Flexible, interactive simulations: SLiM 2 published in MBE

Hi all!  Back in April 2016, I wrote a post about SLiM 2.0, a software package that I've developed in collaboration with Philipp Messer at Cornell.  SLiM 2 runs genetically-explicit individual-based simulations of evolution, on the Mac or on Linux, either at the command line or (on the Mac) in an interactive graphical modelling environment (great for teaching and labs!).  SLiM 2 is scriptable, with an R-like scripting language, making it extremely flexible; the manual for SLiM 2 has dozens of example "recipes" for different types of models that can be implemented in SLiM, including genetic structure, population structure, complex types of selection, complex mating systems, and complex temporal model structure.  Even relatively complex models (quantitative genetics models backed by explicit loci, kin selection and green-beard models, models of behavioral interactions between individuals, models of social learning, etc.) can be written with just a few lines of script.  And yet despite all this flexibility, it's also quite fast, and it works well on computing clusters if you have projects with long runtimes.

What I'm announcing today is that our paper on SLiM 2 has now been published online by Molecular Biology and Evolution.  This paper introduces the software and provides an interesting model as an example (a CRISPR/Cas9-based gene drive in an stepping-stone island model with spatial variation in selection acting on the drive allele).  It also provides performance comparisons with other forward genetic simulation packages (SFS_CODE and fwdpp).  If you're interested in SLiM, this paper is a good place to start; and if you're already using SLiM, it's now the correct paper to cite, not Philipp's 2013 paper on SLiM 1.0.

If you're got questions or feedback about SLiM 2 you can either contact me by email (bhaller squiggly mac point com), or you can post on SLiM's discussion list, slim-discuss.  Enjoy!


Ref:

Haller, B.C., & Messer, P.W. (2016.) SLiM 2: Flexible, interactive forward genetic simulations.  Molecular Biology and Evolution (advance access).  DOI: 10.1093/molbev/msw211

The healing power of optimism

Recent events can leave one pessimistic about the future of our world and the merits of its humans. Climate change is running amok. Deforestation abounds. Invasive species destroy native communities. Terrorists cause unprecedented fear and suffering. Racist, misogynistic, serial liars are elected to the most powerful positions. Indeed, talking to young people makes clear that they often think the world is spiraling into Hell and taking humanity with it. Biodiversity is destroyed. Our kids have no future. Humans are on the path to extinction. In this miasma of pessimism, it is perhaps useful for us old timers to bring a bit of personal historical perspective.

When I was growing up, nuclear war was the specter hanging over all our heads.

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Many people – including all my friends – were almost sure that we were all going to die in a ball of flame or frozen in the subsequent nuclear winter. Bunkers were constructed. Supplies were stockpiled. Fear shaped nearly all aspects of life. Now, the fear is mostly gone. 

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Another werewolf of my childhood was smog.

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Take Los Angeles as an microcosm. Smog was so bad that people were told not to go outdoors much of the year. Crops withered. People died of lung problems. Then clean air legislation led to emission control devices, particularly the catalytic converter. Now, smog alerts are much less common.

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Then came the ozone layer depletion. 

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CFCs and other pollutants were causing it to shrink, increasing the bombardment of the world’s DNA with damaging UV radiation. We were all going to need umbrellas all day long. But then regulation banned CFCs and the ozone layer stabilized to the point that it is no longer a paramount concern.

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And don’t forget DDT (solved by legislation), acid rain (reduced through emission controls), mercury poisoning (reduced through awareness), eutrophication (reduced through waste processing), George W. Bush (followed by Obama), Stephen Harper (followed by Trudeau), and so on. Sure, some of these problems still exist, especially in the developing world, but they are nowhere near the front of our consciousness and concerns anymore because – to a point – we have learned how to deal with them and have taken steps to reduce them.

Now we have deforestation, climate change, terrorism, Brexit, and – of course – Trump. Just like nuclear war, smog, ozone depletion, DDT, acid rain, and the rest of it, these problems can make it seem like the end of the world is just around the corner. I would submit, however, that these problems will be solved (or at least reduced) through human ingenuity, legislation, and social change. It won’t be instant, it won’t be everywhere (e.g., smog and eutrophication are still huge problems in the developing world), and it won’t be complete. But – just like seemingly unsolvable problems of the past – today’s problems are also solvable.

As today’s problems fade (some of them – most notably climate change – very slowly), new problems will emerge. Those problems will cause pessimism in the future’s youth. But those of us old timers who have seen unsolvable problems emerge and then be solved will be more sanguine about things – optimistic even. Of course, this optimism is no cause for complacency or inaction - in fact, just the opposite. The key is for all of us scientists, citizens, and humans to do what we can to improve the state of the planet and our society.

I expect this post to engender many thoughts and opinions about how I am glossing over how horrible the state of the world is – and will become. Rest assured, I fully acknowledge that yesterday's problems are not entirely (or maybe even mostly) gone and that today’s problems are huge – and will remain so into the future. My point is simply that a personal historical perspective from us old timers can perhaps bring some healing by promoting optimism. That optimism will then hopefully stimulate action than helps to solve the problems. Yes we can.

Street smarts

On a Bajan terrace, under the mystified gaze of local customers, two men stare at a sugar packet that was placed on the next table, without blinking the eyes. Are they waiting for the sugar packet to reveal the answer to life and the universe, or that it shows them the way of the holy sugar cane? In fact, these two seemingly enlightened guys are actually conducting a scientific study. The excellent Simon Ducatez, a French evolutionary biologist and me, Jean-Nicolas Audet, neuroethologist from Montreal, are in Barbados to study bird behavior.

Waiting for the bullfinches. Field work is never easy.

Those that we are waiting for are Barbados bullfinches. When you sit at a terrace in Barbados, it's almost guaranteed that you will share your table with bullfinches. Of all the street smarts (see Figure 4 and sup. 1 and 2 movies) they use to forage, the bullfinch steal sugar packets and they are able to open them to extract the sugar (see movie below). Our multiple terrace visits allowed us to discover that there was independent appearance of this innovation (and not just social transmission).

 Barbados bullfinch opening a sugar packet. (from: http://link.springer.com/article/10.1007%2Fs10071-013-0612-4)

But what about bullfinches that live in the country side, where there are no sugar packets lying around? Would rural bullfinches be capable of accomplishing such feats, if they had the opportunity to do so? My supervisor Louis Lefebvre and we decided to test this idea by comparing the behavior of rural and urban bullfinches.

The goal was to capture bullfinches in places with different degrees of urbanization, from highly rural to highly urbanized (see map below). The northeastern zone of Barbados is one of the few areas that are relatively untouched by human presence, so rural sites are concentrated in this area of the island. In contrast, the west coast is very populated, partly because of the very high tourist activity. Going out in the wild (and in the human wilderness), in uncharted territories to capture birds represents some challenges. We often had to chase out monkeys, mongooses, giant bumblebees or even horses that were too interested by our mist nets but we were also chased out ourselves by angry farmers who though we were poaching on their land. We also needed some street smarts to elaborate the logistics with very limited means and we even had to manufacture some specialized equipment. In any case, this adventure was a lot of fun and it is my best field work experience to date.

Our 8 capture sites. Red indicators designate rural sites and yellow, urban sites.

Once we captured our birds – and many more other wonderful bird species that happened to fly in the nets – we brought the bullfinches in the “lab” at the Bellairs research institute. The “lab” was in fact 4 walls and a roof. For the rest, we had to figure out how to make it look like an aviary.  Again, a lot a streets smarts was needed there.

Me, proud of my artisanal mist net installation on a rural site.

And that is when, finally, the real science began. Our first behavioral task aimed at measuring the birds’ boldness, by recording how long it takes for the birds to come at the feeder after a human disturbance. Expectedly, the urban birds were bolder, probably because they are more habituated to the human presence. We also measured neophobia, the fear of novelty. We used the same protocol as for boldness but a novel object was placed beside the feeder. Surprisingly, the urban birds were more neophobic than the birds from rural areas. While we don’t know the real reason for this, this could be explained by the fact that birds living in urbanized areas learn to fear the novel situations because of their potential danger, whereas rural birds live in very predictable environments and never learn to fear weird situations. For more details on the temperament results, see the original article.

Our most striking result is the finding that urban bullfinches are more street smart than country birds, as reported by IFLScience. In fact, birds captured in urbanized areas were faster at solving two different problem-solving tasks. Those problem-solving tasks (see video made by National Geographic, below) were specifically designed to mimic technical foraging innovations in the wild, like the sugar packets opening. Having a better ability to solve problems in a city could mean life or death.

We have also measured immunocompetence in birds from both environments. To do so, we injected PHA into the wing of bullfinches and 24 hours later we measured the intensity of the reaction. This measurement is a proxy for the strength of the immune system. We first hypothesized that the immunity would be reduced in animals that have better cognitive abilities, since it is costly to maintain both systems at the same time. We imagined that the immunity would be a good candidate for a trade off trait against problem-solving ability. We were wrong. It appears that the urban birds’ immunocompetence is much higher than in rural birds. It seems that in this case, the urban birds have it all, although I find this hard to believe. Another possibility is that the city birds live well, but they die faster than country birds. In fact, in a study involving great tits, telomeres were found to be shorter in urban birds compared to rural birds. In any case, if I were a bird, I would probably be an urban bullfinch.

The article « The Town Bird and the Country Bird: problem-solving and immunocompetence vary with urbanization. » was published in Behavioral Ecology, 2016; 27(2):637. http://beheco.oxfordjournals.org/content/27/2/637