Data sharing, reproducibility and peer review

I just reviewed my first manuscript where the authors provided a reproducible analysis (i.e., they shared their data and analysis script with the reviewers). This is something my coauthors and I have tried to provide with our recent studies, but it was my first time experiencing it as a referee.

I think it really helped, but it also raised new questions about traditional peer review.

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Troubleshooting and iteration in science

The scientific method is taught as far back as elementary school. But students almost never get to experience what I think is the best part: what you do when something goes wrong. That’s too bad because self-correction is a hallmark of science.

In ecology and evolution, most graduate students don’t get to experience iteration firsthand, because they are often collecting data right up until the end of their degree. I didn’t experience it until my postdoc, when we failed to repeat a previous experiment. It took several experiments and a lot of time  – two years! – to figure out why. In the end, it was one of the most rewarding things I’ve done.

Wouldn’t it be great if undergraduate students actually got to do this as part of their lab courses (i.e., revise and repeat an experiment), rather than just writing about it?

One thing that can come close – teaching you how to revise and repeat when something doesn’t work – is learning to code.

A bad year for birds

June 2013 was bad for tree swallows. At the Queen’s University Biological Station, over 90% of nests failed as a result of persistent cold, rainy weather.

This happened to be the same year we were conducting an experiment on the hormonal mechanisms of parental care in these birds. The bad weather made for a disastrous field season. Just a couple of weeks in, and we were turning up cold lifeless chicks in nearly every nest. The upside was that it led to some potential insights into the way stress hormones and tough weather conditions interact. My coauthors Jenny Ouyang and Ádám Lendvai were invited to write an excellent blog post about it here:

Terrible weather provides insight into a bird’s life

It was remarkable how closely the nest failure rates tracked the fluctuating air temperature. This could be caused by a couple of factors, with a major one being that tree swallows rely on flying insects to feed their young, and the ability of insects to fly depends on temperature. Persistent cold weather means that parent tree swallows cannot find enough food to support their offspring.

The corticosterone hormone implants made the treatment birds more susceptible to faster brood mortality, even during benign weather. It should be noted that the implants were deployed before the bad weather struck, and we would not have performed this experiment if we had known in advance that this would be such a tough year! Hopefully, though, the results provide some insight into the role of stress hormones as mediators of a sensitive period in the life history of these birds.

Read the study here:

Ouyang et al. 2015. Weathering the storm: parental effort and experimental manipulation of stress hormones predict brood survival

How to loop efficiently in R

My learning curve with the statistical software R has been a long one, but one of the steepest and most exciting times was learning how to write functions and loops. Suddenly I could do all kinds of things that used to seem impossible. Since then, I’ve learned to avoid for loops whenever possible. Why? Because doing things serially is slow. With R, you can almost always reduce a big loop to just few lines of vectorized code.

But there’s one situation where I can’t avoid the dreaded for loop. Recently, I learned how to make for loops run 100s of times faster in these situations.

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Brawn over brains?

There’s no question that broadly speaking, big brains are smart. Take humans, for instance: our brains weigh in at about 3 pounds on average, nearly four times the size of the brains of chimpanzees (whose brains weigh in at less than a pound apiece).

What’s less clear is why. There are a number of theories: maybe intelligence evolved to give us a competitive edge in foraging, or maybe it helped us keep track of increasingly complex social interactions. Ideally, we’d like a theory to explain the evolution of intelligence broadly, so researchers have tried to these hypotheses across multiple species (for instance, comparing relative brain size and social group size among hoofed mammals like horses and deer1).

But brain size alone – even when scaled as a proportion of overall body size – is not an ideal measure of intelligence. The trouble is that small animals often have considerably higher brain-to-body mass ratios – ant brains, for instance, can weigh nearly 15% of their total body mass (the equivalent of a 20 pound human head!), and mice have about the same brain-to-body mass ratio as we do. So how can we study brain evolution, when even primates span a 3000-fold difference in body size (comparing a gray mouse lemur and a gorilla)?

Enter the encephalization quotient, or EQ, a measure of brain size relative to what we would predict, given that there is a curved relationship between brain size and body size (allometry is the technical term for this). It’s the best yardstick we have for the evolution of intelligence. Until now, that is.

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Nest in the city

One of the most incredible things about peafowl is how well these birds thrive in the suburbs. There were hundreds in Arcadia, CA, where I studied them, and every once in a while I hear about some other town where they’ve taken over – Orange County, Palos Verdes, Miami – they even disperse and occasionally pop up somewhere new (like here, or here). I’ve been told that in India (where the species is originally from), flocks also tend to settle down in villages. (And the name for a group of peafowl? A muster!) And peacocks are now on the cover of a book on urban birds1.

So what makes peafowl so much better at urban living than other, similar species?

It could be that they’re catholic about their diets, or that they’re tolerant of a broad range of environmental conditions2. Other research has suggested that, in mammals at least, successful invaders tend to have relatively large brains3 – possibly because a large brain confers the ability to respond flexibly to new situations. American crows fit this theory, as an urban success story with relatively large brains. But peafowl are some of the smallest brained birds out there, when you consider brain size relative to body size – and pigeons, starling and house sparrows aren’t particularly well-endowed, either. So what if it has more to do with how they use their brains to adapt?

A new study points to an intriguing benefit of city life for some birds, and it has me wondering about learning as a mode of urban adaptation. Apparently, some urban birds use cigarette butts to build their nests – and researchers have now shown that the cigarette butts actually improve the living conditions for young birds.

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Is animal care due for an update?

Canadians will fiercely defend nearly any Canadian-made thing, and we have an uncanny ability to keep track. Insulin? Discovered by a Canadian. The telephone? Also Canadian. Sir Sandford Fleming and his time zones? Canadian too. Tom Cruise? Spent his childhood here.

At the philosophy symposium here in September on ethics and animals, I learned of yet another point of pride: our national body governing the care of animals in research was one of the first in the world. Although the first official law to prevent cruelty to animals was passed in Britain in 1876, and the US had its Animal Welfare Act a few years before Canada’s Council on Animal Care (CCAC) was official, the CCAC had its beginning in the early 1960s – and it was revolutionary at the time.

But is it due for an update?

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Chicken of the trees

This month has been an eye-opener for me. Two weeks ago, I was rubbing shoulders with animal rights activists. One week later, I was hunting at the Croskery farm. And last night, we dined on the spoils – a fantastic squirrel stew that gave Thanksgiving dinner a run for its money.

How did it happen?

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A microscopic predator-prey chase

In terms of behaviour, animals have plants beat – though some would argue that plants have their own brand of intelligence.

Not all photosynthesizing beasts are firmly planted, though, and many that live in the water can move. Aquatic algae, for instance, often have whip-like structures (called cilia and flagella) that they can use to propel themselves along in the water. Some land plants also produce flagellated sperm that can move on their own volition.

H. akashiwo

A single-celled marine algae with flagella for getting around. From Wikimedia.

In the ocean, the ability to move can be beneficial, allowing algal cells to find food or move to a suitable environment. Motile cells can also avoid their predators by swimming away – something land plants definitely cannot do. Swimming algae incredibly slow, topping out at about half a centimetre per minute – but a new study suggests that the slow race between algae and their predators might be responsible for a far bigger, more dangerous phenomenon.

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Neanderthals were into birds

Well, into their feathers anyway. Thanks to a new study out this week, we now have paleontological proof that Neanderthals collected birds for more than just food. They probably used bird feathers for decoration – just like we do – suggesting that we aren’t the only hominid species to have developed an artistic culture1.

The research team – led by Clive Finlayson – used a combination of archaeological and paleontological evidence from several different sites where Neanderthals lived during the Paleolithic, ranging from Gibraltar in southern Spain to sites in the near East. For each site, the researchers tallied up the number of different bird species found in the fossil record at the same time and place as the Neanderthals, and they discovered that certain species were most frequent. The most common species were raptors (like vultures, kites and golden eagles) and corvids (like crows and choughs). Crucially, the researchers found that the remains of these particular species are far more abundant at the Neanderthal dwellings than they are at other paleontological sites – suggesting that the bird bones were there for a reason.

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Innovative, naturally

bluegill sunfish field work

Chandra Rodgers sampling bluegill sunfish on Lake Opinicon.

This spring I had the opportunity to write a feature article on the Queen’s University Biological Station, a site just north of Kingston where researchers have a long history of major scientific breakthroughs involving modest Ontario wildlife. Several of these discoveries have proved to be as useful as they are compelling. The story was published in the Kingston Whig Standard, and on the web through the Queen’s Alumni Review and Funding for photography was provided by the CFI’s 2011 Emerging Science Journalists Award.

Talking to scientists about their research was by far the best part of this project – much more fun than I expected! And even the toughest interviews were a gold mine of ideas. Thanks to everyone who participated. The full story is posted below…

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Life imitates [filmmaking] art

Congratulations to Myra Burrell – her peacockumentary has been short-listed for the Animal Behavior Society’s film festival!

Myra, a veteran of the natural history film program at the University of Otago in New Zealand, traveled to California with me in 2010. She helped with peacock field work, capturing more females than anyone thought possible. Somehow, in the meantime, she made a movie about the birds. It’s a short film that gives you an idea about what happens on a peacock lek, from the hen’s point of view.

It’s quite an honour to be among the 6 films selected for festival screening, since they must get on the order of ~100 applicants. If Myra wins, it would be oddly fitting: a wildlife film straight out of a park that moonlights as a real Hollywood set.

You can watch “Hen’s Quest” here.

The best parts? I love the music and Myra’s cinematography. I contributed writing (including the title!) and did the artwork; Brian McGirr turned my map drawing into a fantastic animation. Good luck, Myra!

To save trees, major rethink is needed

When you stop to think about it, few things are weirder than a tree. Like us, they’re largish organisms made up of many cells, each with a central nucleus – but we have little else in common. Plants diverged from our early ancestors well before there was anything bigger than a single cell around. They split from the animal lineage even before fungi, which leads to a shocking conclusion. That spot of mould in the vegetable drawer? It’s more closely related to you than the plants upon which you both depend.

Small wonder, then, that plants don’t live and die by the same rules as animals – but this could have dire implications. That’s the message of a new study by Jonathan Davies of McGill University, published in PLoS Biology. Davies and his international collaborators have shown that the factors causing extinction in plants are entirely unexpected, and the upshot is that the current IUCN Red List criteria for listing endangered species – which are based on animal studies – might be useless when it comes to plants.

Davies and his team used the latest the comprehensive Red List data for all flowering plant species in two locations: the United Kingdom and the South African Cape. The Cape is a biodiversity hotspot with thousands of endemic species: plants that evolved there, and that can be found nowhere else. The UK flora, in contrast, is made up of species from other regions that moved in after the retreat of Pleistocene glaciers.

Previous work has shown that among mammals, we are most likely to lose species with large body sizes and long generation times – giant pandas and elephants are classic examples. But according to the new analysis, plants break the mold. Davies and coauthors found that the kinds of plants most at risk in the UK are different from those at risk of extinction in the Cape, indicating that basic traits like size have nothing to do with it. Using a detailed evolutionary history of the Cape species, the team also found evidence that extinction risk in plants is tightly linked to mode of speciation: the Cape species most at risk tend to be ones from the younger, rapidly-evolving lineages.

This implies that in plants, extinction is pruning the tips of the evolutionary tree. The authors suggest an explanation: unlike animals, new plant species tend to arise from small isolated populations that are at the extremes of a much larger ancestral range. Thus, a new plant starts off with a limited distribution, and because range size is an important criteria for Red List risk, it is also highly vulnerable.

The team’s analysis of anthropogenic factors turned up an additional surprise. For the Cape flora, human-induced habitat changes such as urbanization and agriculture cannot explain extinction risk of local plants. In other words, there is no simple geographic correspondence between human activity and plant decline. As the authors put it, places like the South African Cape might therefore be both “cradles and graveyards of diversity”, regardless of human activities.

This study suggests that a major strategy revision is in order if we want to conserve the world’s plants – a group that we all depend upon for oxygen and energy. More generally, risk criteria for one taxonomic group cannot necessarily be applied to another, since the pathways to rarity may be as foreign as the species themselves.

Further Reading

Davies, J. T. et al. 2011. PLoS Biology: 9(5): e1000620.

Cuttlefish strike a pose for 3D camouflage

In the game of hide and seek, cuttlefish have the upper hand. These chameleons of the sea are astonishingly good at disappearing: they can instantaneously change the colour of their skin to blend in with the background, matching even the finicky details like the pattern of coloured rocks on the ocean floor.

Divers have long known that cuttlefish are masters of the 3D camouflage game, too, and new research from the Wood’s Hole Oceanographic Institute has revealed how they do it.

Alexandra Barbosa, a graduate student, and Dr. Roger Hanlon were interested in the way cuttlefish strike a pose when trying to hide. After encountering a predator, these octopus-like animals will flee among the corals, rocks and algae, and freeze with their arms contorted into shapes that mimic nearby objects – a feat made all the more impressive by the fact that cuttlefish arms can bend in any direction. Some birds and insects are also known to camouflage themselves with body posture, but few come close to cuttlefish in shape-shifting flexibility (see photos of cephalopod camouflage in the wild here).

To understand just how they do it, Barbosa and her colleagues in Dr. Hanlon’s lab presented captive cuttlefish with some highly unusual surroundings: jailbird stripes, in black and white. In response, the cuttlefish got theatrical, raising their arms roughly parallel to the angle of the stripes. And when the researchers shifted the angle of the background image, the cuttlefish stretched their arms into a new position in an attempt to stay hidden.

Cuttlefish posing on artificial backgrounds

Cuttlefish posing against different backgrounds. Modified from Barbosa et al. 2011 (see Figure 1).

Intriguingly, not all of the ten individuals tested were able to match the angle perfectly all of the time – but these quirks may not be surprising given that cuttlefish camouflage is so complex. After all, in nature cephalopods get to choose their own hiding places, a decision that might involve several different factors. According to the researchers, camouflaged cuttlefish are even known to gently wave their arms to match the movement of the underwater plants they are trying to mimic.

These results are a clear demonstration that cuttlefish use vision to guide their 3D camouflage, since the study animals matched a flat background image. Moreover, Barbosa and Hanlon have shown that shape-shifting cephalopods can easily handle scenarios that would never occur in the environment where these behaviours evolved, and adjust just as flexibly to this artificial environment as they do in their natural habitats.

Captive experiments like this are just the first step in understanding how cuttlefish use visual cues to hide, and some big questions remain. For instance, little is known about how cuttlefish can detect and match colours so well despite the fact that they are, in effect, colourblind – Hanlon has found that giant Australian cuttlefish can take on the colouration of rocks on the ocean floor even in the middle of the night.

These remarkable split-second decisions about where, and how, to hide might also help us understand something bigger. Strategic camouflage is just one aspect of the surprising intelligence of cuttlefish, which have the largest brains for a given body size of any invertebrate – these animals are also able to learn and communicate with one another at a level that rivals many land-based animals. It will be intriguing to see where hide and seek fits in to the history of cephalopod brain evolution.

Further Reading

Barbosa, A. et al. 2011. Proceedings of the Royal Society B. In press.

How I learned to respect the peahen

Written for the Los Angeles Arboretum.

Meep meep? More like “Honk honk!”

Arboretum regulars will no doubt recognize the call of a startled peahen, but you may not be aware of the clever ways they use it. Not that they try to boast or taunt the enemy, necessarily, but I’m starting to think that the birds at the Arboretum owe a lot to their version of the Road Runner’s call.

How do I know? Some background is in order here: I’m the tall blond woman who has been hanging around the Arboretum morning and night for the past few years, overdressed and hauling a camera, a pair of binoculars, some peanuts and, if I was lucky, a peacock. Working at the park each spring, I often wished I had more time to chat with visitors. But I was preoccupied, and the life of an ornithologist can sometimes feel like that of Wile E. Coyote on a bad day.

For the past four years, I’ve been chasing peafowl across the continent – from Arcadia in February to Winnipeg, Toronto and New York in May and June. Incidentally, the Bronx Zoo is the only place in North America that even comes close to the Arboretum in sheer number of peafowl. Three years into my PhD in biology, and I’ve spent literally hundreds of hours watching these birds.

You may be wondering what got me into this mess.

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