attitude as I do when I’m doing research. All I have to do to teach students is demonstrate the approach (show them!). Last semester when I was teaching a topic I had never studied myself (cell and developmental biology) I showed them the approach that I was currently taking to learn the topic. There is no good reason we can’t have the same attitude about our large-scale research projects.

Carl Rogers who developed student-centered teaching along with his client-centered therapy (Photo credit: Wikipedia)

I want to emphasize that this is my philosophy of teaching. I am not suggesting that anyone wholeheartedly take on my own philosophy. There are lots of teaching philosophies out there in science education, and I’m glad to see people experimenting. The lecturer I’m working with this semester is one of several who has a reputation for experimentation, and it’s fun being in that setting. If you wanted to pick a teaching philosophy out of a hat, you could. You would be better off to work closely with someone who has a definite philosophy, and then adapt that philosophy based on your own experience.

Much of the research I’ve read falls under the heading of “motivational psychology,” which is largely concerned with (depending on perspective) how to motivate people, or what motivates people. I would suggest reading Alfie Kohn‘s classic book Punished by Rewards for a start on that topic. Much of our theory of education and governmental policy is based on operant conditioning, an adaptation of animal training that was elevated to the status of an all-encompassing scientific theory. Kohn’s book challenges the logic of that in education, parenting and the workplace.

Here’s an excerpt from my teaching philosophy:

Observing children, students and my own learning history has shown me that the energy to learn comes from within students themselves. Spending time at the playground and with my own children, I see that children don’t need to be taught: do children need to learn from a book how a family works before they play house? Children set up organizations, create dramas and negotiate conflicts by figuring it out as they go. They also conduct controlled experiments, especially when playing alone: “If I roll the ball this way, how fast does it go? What if I roll a bigger ball down the same track?” This is exactly what Galileo actually did, and kids do it all the time. Richard Feynman first discovered inertia while playing with a ball and a toy wagon before he was five years old. Note that I’m not saying children would do these things without being told about them; they are not born with the concepts needed to play house or form a club on the playground. But they do figure out how to do it without instruction.

The cost of reproduction in birds

Tags

biology, birds, evolution, Genetic drift, Natural selection, research, science

The concept of trade-off is paradigmatic in life-history theory. an organism can only acquire a finite amount of energy in its lifetime, so it must “choose” how to allocate that energy to growth and survival or reproduction. Reproduction is assumed to be costly so that individuals who spend more on reproduction, for example by laying more eggs, will not survive as well. We suppose that over evolutionary time, natural selection will act on genetic variation for these allocation decisions, so that the sequence of decisions over an individual’s lifetime will represent an optimal allocation of resources.

Unfortunately this intuitively appealing idea has been very hard to find in nature. In fact, many studies have come up with positive correlations: animals that reproduce more tend to survive better. A recent study by Eduardo Santos and S. Nakagawa found that this trade-off was almost impossible to detect in most studies, or non-existent altogether. In a meta-analysis of brood supplementation studies (researchers added eggs to the nests of breeding birds), they found little impact on survival. Their result held across all the major taxonomic groups of birds, the biggest division being between passerines (songbirds, crows, flycatchers, etc) and non-passerines (ducks, loons, parrots, woodpeckers). Regardless of overall “lifestyle” the birds tested in most studies were able to withstand the hypothesized survival cost of additional eggs dumped on them by researchers.

Why would this be the case? As always there is the possibility that the studies were poorly designed, or that brood supplementation is not a good way to test for a trade-off. Particularly, brood supplementation only taxes the parents of their ability to defend and feed offspring; it does nothing to the energy that females put into egg production. The other possibility is that adult birds just don’t put that much effort into reproduction in the first place. Perhaps survival is far more important. The trade-off is still there, but it’s just not important for most birds.

The hypothesis that life is just not as Malthusian as we have often supposed in evolutionary biology intrigues me greatly. If evolution acted in the “well-oiled machine” manner that many laypeople and professional scientists find appealing, then we’d expect selection to push annual reproduction right up to the level allowed by the trade-off. What studies have found is birds putting minimal effort into reproduction, parenting or anything that affects their survival. This means that selection is a lot weaker than we expect: this gives genetic drift a lot more room to account for polymorphism. It also makes sexual selection more plausible: if most species have fairly conservative lifestyles and selection for survival is not that strong, then males (or females) can afford costly ornaments.

An unrelated study also appeared this week that is getting a lot of press: researchers in Iceland found a strong relationship between the age of fathers and mutations passed to their offspring. This is the first study to quantify the per-year effect of paternal age on offspring mutations in humans, so it’s a pretty big deal. I will talk more about this in a future posting since it’s related to my dissertation research, but in the meantime, go read the article and enjoy the flurry of debate surrounding it.

E. S. A. Santos, S. Nakagawa (2012). The costs of parental care: a meta-analysis of the trade-off between parental effort and survival in birds Journal of Evolutionary Biology, 25, 1911-1917 DOI: 10.1111/j.1420-9101.2012.02569.x

Related articles

• Kiwis in ‘severe reproductive bottleneck’ (stuff.co.nz)
• Parent-offspring Conflict: Time to Listen to the Argument (psychologytoday.com)
• Better looking birds have more help at home with their chicks (esciencenews.com)
• Older fathers pass on more mutations (newscientist.com)

The Handicap Principle

Tags

biology, birds, evolution, research, science, sexual selection, theory

Researchers use sexual selection theory to attempt to explain traits that are exaggerated, seemingly unrelated to survival and seemingly costly. I call these characters “ridiculous.” Almost every sexual selection talk starts with a collage of absolutely ridiculous-looking sexual ornaments and armaments. Most biologists have this “biological diversity slide” near the beginning, but other biologists have theirs filled with perfectly sensible looking animals. Animals that are clearly built for survival. Sexual selection, on the other hand, seeks to explain things like this:

Male Blue Peacock in Melbourne Zoo, Australia. (Photo credit: Wikipedia)

One way to explain these extravagances is not to use sexual selection at all, but to say that it is, indeed necessary for survival. In fact, the whole idea of sexual selection arises out of a Bob McGuire argument: “Come on, that can’t possibly be necessary for survival! Chuck, you’re crazy.” Bob McGuire was a timeshare salesman who tried to talk Dr. Adamson and I into buying by saying things like “Come on, you’re not gonna take a baby camping, come on!” These appeals to disbelief are rather common in science, not just in anti-science.

The alternative looks at how ridiculous-looking traits do impact survival: if they are really costly, perhaps that cost relates to their value as signals. Perhaps they tell females something. Perhaps the cost itself is really important, and females should pay attention to that cost. How would a signal convey all that?

These important things to consider are fitness components. We talk a lot about fitness, but there’s no one measurable quantity that actually is fitness. Survival forms one fitness component, attractiveness forms another. When females want to have attractive offspring, one way to get them is just to mate with an attractive male: “You mate with a good-lookin’ bird like me, you’ll have good-looking babies, and good-looking grandbabies and so on. It’s a win!” The trait doesn’t need to be particularly costly to tell females that their offspring will be attractive. But what if the offspring don’t survive to mate?

Handicap to the rescue!

A really costly signal, on the other hand, could tell females that a male not only is attractive, but he’s able to survive well. The signal tells females that males carrying them are able to survive well because their trait does not impact their health as much as it would someone who was less healthy. This is called the handicap principle: if a male shows a handicap, he must be well-adapted and healthy, or else he wouldn’t be able to handle the cost. This idea was first proposed independently by Bob Trivers and Amotz Zahavi, and roundly rejected as completely preposterous. The 1989 edition of The Selfish Gene contains the typical argument: if it’s costly, then it’s costly and it will be selected against.

However, in 1990 Alan Grafen showed that handicap signals are evolutionarily stable: if everyone in the population is using a costly signal, then someone using a non-costly signal to convey the same information can’t make a living. If a signal is truly costly, then you can’t fake it. Grafen showed with his characteristic style that this applied to communication across the board, not just in sexual signals. Some researchers go so far as to say that every signal is a handicap, although I think “the finger” is enough of a counterexample. Incidentally, “the finger” did originally have meaning: it meant you had never been captured in war and were still able to shoot an arrow. I think this meaning has been lost since the Battle of Agincourt.

Kinds of handicap

There are a few different ways to have a handicap. One is called “pure epistasis” or “Zahavi’s Handicap.” In this case, every male grows the same trait, but it kills less-healthy males more often than it kills more healthy males. This is the version that Zahavi came up with originally, and it was widely ridiculed. It turns out the ridicule was partially correct, and this sort of handicap doesn’t really work. Zahavi’s handicap doesn’t work because after selection for survival, all males will start to look pretty much the same, and then females have no incentive to choose among males (a female who mates randomly will get the same good genes as one who goes to the trouble of choosing). Then the trait is useless, and costly, and will be lost from the population.

The second way is the “revealing handicap.” In this case all males grow the trait, but the signal itself has much better quality in more healthy males. The caricature is of a peacock’s tail: all males grow similarly-sized tails, but less healthy males let theirs drag on the ground and get infested with mites. It doesn’t kill them, but it’s not as shiny and dazzling and sexy as it would be for a healthy male. In this case the signal itself tells females how healthy a male is. This kind of handicap can lead to an exaggerated male trait, as long as there is sufficient genetic or environmental variation for the tail dragging on the ground.

The third way is condition-dependent signaling: males who are of good health grow larger traits and are less impacted by the costs of carrying the trait. The nice thing about this theory is that everything seems to work as far as genetic variation. Females benefit by mating with showy males, from having more healthy male and female offspring. Also, if the trait is condition-dependent, there is plenty of mutation in “condition,” which is basically the sum of all the selective forces across the genome. There should always be plenty of genetic variation in condition, so females should always benefit from being choosy.

I study how condition-dependent signaling plays out over the lifespan. If a male is really healthy, he can expect to live a long time, and he could potentially conserve his resources until he gets older. By growing his trait over a long period of time, he would have more opportunities to mate, and be just as sexy in middle- or old-age when selection is less intense. This does present a few problems in how the traits would actually change over time. If selection is intense enough, a male might be killed even for having a small trait, and once he gets older, his sperm will be harboring more deleterious mutations. I’ll go into more detail about these in future posts.

Related articles

• Genetic variation and sexual selection: an introduction to my research (lxmx.wordpress.com)
• What human traits were evolved only for sexual attractiveness? (io9.com)
• Its All About the Mane! (pathpics.wordpress.com)
• Sexual selection in humans: some interesting recent work (lxmx.wordpress.com)

Sexual selection via sensory bias

Tags

biology, evolution, research, science, sexual selection

We study sexual selection mostly to understand the evolution of costly, extravagant traits in males, for example flashy colors. Another reason is that sexual selection may play a role in the formation of new species (speciation). I mostly study sexual selection by female choice, meaning that certain females may prefer these flashy males; one way this could happen is that females might prefer particular males simply because they are conspicuous, or they look like food. This is called sensory bias. The simplest example is the guppy Poecilia reticulata where the females display a preference for orange objects because that’s what they eat. Males mimic this orange color and attract females. This is interesting because natural selection directly sets up the female preference: even if the preference has a cost, natural selection still favors its evolution, because it helps females survive. This could make new species form because different perceptual biases could be favored in different places.

Recent Servedio Lab graduate Alicia Frame asked whether sexual selection can then pick up these preferences and exaggerate them beyond what natural selection calls for. Sexual selection here would be indirect, meaning that the preference itself is no longer acted upon, but sexual selection on the attractive male trait could make the preference stronger. I’ll explain the mathematical details in another post, but basically whenever there’s direct selection on a trait (selection favors a trait), there is indirect selection on other traits that correlate with it. In this case the traits (the signal and the preference) occur in different individuals, but it’s simpler to think of two traits on the same individual organism. A simple example would be size of the brain and size of the body in humans. If there was selection to have a bigger brain in early hominids, then individuals with bigger bodies would also be favored by selection.

Alicia and our advisor Maria used a newer version of a biologically realistic model: there are “yellow fish” and “blue fish” that live in either yellow or blue environments. Males that contrast with their background environment are more conspicuous and thus more easily spotted by predators and preferred by females. Indirect selection is caused by correlations between traits. To have a correlation, you need lots variance in both correlated traits. What Alicia and Maria found was that when all females are choosy (the preference is there because of natural selection), there is not enough variation in the male trait for indirect selection to strengthen the female preference. This was true even when the male trait mutated back and forth between conspicuous and inconspicuous color morphs, creating more genetic variance. They did find exceptions, but I find this general result really interesting: natural selection alone is most important in determining the strength of the trait. If there is any strengthening, making the male trait even more ridiculous and conspicuous, then it will have to be the result of direct benefit to the female. Indirect selection is just too weak.

Alicia published this paper in the Open Access journal Ecology and Evolution, so anyone can read it free of charge. Here’s the abstract:

Evidence suggests that female preferences may sometimes arise through sensory bias, and that males may subsequently evolve traits that increase their conspicuousness to females. Here, we ask whether indirect selection, arising through genetic associations (linkage disequilibrium) during the sexual selection that sensory bias imposes, can itself influence the evolution of preference strength. Specifically, we use population genetic models to consider whether or not modifiers of preference strength can spread under different ecological conditions when female mate choice is driven by sensory bias. We focus on male traits that make a male more conspicuous in certain habitats—and thus both more visible to predators and more attractive to females—and examine modifiers of the strength of preference for conspicuous males. We first solve for the rate of spread of a modifier that strengthens preference within an environmentally uniform population; we illustrate that this spread will be extremely slow. Second, we used a series of simulations to consider the role of habitat structure and movement on the evolution of a modifier of preference strength, using male color polymorphisms as a case study. We find that in most cases, indirect selection does not allow the evolution of stronger or weaker preferences for sensory bias. Only in a “two-island” model, where there is restricted migration between different patches that favor different male phenotypes, did we find that preference strength could evolve. The role of indirect selection in the evolution of sensory bias is of particular interest because of ongoing speculation regarding the role of sensory bias in the evolution of reproductive isolation.

Alicia is now working on a postdoc in toxicology at the EPA in Research Triangle Park.

Alicia M. Frame, Maria R. Servedio (2012). The evolution of preference strength under sensory bias: a role for indirect selection? Ecology and Evolution DOI: 10.1002/ece3.273

New Journal Publishing Models

Tags

open access, publishing, research, science

Really interesting stuff is happening this week in the world of scientific publication. Scientists and editors are trying out new publication models that will change science. This is important because science publication is science. Scientists rely on citing printed works to give credibility to their arguments, their data, and basic knowledge. Everything that scientists put in a new article has to be attributed to an already-printed article, be a new result, or be generally accepted by the community. This last provision doesn’t stop most papers I see from citing Charles Darwin within the first paragraph. Even when we all know who he was and what he said, citing a printed work still lends the most weight to any point a scientist makes.

Why is this true? Because there’s an ironically Darwinian process behind publication called peer review. Once an article has been accepted for publication by a journal, it has been reviewed thoroughly and revised significantly. If it’s published, then several knowledgeable people agreed that it was important and well-done. Here’s a basic run-down of the process: I do some research and I want to tell people about it; I submit that paper to a scientific journal’s editor; the editor gives it to an associate editor who chooses (usually) three reviewers who prepare detailed comments on everything from spelling to the validity and the overall scientific significance of the results; the editor then looks over those comments and decides whether the paper is right for the journal, is well-done, etc. Then he can make one of several decisions (there are many variations, but these are the most common): reject the paper, give the authors a chance to revise and then start the process again, accept it given that the authors do what the reviewers suggest, or accept it outright. The last option is unheard of — except that it happened to me once; that was crazy — but it’s important for understanding new developments in publishing.

The last part of the process is that if the author gets the chance to publish the article, he has to pay to publish it. This is the weird part of scientific publishing that I think many people are unaware of, or might have thought they misheard. Yes, scientists pay to have their work published.

Ideally the process of peer review should live up to the ideals that I outlined above, but there are a lot of people who think it is outdated, unnecessary or evil. There are other problems in the process, such as authors paying for work, and then there is the cost of disseminating the research, i.e. actually getting it to its readers. As of this week, scientists are now toying with every part of this process along with the help of the internet.

The biggest development over the past ten years has been Open Access publishing, which takes care of the last part of the process, the dissemination of research. Open Access articles are reviewed just like other articles, but they are offered free of charge over the internet to anyone who wants to read them. This is unlike most journals that are only available to people with a subscription, for example students at a university where the library subscribes. The biggest argument in favor of Open Access has been that citizens are being made to pay for research twice: federal grants (that originate from tax dollars) pay to do the research and publish it, and then taxpayers have to pay to read the work once it’s published. There are now thousands of Open Access journals and you can read them as easily as you are reading this blog. This is a good thing.

Moving back through the process, a new sort of non-journal is experimenting with publication costs. PeerJ is not really a journal, but promises peer-reviewed publication on the internet for a one-time fee for the authors: you pay only $99 for one publication a year, instead of up to $1000 for one publication at a time. PeerJ also promises to publish articles on the basis of scientific merit rather than impact. Most journals, including my favorites, will only accept paper if the editor and the reviewers can agree that it’s significant to the scientific community. PLoS ONE changed that by accepting papers only based on whether the science was well-done, and PeerJ plans to do the same thing. As you can imagine PLoS ONE publishes a lot of papers: there are over 2,000 a month these days, which makes it really hard to find interesting papers to read. If I publish a paper in PLoS ONE, I will definitely blog about it.

Dealing with the problems of peer review is the goal of Peerage of Science, which is a network of scientists that distribute their work and get it reviewed before submission to a journal. I think the idea here is that you can then submit your paper saying that it’s already been reviewed. I like the idea of forming a community of peers where we can review each others’ work without things becoming competitive. This is one of the biggest complaints about peer review. I’ve never experienced competition during the review process, but I know people who have thought that was going on. Reviews are typically anonymous, but Peerage of Science encourages the breaking of anonymity.

A new microbiology journal called mBio plans on dealing with the editor’s decision-making process. Instead of all the variants, and the reviewers getting whatever they want (“we kindly thank the reviewers for making us do additional experiments that had nothing to do with our hypothesis, but that seem to fit the research program of another biologist we know very well”), mBio promises to either reject a paper or accept it with minor revisions. A minor revision is something like the decision to not include a figure, or to add one or two additional citations. This means that the editor can make a faster decision, but it also means that reviewers are given less (more?) power. Sounds like if a paper needs significant revisions, mBio will just reject it, saving the authors some time.

I think what all these experiments are going for is making scientific publication a lot more like a wiki: a place where people can easily access each others’ work and data, easily share their work and data, and review is still there. Review, with all its problems, is still incredibly important. Lots of people have suggested alternatives, and there are some good ones, but I still appreciate the review process, even if I don’t like it all the time while I’m in the middle of it. I recently had a paper rejected because the reviewers just didn’t get what I was saying, but that is my problem, not theirs, so they did their jobs. Moving scientific publication in the direction of openness, through any of these ideas, is a huge step forward.

We should be a long way from the days when scientists would deliberately obfuscate their results from their peers — Galileo disseminated his results to other astronomers written in a cipher. The biggest thing holding us back is the idea that scientists own their research: I don’t believe I own my ideas, but there are people who want to keep their ideas to themselves as long as possible (i.e. until after it’s been through peer review). And of course there are people who profit from keeping scientific results hard to get at. However, as the free software movement shows, today’s technology (incidentally, built out of free software) makes sharing incredibly easy for those of us who want to share. The people who created arXiv understood this even when it wasn’t so easy.

Thanks for reading.

Sexual selection in humans: some interesting recent work

Tags

biology, evolution, human evolution, research, science, sexual selection

Researchers have found sexual selection important in the evolutionary history of humans, and a lot of researchers are focusing on the roles of mate choice and life history in major transitions in human evolution. I find the transition from hunter-gatherer to agricultural civilization the most interesting. This week I’ve read three interesting papers on three interesting facets of human sexual selection. These studies also did things in three different ways: there is a study of psychological study of modern (i.e. living) human mating preferences, a study of pre-industrial humans using historical data and a theoretical study using mathematical and computer models.

The first study is a twin study of human mating preferences in men and women. Brendan Zietsch and Karin Verweij at the university of Queensland, and Andrea Burri from King’s College, London gave surveys to men and women in both monozygotic (MZ, “identical”) and dizygotic (DZ, “fraternal”) twin pairs, asking them to rank the qualities of mates that they found desirable. The traits were qualities like “kind and understanding,” “healthy,” “intelligent,” “good earning capacity,” “good housekeeper,” “wants children,” and of course “physically attractive.” The most amusing characteristic of their raw data was, of course ,the differences between the sexes. Members of both sexes valued “kind and understanding” the most, and in line with other studies, men valued physical attractiveness more than women did. The least important qualities to men and women were “religious” and “university graduate.”

The evolutionary part of this study was using the twins to find the ability of natural selection to affect these preferences. MZ twins have the same genetic material, therefore differences between them are due to the environment. We can get more information on the role of environment by looking at DZ twins, who share some genes. From these data the researchers quantified the amount of additive genetic variance, dominance genetic variance and environmental variance. When individuals differ in their survival or reproductive success and it’s because of additive genetic variation — the number of certain copies of particular genes — then all those differences in fitness are passed on to their offspring. Additive variation is therefore the raw material for selection. These researchers found that the mating preferences with the highest heritability (biggest differences in preferences due to genes) were those that ranked highest on people’s priority lists. The researchers also questioned why the heritabilities should be so low (around 20% in most cases): though they entertained many possibilities, I think the most promising is that selection is acting very strongly on women’s and men’s mating preferences right now.

That brings us to the second study, from a multinational group of researchers that was published in Proceedings of the National Academy of Sciences (PNAS). The data on marriage (i.e. mating), births and deaths was mostly compiled from church records, family bibles and tax records in pre-industrial Finland. Another really interesting church-record data set producing results on human evolution, was derived from records of the pioneering Mormons of Utah in the late 1800s. The researchers studying the Finnish population asked if they could determine whether natural and sexual selection was acting on this population over the time period of their data, and what the crucial periods in the lifetime were: what fitness components contributed to overall fitness? Was it survival to adulthood? Was it how many times you married? Was it how many children you had? They found that in this society, where serial monogamy (i.e. remarriage) was common, and extramarital affairs and divorce were severely punished, that survival to adulthood made the biggest difference. However, they also found that the raw material for sexual selection in this population: interestingly from my perspective, most men remarried younger women who could still produce more children.

They also found that sexual selection might be able to act on the ability to remarry in women as well as men in this population. Also interesting: the wealth of individuals (whether or not they owned land) was totally unimportant to any fitness component, either under natural or sexual selection. The authors of the paper emphasized that natural and sexual selection can still act in our species, despite the demographic changes that came with the agricultural revolution. This is an important finding, and their data is totally awesome.

The third study I read this week used mathematical models to study the possible transition from a promiscuous mating system in human ancestors to our more-familiar system with long-term pair-bonds. Sergey Gavrilets of UT Knoxville authored this study, also published in PNAS. This is a contentious area, with many sources of interest, including anthropologists, social theorists and evolutionary biologists. I’m glad to see that a theory paper is getting some popular attention, and particularly that anthropologists are paying attention to it.

Gavrilets studied four different models of how males can obtain mates, and how females derive their fecundity, at least partially from male behavior. He used these models to ask if there wa sa relationship between the fighting ability of males and how much they provisioned their mates: we often assume, as is standard in economics as well, that each organism has a finite amount of resources to devote to various activities, so he divided male activities into fighting versus something else. All these models led to a state where males did nothing but fight, and females had lower fitness than if they got some direct, material benefits (food) from their mates. This is a low-fitness state: good for males who can fight to gain more mates and thereby more offspring, but not so good for females, who could have more offspring and survive better if the dudes would just cut it out.

Then Gavrilets added two wrinkles: a negative correlation between male fighting ability and mate provisioning, and female variation in faithfulness to their mates. Using a computer model, he then simulated evolution to show that populations would move more toward monogamy and long-term pair bonds. Gavrilets’ conclusion is that low-ranking males (not as good at fighting) would could increase their reproductive success by provisioning their mates; females can reward and reinforce this by not fooling around, which would force these males to provision offspring who got genes from an aggressive, promiscuous male.

All these studies show some really interesting ways that sexual selection works in humans, and may have played a role in our past. There is male and female mate choice going on. There are factors other than simple mate choice, for example in Gavrilets’ models. There are also life-history factors: as the Finnish study showed, survival to adulthood is a necessary prerequisite for mating success. Also, knowing that sexual selection can still act in humans, who are mostly monogamous, is really exciting.

A few caveats are in order, however: all of these studies emphasize selection. So do I, since I study selection. However, it’s easy to get caught up in the idea that selection is the evolutionary mechanism, when in fact there are other forces that are potentially much more important, particularly genetic drift, which randomly causses alleles to disappear from populations. We often think of genetic drift as something that produces variation between populations: the differences in appearance between Europeans and Asians, for instance, are conceivably due to drift. But who wants to think that critical parts of our identity — for example our mating behavior — could be due to a process even more stupid than natural selection? Drift is not just stupid, it’s stochastic — even worse! In other words, selection at least has the appeal that “it’s not totally random!” as biologists are often heard to say to religious zealots. Drift, on the other hand, is completely random. Not very pretty. The trap of thinking that everything interesting is due to selection is called adaptationism.

The other caveat is that most studies of humans assume that our current monogamous mating system is derived, in other words a recent adaptation. Most studies I hear of, be they from anthropologists, psychologists, or evolutionary biologists, assume that our ancestors were promiscuous or polygynous. This is intuitively appealing for scientific reasons — men are, on average, larger than women — and for social reasons — we like to think of ourselves as new, developed, derived and interesting. Whatever we are doing right now is often seen as a good thing, and we know that in the past what those people did was not a good thing. However, I have yet to see any data that supports this idea. The specific significance of Gavrilets’ paper hinges on the idea that our ancestors were not monogamous. However, this could be a good case of The Platypus Fallacy: just because gorillas and chimpanzees have different mating systems from modern humans does not mean that our ancestors did.

Thanks for reading.

• Zietsch BP, Verweij KJ, & Burri AV (2012). Heritability of preferences for multiple cues of mate quality in humans. Evolution 66 (6), 1762-72 PMID: 22671545
• Alexandre Courtiol,, Jenni E. Pettayd,, Markus Jokelae,, Anna Rotkirchf, and, & Virpi Lummaaa,b (2012). Natural and sexual selection in a monogamous historical human population PNAS DOI: 10.1073/pnas.1118174109
• Sergey Gavrilets (2012). Human origins and the transition from promiscuity to pair-bonding PNAS DOI: 10.1073/pnas.1200717109

The social environment as a source of variation

Tags

evolution, insects, open access, research, science, sexual selection

Some of the most interesting studies on life-histories and mate choice have been done with laboratory populations of insects. Crickets are especially well-suited to these studies because their most salient characteristic, their call, has qualities that are affected by different evolutionary forces. Calls have a frequency (pitch), but males also exert effort calling. Several researchers have picked up on the different meaning of these two variables for sexual selection in crickets. The “ears” of female crickets are probably tuned to a particular frequency, just as (American) human ears seem tuned to 440Hz. This should lead to stabilizing selection: males whose calls are too high-pitched will not attract mates or attract the wrong ones (e.g. from another species); the same should apply to males whose calls are too low-pitched. However, frequency should be mostly independent of the amount of time a male spends calling: this should depend on his health (how much time can he spend?), the predators and parasites that might tune in to his call, and the density of other males, i.e. competitors. The overall effect should be directional selection, i.e. favoring males who call more when they can (condition-dependence).

Michael Kasumovic and his colleagues Matt Hall and Robert Brooks recently raised male Australian Black Field Crickets to determine if their juvenile environment affected their calling effort and their pitch. The researchers ingeniously hypothesized that perceived density of competitors would affect male song in different ways: perceiving more competitors should not affect pitch, whereas competitor density should definitely affect calling effort. If males perceive that they have more competitors, they will have to call more to find mates. This produces directional selection on calling effort. However, females will still tune in to the same frequency, regardless of how many males are around. The effect of juvenile social environment therefore coincided with whether directional selection or stabilizing selection was the dominant force on a particular trait. They fooled the crickets into believing there were more competitors by broadcasting calls to developing males in the lab. Since they also knew that female choice was affected by the females’ perception of male density, they also raised females under similar conditions.

I find this study really interesting because it shows how many possible sources of phenotypic variation there are. When we consider the lek paradox, a big problem is that the conditions under which we expect to lose genetic variation are very narrow: we have to suppose that the genes act in a certain way, that there is no mutation, and so on. We might as well deal with friction-less pulleys and billiard balls. My research focuses on phenotypic variation due to age, and Kasumovic and his colleagues have focused on the social environment. This study reminds us that the complexity of life means that there is a huge number of reasons we should expect lots of phenotypic variation. That phenotypic variation should lead to plenty of ways that we can maintain genetic variation in populations. However, science proceeds in baby steps of understanding: each potential idea has to be tried out and tested to death. We can think of these sources of variation a lot faster than we can do experiments, or even produce worthwhile theory (that is, find out if the ideas really make sense). The lek paradox will therefore be with us for a while.

Another really interesting thing about this article is that it’s published in the new Open Access journal Ecology and Evolution. That means everybody interested can go and read it: while you’re there check out all the other primary research articles you have access to free of charge. This is primary research, i.e. the research papers written by the people who performed the experiments.

Here’s the abstract:

The juvenile environment provides numerous cues of the intensity of competition and the availability of mates in the near environment. As research demonstrates that the developing individuals can use these cues to alter their developmental trajectories, and therefore, adult phenotypes, we examined whether social cues available during development can affect the expression and the preference of sexually selected traits. To examine this, we used the Australian black field cricket (Teleogryllus commodus), a species where condition at maturity is known to affect both male calling effort and female choice. We mimicked different social environments by rearing juveniles in two different densities crossed with three different calling environments. We demonstrate that the social environment affected female response speed but not preference, and male age-specific calling effort (especially the rate of senescence in calling effort) but not the structural/temporal parameters of calls. These results demonstrate that the social environment can introduce variation in sexually selected traits by modifying the behavioral components of male production and female choice, suggesting that the social environment may be an overlooked source of phenotypic variation. We discuss the plasticity of trait expression and preference in reference to estimations of male quality and the concept of condition dependence.

Remember this article is available to everyone for free, so please go read it and learn more about the authors and their other interests.

Genetic variation and sexual selection: an introduction to my research

Tags

evolution, genetics, research, science, sexual selection

One of the biggest problems in evolutionary biology is the maintenance of genetic variation in populations. Without genetic variation, populations do not change in a consistent way over time. Basically, without genetic differences, all the differences between organisms would be erased at reproduction. If natural selection is consistent over time, applying the same winnowing effect to every generation, we should end up with only the alleles that selection favors, i.e. less variation. This is called “directional selection” since it favors the evolution of traits toward a particular size. This is different from “stabilizing selection” that favors one particular size and selects against extreme phenotypes. However, both of these forms of selection yield less genetic variation over time if selection is constant; if selection goes back and forth favoring one phenotype and then another, then it’s easy to maintain genetic variation. Another simple exception is heterozygote advantage, where a particular genotype is favored, rather than particular alleles: the alleles have to occur in a particular combination that does better than either does alone.

Sexual selection, the process that leads to ridiculous looking, dead-sexy animals, is usually conceived of as directional selection. If we think of a process that produces a long tail or big horns or a sexy mind, that process will favor phenotypes on one end of the range in a population. This presents two problems. After a while

1. the genetic variation will all be gone
2. females will not get a better mate by being choosy

This is a particularly bad problem if being choosy is costly. Looking around for a mate might be dangerous: predators could be hiding in the bushes and do you really want to mate with the male that has mated with every other female? Females may get food or resources from males, but in many cases all they get is sexy offspring. Females in many models need to get a really substantial direct benefit for sexual selection to work in the first place. Then consider that when there is no difference in genetic sexiness of males, a female that mates with the first male to come along does just as well: her offspring are just as sexy.

There’s another problem: when we look at sexually selected traits in the wild, we actually find a huge amount of genetic variation. Either these traits are not under directional selection at all, or selection is very weak, or there is something maintaining the variation, propping it up every generation. This could be mutation, or it could be particular combinations of alleles that lead to different phenotypes. If there are a huge number of genes controlling the phenotype we’re looking at, there are a lot of ways for them to combine. All of these problems come under the name “lek paradox,” named for the dancing arenas used by males to attract females. The lek paradox is basically “Why do we see choosy females when all females get from males is sexy offspring?”

Thankfully, there’s another interesting twist: sexual traits are affected by the overall health of the whole organism. Developmental variation or the social environment can lead males to display different traits based on their health, their age or their perceived level of competition. Condition-dependence is variation in traits that depends on the overall health of the individual, and therefore genetic variation in condition is revealed in signals that depend on overall health. This type of signaling is very important in the evolution of sexual signals, as it reveals the health of potential mates to females. Also, it can’t be cheated: if you can produce a big, costly signal indicating health, you must be pretty healthy; you’ll probably make vigorous, not just sexy babies. This is one type of “handicap signal.” Jerry Seinfeld explained handicap signaling best in an early episode of Seinfeld: why give someone the finger, when it takes a lot more effort to give someone the toe?

My research deals specifically with the noise introduced by age: if the signal a male displays depends on his age and his health, or his particular genes, then males of different genotypes and ages can have similar display traits. Mutations in overall condition should maintain genetic variation in the signaling trait. Some scientists have looked at a similar idea before: if a male is old, he has proven that he can survive and therefore probably has good genes. Old males should be a attractive. Some have said that it can work, and other have said it’s unlikely. I ask a different question: can those traits actually evolve? There are several problems: males with slow-growing traits, that enable to live a long time will be rare, they may never grow old enough to be sexy. If they display their sexy trait at a young age, they will be killed for it. Another problem with old males becoming attractive is that most mutations come from old, backdated sperm: will the offspring of a sexy, old male be even as sexy as their father?

My goal is to find the conditions under which males will evolve to display age-dependent traits using mathematical models and computer simulations of evolution. Age-dependent traits should help maintain genetic variation in sexual traits because males who survive differently should display differently: males in good health, with lots of good genes should wait until they get old to display their sexiness; males in not-so-good condition should display earlier in their lives, because they won’t get old. The point is that females can’t tell the difference — or we should have to demonstrate that they can, which means the evolution of an age-dependent trait! — and mate choice will thereby maintain the variation in condition.

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