Field of Science

The simulations behind the fitness landscape visualizations

We now have two videos out featuring evolving populations in two-dimensional fitness landscapes.

Using fitness landscapes to visualize evolution in action Youtube Vimeo
Visualizing coevolution in dynamic fitness landscapes Youtube Vimeo

(Best to watch the first one first for some background information about fitness landscapes.)





These movies are based on simulations of organisms evolving by reproduction, mutation and selection. Populations move around on a map that depict fitness as a function of phenotype (i.e., the biological and physical characteristics of an individual organism).

The following is a semi-technical description of the simulations, so be warned. If you have questions about some details, let me know in the comments.

Phenotype. The fitness landscapes that you see are phenotype-fitness maps. That means that for each possible phenotype there is an associated fitness value (which is a scalar - a single number). The phenotype of these simulated organisms consist of two traits. Both of these traits are numbers that range between 1 and 200. A phenotype of (10, 10) means that the organisms is situated near the lower corner of the fitness landscape, and a phenotype of (195, 3) means that the organism is situated near the right corner.

Sympatry. All simulations shown in the videos have no spatial component. The moving around in the landscape is only caused by changes in the phenotype, not geographically, and the population is therefore said to be strictly sympatric or well-mixed. If the individual organisms did move around in physical space, then where they are located relative to each other could have an influence of who they interact with, which could change things further. Structured populations are known to affect evolutionary dynamics through social interaction, competition for resources, and mating.

Mutations in these simulations work like this: Each of the two traits mutate at a set mutation rate. Every time an organisms reproduces, the new organism has a chance to mutate which is equal to the mutation rate. This is true for each trait, so that a mutation rate of 0.05 means that trait 1 has a 5% chance of changing, and trait 2 also has a chance of changing. These two events are independent of each other. When a trait mutates, the trait value is either increased or decreased by one. In other words, if the trait value of the parent was 142, the offspring will have a value of 141 or 143 with equal probability. There is no underlying genetics in these models, and the phenotype is directly inherited.

Selection.  Organisms reproduce asexually. Every offspring is a clone of the parent, except for any mutations. Every computational update some organisms die and some reproduce. Death is completely random, so that every organism has an equal chance or being removed every update. Who gets to reproduce is also random, but fitness affects this chance. For example, an organism that has twice the fitness of another organisms has a probability of reproducing that is twice as high. This doesn't guarantee that it will have twice as many offspring - but on average it will be approximately so.

Population size. Competition in these simulations is for space. Some simulations have a constant population size. In this case, a small percentage of the population is killed every update, and those empty spots are filled by selecting among the survivors. Other simulations have variable population sizes. In these vases every surviving organism has a chance to reproduce once every computational update that is equal to their normalized fitness. The variable population size simulations results in stable populations where the population size fluctuate around a value which is ultimate given by the average fitness. For example, when the population climbs a peak the average fitness of organisms increases, and the average chance of reproducing goes up. This means that the population grows in size. The way this is implemented is such that there is a carrying capacity set to 2,000 individuals. If the population reaches this size, 50% are moved next update, and the other 50% then has a chance to reproduce. If they all had the maximum fitness (a set value), then they would all reproduce, and the population size would be back to 2,000. This doesn't happen, because mutations would make some individuals have a fitness lower than the maximum. If the population size gets very low, the number than is killed every update is set to less than 50%, so that more than half of the organisms survives. The precise fraction killed goes from zero at population size zero linearly through 50% at 2,000. This most often results in population of around 1,600 organisms. Most published simulations studies of evolution use constant population sizes.

Dynamic landscapes. In the second video of coevolution systems the fitness landscape of one population changes over time because they are affected by another population. In the moth-orchid simulation, the length of the moth proboscis needs to be longer than the orchid spur length to be able to get to the nectar at the bottom. If every individual orchid has a spur that is longer than the proboscis, then moth fitness is low (but non-zero). Having a proboscis that is as long as the spurs of half of the orchid population will give the moth an intermediate fitness. The fitness landscape of the orchids is similarly affected by the moth population, with the orchids needing spurs that are longer than the proboscis in order for the feeding moth to get pollen on their faces. This drives the evolution of longer proboscises and spurs as dictated by the two changing fitness landscapes. In the rock-paper-scissors simulation, the fitness landscape of each population is affected by the phenotype values of the other two populations.

How the woman got her period

Guest post by Suzanne Sadedin. This is reposted from Quora.

Suzanne got her PhD in biology from Monash University, and has done postdoctoral research at Monash University, University of Tennessee, Harvard University, and KU Leuven.




What is the evolutionary benefit or purpose of having periods?

 I'm so glad you asked. Seriously. The answer to this question is one of the most illuminating and disturbing stories in human evolutionary biology, and almost nobody knows about it. And so, O my friends, gather close, and hear the extraordinary tale of:

HOW THE WOMAN GOT HER PERIOD

Contrary to popular belief, most mammals do not menstruate. In fact, it's a feature exclusive to the higher primates and certain bats*. What's more, modern women menstruate vastly more than any other animal. And it's bloody stupid (sorry). A shameful waste of nutrients, disabling, and a dead giveaway to any nearby predators. To understand why we do it, you must first understand that you have been lied to, throughout your life, about the most intimate relationship you will ever experience: the mother-fetus bond.

Isn't pregnancy beautiful? Look at any book about it. There's the future mother, one hand resting gently on her belly. Her eyes misty with love and wonder. You sense she will do anything to nurture and protect this baby. And when you flip open the book, you read about more about this glorious symbiosis, the absolute altruism of female physiology designing a perfect environment for the growth of her child.

If you've actually been pregnant, you might know that the real story has some wrinkles. Those moments of sheer unadulterated altruism exist, but they're interspersed with weeks or months of overwhelming nausea, exhaustion, crippling backache, incontinence, blood pressure issues and anxiety that you'll be among the 15% of women who experience life-threatening complications.

From the perspective of most mammals, this is just crazy. Most mammals sail through pregnancy quite cheerfully, dodging predators and catching prey, even if they're delivering litters of 12. So what makes us so special? The answer lies in our bizarre placenta. In most mammals, the placenta, which is part of the fetus, just interfaces with the surface of the mother's blood vessels, allowing nutrients to cross to the little darling. Marsupials don't even let their fetuses get to the blood: they merely secrete a sort of milk through the uterine wall. Only a few mammalian groups, including primates and mice, have evolved what is known as a “hemochorial” placenta, and ours is possibly the nastiest of all. 

Inside the uterus we have a thick layer of endometrial tissue, which contains only tiny blood vessels. The endometrium seals off our main blood supply from the newly implanted embryo. The growing placenta literally burrows through this layer, rips into arterial walls and re-wires them to channel blood straight to the hungry embryo. It delves deep into the surrounding tissues, razes them and pumps the arteries full of hormones so they expand into the space created. It paralyzes these arteries so the mother cannot even constrict them.

What this means is that the growing fetus now has direct, unrestricted access to its mother's blood supply. It can manufacture hormones and use them to manipulate her. It can, for instance, increase her blood sugar, dilate her arteries, and inflate her blood pressure to provide itself with more nutrients. And it does. Some fetal cells find their way through the placenta and into the mother's bloodstream. They will grow in her blood and organs, and even in her brain, for the rest of her life, making her a genetic chimera.

This might seem rather disrespectful. In fact, it's sibling rivalry at its evolutionary best. You see, mother and fetus have quite distinct evolutionary interests. The mother 'wants' to dedicate approximately equal resources to all her surviving children, including possible future children, and none to those who will die. The fetus 'wants' to survive, and take as much as it can get. (The quotes are to indicate that this isn't about what they consciously want, but about what evolution tends to optimize.)

There's also a third player here – the father, whose interests align still less with the mother's because her other offspring may not be his. Through a process called genomic imprinting, certain genes inherited from the father can activate in the placenta. These genes ruthlessly promote the welfare of the offspring at the mother's expense.

How did we come to acquire this ravenous hemochorial placenta which gives our fetuses and their fathers such unusual power? Whilst we can see some trend toward increasingly invasive placentae within primates, the full answer is lost in the mists of time.

Uteri do not fossilize well.

The consequences, however, are clear. Normal mammalian pregnancy is a well-ordered affair because the mother is a despot. Her offspring live or die at her will; she controls their nutrient supply, and she can expel or reabsorb them any time. Human pregnancy, on the other hand, is run by committee – and not just any committee, but one whose members often have very different, competing interests and share only partial information. It's a tug-of-war that not infrequently deteriorates to a tussle and, occasionally, to outright warfare. Many potentially lethal disorders, such as ectopic pregnancy, gestational diabetes, and pre-eclampsia can be traced to mis-steps in this intimate game. 

What does all this have to do with menstruation? We're getting there.

From a female perspective, pregnancy is always a huge investment. Even more so if her species has a hemochorial placenta. Once that placenta is in place, she not only loses full control of her own hormones, she also risks hemorrhage when it comes out. So it makes sense that females want to screen embryos very, very carefully. Going through pregnancy with a weak, inviable or even sub-par fetus isn't worth it.

That's where the endometrium comes in. You've probably read about how the endometrium is this snuggly, welcoming environment just waiting to enfold the delicate young embryo in its nurturing embrace. In fact, it's quite the reverse. Researchers, bless their curious little hearts, have tried to implant embryos all over the bodies of mice. The single most difficult place for them to grow was – the endometrium.

Far from offering a nurturing embrace, the endometrium is a lethal testing-ground which only the toughest embryos survive. The longer the female can delay that placenta reaching her bloodstream, the longer she has to decide if she wants to dispose of this embryo without significant cost. The embryo, in contrast, wants to implant its placenta as quickly as possible, both to obtain access to its mother's rich blood, and to increase her stake in its survival. For this reason, the endometrium got thicker and tougher – and the fetal placenta got correspondingly more aggressive.

But this development posed a further problem: what to do when the embryo died or was stuck half-alive in the uterus? The blood supply to the endometrial surface must be restricted, or the embryo would simply attach the placenta there. But restricting the blood supply makes the tissue weakly responsive to hormonal signals from the mother – and potentially more responsive to signals from nearby embryos, who naturally would like to persuade the endometrium to be more friendly. In addition, this makes it vulnerable to infection, especially when it already contains dead and dying tissues.

The solution, for higher primates, was to slough off the whole superficial endometrium – dying embryos and all – after every ovulation that didn't result in a healthy pregnancy. It's not exactly brilliant, but it works, and most importantly, it's easily achieved by making some alterations to a chemical pathway normally used by the fetus during pregnancy. In other words, it's just the kind of effect natural selection is renowned for: odd, hackish solutions that work to solve proximate problems. It's not quite as bad as it seems, because in nature, women would experience periods quite rarely – probably no more than a few tens of times in their lives between lactational amenorrhea and pregnancies**.

We don't really know how our hyper-aggressive placenta is linked to the other traits that combine to make humanity unique. But these traits did emerge together somehow, and that means in some sense the ancients were perhaps right. When we metaphorically 'ate the fruit of knowledge' – when we began our journey toward science and technology that would separate us from innocent animals and also lead to our peculiar sense of sexual morality – perhaps that was the same time the unique suffering of menstruation, pregnancy and childbirth was inflicted on women. All thanks to the evolution of the hemochorial placenta.

Links:
The evolution of menstruation: A new model for genetic assimilation
Genetic conflicts in human pregnancy
Menstruation: a nonadaptive consequence of uterin... [Q Rev Biol. 1998]
Natural Selection of Human Embryos: Decidualizing Endometrial Stromal Cells Serve as Sensors of Embryo Quality upon Implantation
Scientists Discover Children’s Cells Living in Mothers’ Brains

Credits: During my pregnancy I was privileged to audit a class at Harvard University by the eminent Professor David Haig, whose insight underlies much of this research. Thanks also to Edgar A. Duenez-Guzman, who reminded me of crucial details. All errors are mine alone.

*Dogs undergo vaginal bleeding, but do not menstruate. Elephant shrews were previously thought to menstruate, but it's now believed that these events were most likely spontaneous abortions.

**One older published estimate for hunter gatherers was around 50, but this relied on several assumptions that suggest it's a significant overestimate. In particular, it includes 3 whole years of menstruation before reproduction (36 periods) for no obvious reason.

We can make an estimate from studies of the Hadza of Tanzania, who reach puberty around 18, bear an average of 6.2 children in their lives (plus 2-3 noticeable miscarriages) starting at 19, and go through menopause at about 43 if they survive that long (about 50% don't). Around 20% of babies die in their first year; the remainder breastfeed for about 4 years. So this is 25 years of reproductive life, of which about 20 are spent lactating, and 4.5 pregnant. That would leave only about 6 periods, but amenorrhoea would cease during the last year of lactation for each child, so this figure is too low. On the other hand, this calculation ignores the ~50% of women who died before menopause, miscarriages, months spent breastfeeding infants who would die, and periods of food scarcity, all of which would further reduce lifetime menstruation. Stats from: http://www.fas.harvard.edu/%7Ehb...

Not dead yet: When do we give up on an idea?

Guest post by Carina Baskett written in response to Angela Moles and Jeff Ollerton's post on Dynamic Ecology: Is the notion that species interactions are stronger and more specialized in the tropics a zombie idea?

Carina Baskett is a PhD candidate at Michigan State University in the Department of Plant Biology and the Ecology, Evolutionary Biology, and Behavior Program. She posts photos from her fieldwork and occasional articles about tropical natural history, among other things, at Wandering Nature.




ResearchBlogging.orgIf you’ve traveled to the tropics, you know the drill. Get your shots for typhoid and yellow fever, and your meds for malaria (try to avoid the one with psychotic side effects). Don’t drink the water, and avoid the lettuce.

This over-abundance of diseases and parasites in the tropics is not just because sanitation is lacking in developing countries. Both diversity and severity of human parasites are higher in the tropics (Cashdan 2001; Guernier, Hochberg et al. 2004).

Could the same be true for plant enemies? What about other biotic interactions, like predator-prey relationships, and plants and pollinators? And why?

The first person to suggest that biotic interactions are somehow different in the tropical and temperate regions was Alfred Russell Wallace. Not only did he independently conceive of natural selection around the same time as Darwin (during a malarial fever in Malaysia, speaking of tropical diseases!), he was also a great tropical naturalist.

In the book Tropical Nature in 1878, he said, “Equatorial lands must always have remained thronged with life; and have been unintermittingly subject to those complex influences of organism upon organism, which seem the main agents in developing the greatest variety of forms and filling up every vacant place in nature.”

The “biotic interactions hypothesis” to explain high tropical diversity* is a descendent of Wallace’s beautifully stated explanation, with contributions from Dobzhansky (1950), Fischer (1960), and Schemske (2009). At its core, skipping over tangents about coexistence and specialization, today’s conception has three testable parts:
  1. The relative contribution of biotic interactions to variation in relative fitness of organisms is greater at lower latitudes.
  2. Biotic selective agents drive faster divergence of allopatric populations than abiotic selective agents due to coevolution.
  3. Therefore, isolated populations speciate faster when the main selective agents are biotic.
For parts B and C, I’ll just tease you with some references that explore or show evidence for these hypotheses in very different ways: Farrell, Dussourd et al. 1991; Schemske 2009; Paterson, Vogwill et al. 2010; Jablonski, Belanger et al. 2013.

I’ll focus the rest of this on part A, which was recently labeled a “zombie:” false, dead, disproven. I’ll try and convince you that it’s nowhere near dead yet. I’m NOT trying to convince you that the hypothesis is true, because I think the answer is very much up in the air, but rather that it’s plausible and that we need more data.

First, the dissection. Part A is represented graphically in Figure 1 (Schemske 2009). Each arrow is the proportion of variation in fitness for the focal species caused by different selective agents: mutualists, antagonists, and the abiotic environment. A wider arrow is a greater proportion. A solid line shows a positive effect on fitness, while a dashed line is negative. (Note that the arrows go both ways for the biotic agents. They coevolve, while abiotic agents do not, which gets into parts B and C of the hypothesis.)

Here’s what this abstract figure would look like on the ground. This past winter here in Michigan was, to put it lightly, a doozy. Two years ago, it was so mild that I was told that my first Michigan winter didn’t even count. It’s not hard to imagine that even after lineages have evolved to tolerate freezing (which is a big deal—it kills cells!), there can still be a lot of variation in fitness depending on the weather.

Think of a plant that lives for a few years, flowering in the summer, producing fruit in the fall, and dying back over winter. Let’s assume that there’s a resource tradeoff between manufacturing antifreeze and producing fruits.** This past winter, plants that invested a lot in antifreeze would have had high relative fitness in the population, because they alone survived. Two years ago, that same strategy would have had low relative fitness, because plants that produced less antifreeze would have survived the winter too, but had higher fruit production. In this hypothetical situation, there is some variation in fitness due to herbivores and pollinators etc., but most of it is due to the wildly variable weather.

In contrast, imagine a similar plant in a tropical habitat, growing in full sun. It experiences temperature stress too. The sunshine is actually more intense in the tropics because it’s hitting the Earth straight on instead of at an angle, so its energy is concentrated in a smaller area. It’s HOT! But it’s hot almost every single day of the year, so all the plants in the population invest in tolerating the heat to the same degree. Temperature isn’t contributing much variation in fitness in this population.

Life here is more like the Hunger Games. Who can grow the fastest? Who can avoid death by enemy herbivores and diseases? Who can form the strongest alliances with pollinators and fruit dispersers? Competition, antagonism, and mutualism is what determines fitness here, not the weather.***

Now that I’ve painted a picture of what Figure 1 could hypothetically look like in the real world, how can we figure out whether or not it’s true?

Ideally, you would pick a focal species and do an observational or experimental path analysis (e.g., Schemske and Horvitz 1988) to determine the relative contributions of various selective agents at different latitudes. Make sure you have an army of assistants, because you’ll need massive sample sizes. Did I mention you’ll have to do it for many years? You won’t want to miss important events like unusually bad winters or pest outbreaks. By the way, even though this kind of study would probably be impossible in animals, it’s also nigh-impossible to find an abundant plant species whose native range encompasses tropical and temperate latitudes, avoiding really dry places and high altitude. (If you know of one, please let me know!!)

Needless to say, filling in Figure 1 with real data has not yet been done, and given our funding climate, it probably never will. But, there are other ways to approximately test the hypothesis (Schemske, Mittelbach et al. 2009).

What we CAN ask is, what is the “intensity” of the interaction today? What do today’s traits tell us about selection in the past? And what is the frequency of an interaction in the community?

To illustrate each question in terms of pollination, we can ask how much do tropical plants rely on self-pollination vs. outcrossing; do tropical plants invest more in pollinator attraction and reward; and, do tropical plant communities show a higher frequency of animal vs. wind pollination? Fill in the blanks with your favorite interaction.

To build a relatively complete approximation of Figure 1, we should be asking these questions in many systems, across many types of interactions, and at many spatial and phylogenetic scales. For example, asking these questions within widely-ranging species (Salazar and Marquis 2012) is quite different from asking them at the community level, with disparate habitats, community membership, and growth forms (Moles, Wallis et al. 2011). Both approaches are needed, because each has huge advantages and severe limitations.

The most comprehensive review of the available data is a 2009 Annual Reviews paper by Schemske et al. (see their Table 1). They noted that the data was insufficient for meta-analysis. Nevertheless, they found that most interactions show greater “importance” at lower latitudes; that is, the interaction is more intense currently, the traits show that it was more intense in the past, or it is more frequent. None of the interactions shows greater importance at higher latitudes.

For example, in the tropics, predation rates on birds’ nests are higher. Ant predation rates on insect bait are higher. Parasite pressure is higher. Palatability of marine worms, salt marsh plants, leaves, and butterfly larvae is lower. The frequency of animal pollination, animal seed dispersal, ant-plant mutualisms, endophytes, and cleaning symbioses is higher. The review also finds that herbivory rates are higher and plants are better defended at lower latitudes, but a recent meta-analysis on herbivory came to different conclusions (Moles, Bonser et al. 2011).

Although the results are necessarily qualitative and we can’t put a p-value on this statement yet, this review shows that looking across many types of interactions, many ways of quantifying their importance, and over many spatial and phylogenetic scales, the weight of the available evidence supports Figure 1.

But I would be the last person in the world to tell you that we’re done testing part A of the biotic interactions hypothesis. Much of the available data was not generated to explicitly address it, so there’s always something missing. For example, herbivory rates could be the same at different latitudes, but tropical plants may be better defended, indicating that greater herbivore pressure has selected for stronger defense. You need both pieces of the puzzle, preferably measured at the same time on close relatives, to be able to say whether herbivore pressure is greater in the tropics.

I’ve spent the last three years thinking about how we can fill in the missing gaps. There are so many ways to test these questions, so many interactions and species to choose from. Each approach is limited in some key way; otherwise, the end-all, be-all experiment would have already been done! One could easily spend a lifetime chipping away at this question from different angles, without even addressing the bigger picture of whether this has anything to do with the latitudinal diversity gradient. (I’m working on that too though!)

Therefore, I was dismayed when I woke up on Tuesday to a post on a widely-read ecology blog that claimed that the hypothesis that biotic interactions are stronger in the tropics is a “zombie idea.” Meaning that it’s dead, it’s been disproven, we can all go home now, and anyone who studies it is just wasting their time.

Whoa. Not enough data for a meta-analysis, but we’re done with this question? A recent review concluded that there is support for the hypothesis, but now it’s been totally debunked? Did I miss something here?

In fact, I haven’t missed anything. As with any scientific controversy worth its salt, there are contradictory reviews, there are people who are highly skeptical, there is massive confusion about what the hypothesis is and how to properly test it. That’s all fine and good. It’s exciting, even.

What is not fine and good, in my book, is to proclaim from the rooftops that we’re done with a question that we’ve barely begun to address. To claim that a handful of publications on latitudinal gradients in herbivory are the end-all, be-all, period end of story of decades of research. To claim that any one of us has the final authority on how to define, test, and interpret an area of science.

A debate about an idea can be constructive and fun. But both my scientific and journalistic selves cry fowl when a story is presented hyperbolically from one point of view. I believe that it’s irresponsible and polarizing to instigate a debate by claiming that the problem is solved and there is no debate.

I’m glad that people are talking about the topic, though I wish it had been inspired by less inflammatory language. I hope the conversation inspires us to clarify what our questions are and how we can test them. I hope also that you agree that we don’t need more catchy metaphors (zombies, old clothes, lemmings, sheep). We need more data and more conversation. Period. But not the end of the story.


*There are so many species in the tropics! There are over 22,000 tree species in the Amazon, compared to 620 in temperate North America (Currie and Paquin 1987; Fine and Ree 2006). This pattern of higher species diversity in the tropics is remarkably consistent across different types of organisms and through time and space. How can the same underlying processes of ecology and evolution produce such different outcomes? We don’t really know! Sure, there are ideas. In fact, Palmer (1994) lists 120 hypotheses to explain it! But given the massive scale of space and time, it’s really hard to test these hypotheses, so a definitive answer remains elusive. See Mittelbach, Schemske et al. (2007) for a great review.

**For any of this to matter for evolution, we are also assuming that allocation strategies are not very plastic; that they are heritable; and that there is genetic variation for these strategies in the population.

***Why am I focusing so much on temperature? Lots of studies show that climatic variables, especially temperature, are tightly correlated with global diversity patterns (e.g., Currie, Mittelbach et al. 2004). In my opinion, for a few reasons, the biotic interactions hypothesis is the only latitudinal diversity gradient hypothesis that provides a plausible mechanism by which temperature can affect diversity. But actually, the hypothesis is generalizable to any gradient in abiotic stress. Although it was proposed to address the LDG, it applies to other gradients in abiotic stressors that covary with species diversity: altitude, ocean depth, precipitation, etc (Schemske, Mittelbach et al. 2009). This is a practical strength because components of the biotic interactions hypothesis can be tested in other systems, which may be more tractable than latitude. More importantly, it is a theoretical strength because confirming this hypothesis could revolutionize our approach to studying the origins of diversity in many systems.

References:
Cashdan, E. (2001). "Ethnic diversity and its environmental determinants: Effects of climate, pathogens, and habitat diversity." American Anthropologist 103(4): 968-991.
Currie, D. J., G. G. Mittelbach, et al. (2004). "Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness." Ecology Letters 7(12): 1121-1134.
Currie, D. J. and V. Paquin (1987). "Large-scale biogeographical patterns of species richness of trees." Nature 329(6137): 326-327.
Dobzhansky, T. (1950). "Evolution in the tropics." American Scientist 38: 209-221.
Farrell, B. D., D. E. Dussourd, et al. (1991). "Escalation of plant defense: Do latex and resin canals spur plant diversification?" American Naturalist 138(4): 881-900.
Fearnside, P. M. (2005). "Deforestation in Brazilian Amazonia: History, rates, and consequences." Conservation Biology 19(3): 680-688.
Fine, P. V. A. and R. H. Ree (2006). "Evidence for a time-integrated species-area effect on the latitudinal gradient in tree diversity." American Naturalist 168(6): 796-804.
Fischer, A. G. (1960). "Latitudinal variation in organic diversity." Evolution 14: 64-81.
Guernier, V., M. E. Hochberg, et al. (2004). "Ecology drives the worldwide distribution of human diseases." Plos Biology 2(6): 740-746.
Jablonski, D., C. L. Belanger, et al. (2013). "Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient." Proceedings of the National Academy of Sciences of the United States of America 110(26): 10487-10494.
Mittelbach, G. G., D. W. Schemske, et al. (2007). "Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography." Ecology Letters 10(4): 315-331.
Moles, A. T., S. P. Bonser, et al. (2011). "Assessing the evidence for latitudinal gradients in plant defence and herbivory." Functional Ecology 25(2): 380-388.
Moles, A. T., I. R. Wallis, et al. (2011). "Putting plant resistance traits on the map: a test of the idea that plants are better defended at lower latitudes." New Phytologist 191(3): 777-788.
Palmer, M. W. (1994). "Variation in species richness: towards a unification of hypotheses." Folia Geobotanica & Phytotaxonomica 29(4): 511-530.
Paterson, S., T. Vogwill, et al. (2010). "Antagonistic coevolution accelerates molecular evolution." Nature 464(7286): 275-U154.
Salazar, D. and R. J. Marquis (2012). "Herbivore pressure increases toward the equator." Proceedings of the National Academy of Sciences of the United States of America 109(31): 12616-12620.
Schemske, D. W. (2009). Biotic interactions and speciation in the tropics. Speciation and Patterns of Diversity. R. K. Butlin, J. R. Bridle and D. Schluter. Cambridge, United Kingdom, Cambridge University Press: 219-239.
Schemske, D. W. and C. C. Horvitz (1988). "Plant-animal interactions and fruit production in a neotropical herb: a path analysis." Ecology 69(4): 1128-1137.
Schemske, D., Mittelbach, G., Cornell, H., Sobel, J., & Roy, K. (2009). Is There a Latitudinal Gradient in the Importance of Biotic Interactions? Annual Review of Ecology, Evolution, and Systematics, 40 (1): 245-269 DOI: 10.1146/annurev.ecolsys.39.110707.173430.

Nature Communications faux pas

This article in Nature Communications


has this figure showing the phylogenetic relationship between "contemporary human populations and Neanderthals":

Basically, the contemporary "out-of-Africa" individual is in a suit and a bowler hat, and the individual of "purely African ancestry" looks like a thug.

How does something like this get published in a prestigious journal nowadays?

Ignored

There is a website I am ignoring.

Sometimes the best action to take is to ignore. The organization and the man leading it want to influence society in a major way, and I disagree with their agenda. If I were to share with readers who they are, some people would go to their website, and they would get even more attention (and considering the huge amounts of traffic I get, it would be a lot*).

But I wanted to say that on this website they are talking about a certain event that was much covered in the media recently. I vehemently disagree with their views in general, and I think they are misrepresenting the event in question.

Their views are factually wrong, which I know based on a lot of evidence. I'd love to share this publicly, but again, more attention probably benefits said organization, and so I think the best solution is to ignore them.

Hereby ignored.

* Ha!


Tadpole plasticity triggered by dragonfly nymph predation (video)

Professor Rick Relyea from the University of Pittsburgh gave a fascinating seminar today: "Phenotypic Plasticity: Stress-Induced Changes in Behavior, Morphology, and Life History of Aquatic Organisms".

He showed this amazing and somewhat scary video of dragonfly nymphs and tadpoles.



Rick's lab website. Movie is downloaded from here.

Pragmatic definitions in biology

Biology is littered with concepts that biologists cannot always agree on how to define or where there are special cases where the common definition have to be amended. Species. Complexity. Modularity. Evolvability. Evolution. Genes. Community. Robustness. Open-ended evolution. Fitness. Life.

Take species. The current state of affairs is that there are many different definitions, and people can't always agree which one is best. Each one of us may have a favorite. (Mine is the Ecological Species Concept by Van Valen (1976) Ecological Species, Multispecies, and Oaks. Also, best title ever.) This often leads to more or less antagonistic attitudes among people, and can have negative effects on the review process.

As far as I'm concerned John Wilkins is the man to go to for species definitions. He lists 26 of them.

In this case, "species" is the concept, and curse Ernst Mayr for being first to call a proposed definition a "concept" (i.e., the Biological Species Concept - which should also really have been the Reproductive Species definition).

What I propose is the stop calling the proposed definitions "definitions", and instead call them "criteria".

That would make it

  • The Reproductive Species criterion
  • The Ecological Species criterion
  • The Phylogenetic Species criterion
  • The Taxonomic Species criterion
  • ... et cetera.

When determining if two groups of living organisms are different species, all you'd have to do is go down the list and check off those criteria that are met (easier said that done, I know). And then when talking about this, qualify the type of species by naming it according to the matching criteria. Your two closely related groups of organisms would then be ecological and phylogenetic species in the case brown bears and polar bears, and reproductive species in the case of horses and donkeys.

The reason I propose this is that this sort of pragmatic meta-definition has the potential to end unproductive arguments and replace them with clarity - a clarity that emphatically depends on people qualifying the type of species/complexity/modularity or whatever else they are talking about.

Same thing for the other difficult-to-define concepts. Open-ended evolution is the idea that evolution just keeps going, and new forms and features (species, traits, genotypes, etc.) keep appearing. But for how long? Forever? That's longer than anything, so thats not very pragmatic, i.e. it is not a definition that can be applied, because we are too impatient to wait forever. Is natural evolution on Earth even open-ended? Would life on Earth ever reach a steady state after which evolution does not produce new things? Does co-evolution count if this produces new forms that have already existed in the past? Life on Earth is very much affected by the changing fitness landscapes when meteors arrive, volcanos erupt, and solar winds fry the planet, or whatever. Can we just create an evolving computational system in which huge disasters cause mass-extinctions at arbitrary intervals, and then say that the system exhibits open-ended evolution because it keeps evolving? How about these criteria:

  • System evolves in never-ending cycles (revolving open-ended evolution)
  • System reaches steady-state but is reset/interrupted by disasters (reboot open-ended evolution)
  • System continues to evolve new forms for as long as we could wait (temporal open-ended evolution)

The point is to move research forward, rather than letting it be mired in argument, and I think that can be done by simply being more explicit about what we mean when we say something.

Anybody feel like taking a crack at evolvability or life?

Origin of life video

I just did a reddit Science AMA today, and whenever you talk about evolution, invariably the question of the origin of life comes up. It's not my field, as I am not a chemist, but here is a great video explaining a model of how life could have formed spontaneously from chemical elements in the pre-biotic Earth. It is based on research from Jack Szostak's lab.



From now on I will be pointing to this whenever I'm asked how the first cells came about.

Evolutionary dynamics in holey fitness landscapes

ResearchBlogging.orgWhat do real fitness landscapes look like? Do they look more like the image on the left, a nearly-neutral holey fitness landscape, or the one on the right, a rugged fitness landscape with many distinct peaks?



Those are only in two dimensions, so the question is also if depicting anything in two dimensions conveys intuitions that are at all correct.

Holey fitness landscapes (Gavrilets and Gravner, 1997, Gavrilets 1997) are approximations of real fitness landscapes where all genotypes are assigned a fitness value of either zero or one. After normalizing fitnesses to be between zero and one, those that are lower than one are assigned a fitness of zero1. Because real fitness landscapes are of extremely high dimensionality2, and assuming that genotypes have fitnesses that are randomly distributed3, it follows that there exist a nearly-neutral network of genotypes connected by single mutations that has fitness (effectively) equal to one.

The proposition is then that this holey landscape model is a good approximation of real fitness landscapes. It hypothesizes that the evolutionary dynamics on real fitness landscapes is similar to that on holey landscapes, and that distinct peaks like in the image on the right do not really exist. And this is a testable prediction.

Take a look at these videos. They depict populations evolving in two-dimensional fitness landscapes at a very high mutation rate. (You can also download the videos from my research website.)


In all three cases the population size is 2304 (that's (3*16)2, in case you're wondering), mutation rate is 0.5, the grid is 200x200 pixels (i.e. genotypes), and mutations cause organisms to move to a neighboring pixel. Ten percent of the population is killed every computational update (which gives an approximate generation time of 10 updates), and those dead individuals are replaced by offspring from the survivors selected with a probability proportional to fitness (asexual reproduction). Top: neutral landscape where all genotypes have the same fitness. Middle: Half-holey landscape with square holes of 10% lower fitness (size of holes is 14x14 pixels). Bottom: Holey landscape where the genotypes in the holes have fitness zero.

The proposition is that the dynamics of the populations should be the same no matter how deep the holes are. The populations in the half-holey and in the holey landscapes should evolve in comparable ways if the holey landscape is a good approximation.

So what do you think?

What I think is that the evolving population in the top (neutral) and middle (half-holey) landscapes resemble each other, whereas they look nothing like the bottom (holey) landscape. In the half-holey landscape the population takes advantage of the holes all the time, meaning that many individuals who are in them reproduce, even though they have a clear fitness disadvantage. The lesson is that being disadvantaged is just okay, and populations can easily cross quite deep valleys in the fitness landscape. But obviously not when the valleys consist of genotype with zero fitness; evolution in holey landscapes is much impeded compared to rugged landscapes, which is why I think they are not a good approximation.

Caveats: These populations are evolving at a very high mutation rate. When I redid it with a much lower mutation rate (0.05), the neutral and half-holey landscapes stop resembling each other, and the half-holey and holey landscapes look more alike. However, evolution happens so slowly in this case that it is difficult to distinguish the dynamics, so the matter is unresolved so far (however, I have other evidence that lower and more realistic mutation rates do not change this conclusion - some preliminary data in Østman and Adami (2013)). A second caveat is that the whole holey landscape idea relies on the fitness landscape being multidimensional, and so how can I even allow myself to compare evolution of populations in half-holey and holey landscapes in just two dimensions? That is valid question: the intuitions we get from these animations may lead us to think we know something about evolution in multi-dimensional landscapes, while the original premise of Gavrilets' idea was that we exactly cannot. Unfortunately, while this is an empirical question - meaning that it could be tested - the holey landscape model posits that the neutral network appears at very high dimensionality. What this dimensionality is is unclear, so even if I were to evolve populations in 2,000 dimensions (which is not computationally feasible - the limit is a little over 30 binary loci), one could always claim that not even that many are enough. Sighs.


1 Genotypes with fitness greater than 1 divided by the population size, N, are effectively the same, because selection cannot "see" differences smaller than 1/N.
2 High dimensionality means a large number of genes (loci) or number of nucleotides.
3 We already know that this is not a very good assumption, as there are indications that fitness landscapes are non-randomly structured with high fitness genotypes clustered with other fit genotypes (Østman et al, 2010), but we don't know if it is enough to render the holey landscape model useless.

References
Gavrilets S, and Gravner J (1997). Percolation on the fitness hypercube and the evolution of reproductive isolation. Journal of theoretical biology, 184 (1), 51-64 PMID: 9039400

Gavrilets S (1997). Evolution and speciation on holey adaptive landscapes. Trends in ecology & evolution, 12 (8), 307-12 PMID: 21238086

Østman B and Adami C (2013). Predicting evolution and visualizing high-dimensional fitness landscapes, in Recent Advances in the Theory and Application of Fitness Landscapes" (A. Engelbrecht and H. Richter, eds.). Springer Series in Emergence, Complexity, and Computation DOI: 10.1007/978-3-642-41888-4_18

Why do you believe?

Important update April 22nd, 2014: I have been corrected on the usage of the phrases "believe in" and "believe that". In the first sentence below I wrote "believe in something", but what I really meant was "believe that something". Thus, saying "I believe in evolution" is wrong, because it is not a matter of faith. People often respond to this by saying "No, I don't believe in evolution. I accept that evolution is true based on the overwhelming evidence." I have objected to this on several occasions before, but now see the difference. I prefer to say "I don't believe in evolution, I believe that evolution is true (based on the evidence)".

If you say you believe in something, what is it that you mean by that? For example, if you say you believe you will find a hundred-dollar bill today, what is that belief built upon?

I posit that what you actually believe (as opposed to what you say you believe) is really based on probabilities. Perhaps not accurately so, but all future events are of course unknown, though some come very close to 100% certainty, and it is thus really the only way to predict anything with any kind of accuracy.

Trivial example: If you roll a die, you might say that you believe you will get a six. But if we assume this is a fair die, you must assess that the chance is about one in six, so your belief should really be that you do not get a six. In that case you really can't have a rational belief that any one side will come up, though you do of course know with almost 100% certainty (i.e., 100% probability) that one of the six numbers will come up (the die could land on an edge).

In science we make models. That is the essence of the scientific endeavor. A model is basically some explanation of something; hypotheses and theories at opposite ends of a spectrum of explanatory depth are models. So if you as a scientists say you cannot imagine how something would work, how something could have happened, etc., then you basically aren't doing your job. People who dismiss science as rigid and uncreative have not understood what it really entails. Coming up with explanations is among the most creative things people can do. If you're writing a work of fiction, it would surely be defeat if you cannot think of a way to make something click in the story. Same thing with science. If you observe something and you can't imagine how that could occur, then get to work!

Positing a hypothesis is emphatically not the same as "believing" it to be true. That I come up with one hypothesis to explain something doesn't mean that I think it is the most likely explanation, nor does it mean that I can't come up with anything else.

For example, why do I think John Travolta said Adele Dazim when referring to Idina Menzel at the Oscars?

Hyp1: He was high as a kite and just mixed up some slightly related names.

Hyp2: Someone played a joke on him and told him that was her name.

Hyp3: It was on purpose because he thinks that Adele Dazim is a prettier name for her.

Hyp4: He wanted to rock the establishment to secure a role in a new indie film.

Hyp5: He has an occasional speech impediment.

Hyp6: It's a special Scientology accent.


I can assign probabilities to each of these. It may not be accurate (they don't need to add to one, and can actually add to more than one since they overlap somewhat), but at least approximate values or perhaps just a relative ranking of them. Each of these hypotheses could be tested, and my personal belief doesn't really have much to do about anything. I don't yet have any evidence either way, and evidence is of course the only thing we can really base rational belief on, though oftentimes that evidence is reflected in theories about, say, human behavior, in which case I can say I find Hyp1 more likely than Hyp6, because I have seen evidence of only one of them happening before.

The answer is evidence. If you have none, they you have no reason to believe anything. Hypothesizing is not the same as believing, and can be done freely without repercussions. At least that is how things ought to be, everywhere and always.

Bill Nye totally won that debate

The debate tonight between Bill Nye and Ken Ham was won by Nye hands down. Hands up.

Take a look at this lovely slide:


That is a fantastic point. I have not seen it made before. The point is that if there were only 7,000 "kinds" on Noah's Arc, then with the conservative estimate of 16 million species today, then an average of 11 new species should have evolved (even in Ham's creationist model) every day. There should have, in Bill Nye's words, a daily newspaper column listing the new species. Yet nothing like that has ever been observed.

So that was one thing that made this whole debate really enjoyable or me.

Bill Nye did the right thing. In his opening 30 minutes he went right for the jugular of the creationism model. The question to debate was "Is creation a viable model of origins?", and Nye attacked that directly by making several points that shows that it is direct contradiction with science:

  • Antarctic ice-cores show that the first snow that fell and made the bottom layer of the ice is 680,000 years old.
  • There are trees  that are more than 9,000 years old.
  • Grand Canyon is many millions of years old.

These are all dated by different scientific methods, and directly contradict an Earth that would be only 6,000 years old.

Other points from the opening remarks:

  • If fossils all died during the flood, then similar species should not necessarily be found in the same sedimentary layers, but should be mixed.
  • If kangaroos walked from Mount Ararat to Australia (via a land-bridge for which there is no evidence), then there should be remains of dead kangaroos along the way, and yet there is not a trace.
  • The Arc as described in the Bible is simply too large to function when made of wood.
Ken Ham also said some things. The main point he made, which he made very many times, was that there is a difference between observational science and historical science. Historical science is not valid science, according to Ham, who said that if you weren't there, then you can never know. But since God was there, and because he wrote it down in the Bible, we can only know what happened by reading the Bible. This stance of course eliminates our ability to conduct criminal investigation, but no one would actually be that dumb. I have at least never heard of any creationist picketing crime scenes and courthouses when they obtain and allow historical evidence.

I predicted that Bill Nye would win this debate. What I meant was in the long term. What matters is inviting young people and children to explore science, and showing them that there is another model than creationism that in fact most people in the world find more credible. That was the goal, also as stated by Bill Nye.

However, I also think that Nye won in the short term. He clearly came away looking way better than Ken Ham, having presented his case with a confidence that I think most viewers noticed. He made great points that hopefully will make young creationists think twice and make them go look at the science for themselves (thank goodness for the internet) before they become hardened creationists heavily invested in creationism.

The fear of some people, like Richard Dawkins and Jerry Coyne, was/is that debating at all lends credibility to the creationists: "Well now, if Bill Nye takes Ken Ham seriously enough to publicly debate him, then maybe there really is something to creationism", or "That Bill Nye shows up in the first place confirms my belief that Ham's creationism model is correct". I just really, really don't think this is the case anywhere. I'd love some data on this, and to change my mind the data should show that this effect is greater than the effect of getting children interested in (real) science.

I think Nye did an excellent job, thank you very much.


Why Bill Nye will win this debate

In just two days Bill Nye and Ken Ham are having a public debate in Kentucky over evolution vs. creationism. The question to be debated is “Is creation a viable model of origins?”



Update: Sign up for free live streaming of the debate.

The meta-debate is whether it was clever or not of Bill Nye to accept the invitation to debate in the first place. Many people believe that Ken Ham has already won just because Bill Nye has agreed to debate. Debates are not the way science is done, and obviously both parties are going to stand their intellectual ground and not move an inch. What scientists seem to fear the most is that accepting to debate science with creationists lends them credence, that creationists looks like they are being taken seriously, and as a consequence that their theory, creationism, in the eyes of the public is afforded credibility.

Jerry Coyne, for example:

He thinks there are better ways for Bill Nye the Science Guy to make use of all the good will he's earned from his science TV shows. 
"I'd tell him, 'Keep going around giving talks about evolution. Write about it. Give lectures.' People love that," Coyne said. "He's greatly beloved by a large number of Americans. But don't get into a one-on-one with a creationist. If you show up for a debate like that, you lose."
"Poeple?" What people? Yes, people who watch science programs on the TV in the first place. But many of the creationists don't let their children watch them at all! With a debate like this, it is possible that Bill Nye can reach some of those, and sow a few seeds of enlightenment, so to speak.

I don't think there is anything to worry about for one simple reason: the facts are on our side. Evolution really is true, science really does work, and prayer really, really doesn't. Therefore, the more this debate is made public, the more children and high schoolers are made aware of the opposing sides, the more people will understand and believe in evolution (i.e., accept the evidence) in the future.


All Bill Nye has to do is calmly (or not calmly) explain why evolution is true and why creationism is not, and sit back and let Ken Ham make a fool of himself. Ham can go ahead and sound as eloquent and wise as he wants - the bottom line is that his view of the world is the wrong one, and there is nothing he can do to stop the coming generations from learning that, save for stalling it by affecting the school boards across the country that determines what is taught in school.


I predict that whatever commentators will say in the days following the debate on February 4th about who won and why, the real test will be determined years ahead when we see that, indeed, more and more young people flee from creationism and realize that science is the only reliable way to learn about the natural world, and that creationism can teach us nothing about it. That will be the real victory, and Bill Nye will have been part of it.


Besides, it's going to be a good old laugh, and you know it!

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Got a new question on the reddit AMA

from NorrisChuck via /r/IAmA/ sent  ago
Who is more evolved? White man or a Black man?