Sequencing: The Next Generation

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

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

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

Science online, gluteal symmetry edition

Is that a tennis ball in your pocket, or asymmetric hypertrophy of your iliopsoas? Oh. It’s a tennis ball. Photo by Steve9091.

Flowers stay open for pollinators, not daylight

A honeybee explores the depths of a dandelion, one of the species used in Fründ et al.‘s experiments. Photo by je-sa.

ResearchBlogging.orgIf you’ve ever stopped to admire morning glory flowers opening first thing in the morning, then noticed they’ve closed by evening, you’re at least dimly aware of one of the longest-established ideas in plant biology: that flowers open and close on a reliable daily schedule. Different species are open at different times of day, of course, but each flowering plant has its preferred open period, and it sticks to that schedule during its flowering season.

This idea led Carolus Linneaus, the father of modern biological taxonomy, to propose an Horologium florae, or “floral clock” using plantings of species with known flowering times to mark the hours. You can find his table of proposed species in the online version of Linneaus’ 1783 treatise Philosophia Botanica, if you’re not averse to Latin. Studies of flowers’ daily schedules go back to well before English was the language of international science, and continue to the present day [$a].

Yet no one seems to have spent much time considering how flowers’ schedules might respond to the activity of their very reason for being: pollinators. Flowers don’t open just to be open in a particular kind of sunlight—they’re open to attract animals that can carry pollen to another plant, and maybe leave some, too. If a flower receives enough pollen to make seeds by noon, why would it stay open until two o’clock?

According to some new experimental results, the answer to that question is that they don’t [$a].

Jochen Fründ, Carsten F. Dormann, and Teja Tscharntke set out to see whether a selection of European wildflowers adjusted their opening schedules in response to pollination, with two major experiments and a broader-scale observation project. The experiments address whether pollinator activity could change flowers’ schedules; the observations help determine how important those changes might be in studies of plant-pollinator interaction.

A floral clock in Geneva—not quite what Linneaus had in mind. Photo by aranmanoth.

In the first experiment, the team planted wildflowers—Crespis capillaris, a close relative of common dandelions—in experimental plots spaced across a field. Plots were either caged or left open to insect visitors, and Fründ et al introduced bees into some of the caged plots. So some plots had a controlled set of pollinators, some had none at all, and some had whatever pollinators were already active in the field.

The team then watched the flowers’ daily opening and closing in the experimental plots. (They had a lot of help—a long list of names in the paper’s Acknowledgements section ends with “and many others.”) Over the same period of time, flowers in the un-caged plots received more insect visitors than flowers in either other treatment, and had mostly closed by midafternoon; flowers in the caged plots with bees introduced received fewer visitors and closed hours later; and flowers in the plots with no pollinators at all stayed open till evening.

So flowers experiencing the same daylight pattern closed earlier if they received more pollinator visits. The team followed up this result by hand-pollinating flowers of C. capillaris and a handful of closely related species growing in the same field, including dandelions—and flowers of three out of four species closed more rapidly when hand pollinated. Dandelions didn’t respond to hand pollination, a result the authors explain by noting that dandelions often self-pollinate, and so don’t need to wait for animal pollinators.

Finally, the team compiled observations of plant-pollinator interactions from sites similar to their study field located across Germany, and divided them into observations taken before solar noon, when the focal flower species from the experiments above tend to be open, and after solar noon. Which pollinator species visited which flowering plants depended significantly on when the observations were made—to the extent that the apparent importance of C. capillaris and its relatives is entirely different before and after noon.

Of course, these results apply directly to only a handful of species representing a particular group of flowering plants—but it’s a group with a lot of widespread and abundant members, and the result is straightforward and striking. Animal-pollinated plants may not behave much like clocks at all. Instead, they’re more like the patrons of a singles bar: they show up at about the same time and hang around until they find someone to buy them a drink. That’s a dynamic worth keeping in mind for studies of plant-pollinator interaction, since it suggests that the partners a pollinator chooses will depend, at least in part, on whether or not it’s out after closing time. ◼

References

Ewusie, J., & Quaye, E. (1977). Diurnal periodicity in some common flowers. New Phytologist, 78 (2), 479-485 DOI: 10.1111/j.1469-8137.1977.tb04854.x

Fründ, J., Dormann, C., & Tscharntke, T. (2011). Linné’s floral clock is slow without pollinators – flower closure and plant-pollinator interaction webs. Ecology Letters DOI: 10.1111/j.1461-0248.2011.01654.x

von Hase, A., Cowling, R., & Ellis, A. (2005). Petal movement in cape wildflowers protects pollen from exposure to moisture Plant Ecology, 184 (1), 75-87 DOI: 10.1007/s11258-005-9053-8

#ESA2011 #ESA11: Who to follow

Update, 9 August 2011: I seem to have picked the wrong hashtag–there’s more activity at #ESA11.

Western scrub jay. Photo by Minette Layne.

The annual meeting of the Ecological Society of America is underway in Austin, Texas, this week. If, like me, you’re not anywhere near Austin, do not despair. There are people who will use the Internet to tell you what is going on at the meetings anyway, out of sheer enthusiasm for ecology! Here are the ones I’m following:

Thanks in part to readers like you, Sarcozona will be covering the meeting at Gravity’s Rainbow. Zen Faulkes of NeuroDojo has apparently been there since Day 0. And Jeremy Fox has been anticipating the meeting for the last week over at the OIKOS blog. Finally, you can follow the official ESA twitter feed and the hashtag #ESA2011 #ESA11 for continuous updates. ◼

Science online, migrating sushi edition

You must admit, it doesn’t look comfortable. Photo by Soller Photo.
  • A movable feast. The neurochemical explanation for those viral videos of dancing squid sushi.
  • Or, you know, don’t fragment the habitats. To offset the effects of habitat fragmentation and help natural populations adapt to changing climate, just add gene flow.
  • The knight’s burden is a heavy one, literally. Was medieval chivalry undone by the sheer weight of knights’ armor?
  • Coming soon: age-defying low-iodine diets. Axolotls are neotenic salamanders, meaning they become sexually mature without developing the “adult” characteristics other salamander species typically have—unless you dose them with iodine.
  • Reviving, not revived. After being fished nearly to extinction, the Atlantic cod population—and rockfish, and haddock—may finally be reviving.
  • We traded guts for brains. Compared to other mammals, humans have unusually big brains for our body size, which means that we also have rather odd bodies.
  • And we’re not talking about “Tag” body spray. The African crested rat deters predators by slathering itself in poison.
  • These congratulations will not be withdrawn later. Retraction Watch completed its first year of following up on post-publication reviews and refutations this week—well done!

Carnival of Evolution, August 2011

Grizzly bear. Photo by Alaska Dude.

The latest edition of the Carnival of Evolution, a monthly collection of online writing about evolution and all its ramifications, is online at Sandwalk. Check it out to learn why genetic testing for grizzly bears is important, what new fossil may have taken the place of Archeopteryx in the evolutionary history of birds, and what pioneer of evolutionary biology will soon be on a U.S. postage stamp.

Science online, urban evolution edition

Freddie Fungus and Alice Algae have no likin’ for prions. Photo by 0olong.
  • Genetically determined, except when it isn’t. The evolutionary context of misogyny.
  • Queering evolution? The new frontier for evolutionary biology may be tracking adaptation to human-built environments.
  • Mad lichen disease? Some lichens can apparently break down prions.
  • Really, where would it have gone? That big underwater plume of oil spilled into the Gulf of Mexico is still there.
  • No surprise to field scientists, I suspect. Commercial GPS systems have some downright dangerous issues with their databases for rural and wilderness areas.
  • “This was the original peer review: immediate and open” The increasing use of online platforms for post-publication peer review may be taking scientific discourse back to its Enlightenment-era roots.
  • Guess I’d better get some more gel packs. Carbohydrate supplements during exercise do, in fact, help you work longer
  • I’m sure that if/ I took even one sniff/ It would bore me terrifically, too … Pair-bonding with a mate seems to make voles less prone to amphetamine addiction.
  • Time to revise the bat “pollination syndrome.” A bat-pollinated tropical vine has leaves that collect and reflect its pollinators’ echolocation signals.

Of mice and men, making a living in rarefied air

(A)

High-elevation populations of deer mice have evolved “stickier” hemoglobin to cope with the thin atmosphere. (Animal Diversity Web)

ResearchBlogging.orgIt’s easy to walk through the woods and fields of North America and never spot Peromyscus maniculatus, the deer mouse, but you’ve probably heard them scampering off through the leaf litter or under cover of tall grass. They’re exceptionally widespread little rodents, found in forest undergrowth and fields from central Mexico all the way north to the Arctic treeline. In all this range, they look about the same: small and brown, with white underparts and big, sensitive ears.

That apparent sameness is deceptive, however.

A big, varied range presents lots of different environmental conditions to which a widespread species must adapt. And when that big, varied range includes the Rocky Mountains, one of those environmental conditions is as basic as the air itself. At high altitudes, atmospheric pressure is lower, which means lower partial pressure of oxygen, the gas that makes life as we know it work.

The fundamental problem at high altitude is to pull more oxygen from thinner air. Natural selection is good at solving problems, and it has multiple options for adapting a mammal to thinner air at high altitudes, to the extent that these traits are heritable. Selection could favor individuals who more readily respond to thin air by breathing faster and deeper, pulling in more air to make up for its lower oxygen content. Or selection could favor individuals who produce more red blood cells, so that a given volume of blood pumped through their lungs picks up more oxygen. Or, at the most basic level, selection could favor individuals whose individual red blood cells are better at picking up oxygen, via a new form of hemoglobin, the oxygen-binding molecule that packs every red blood cell.

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Science online, certified organic breakfast edition

This organic breakfast may not be “chemical free,” but it could change your brain. Photo by lauren glanzer.

Special congratulations this week to Ed Yong, who is officially a full-time freelance writer as of Wednesday. I can only imagine what he’ll achieve now that this science writing thing isn’t restricted to his spare time.

  • Please note that “direct” experiments ≠ clearer results. Groundbreaking experiments that would be ethically impossible to conduct.
  • Pre-emptive incest? Hermaphroditic scale insects impregnate their offspring just after conceiving them.
  • In other words, bugger off, Senator McCain. Why would you want to sample bears’ DNA? Because bears are actually pretty important, for starters.
  • No word on whether they also dance quadrilles. Teeny-tiny lobsters buzz to scare off predators.
  • The first one alone may cause a spit-take. Four myths about organic agriculture may surprise you quite a bit.
  • Or, less likely to draw, anyway. You’re more likely to win at “rock-paper-scissors” if you play blindfolded.
  • “Ooooh, changes in grey matter.” Scicurious soft-boils a study purporting to show that eating breakfast changes your brain.
  • Population control. When doing observational research on humans, the way you group people into populations may make a big difference.

Science online, indirect costs of royal jelly edition

A queen bee, indicated with a red dot of paint. Photo by reway2007.
  • Not so much explanation as warning, really. The intricacies of indirect costs in grant funding, explained.
  • Motivation is key. Anoles demonstrate learning ability in an experiment that has them playing find-the-worm.
  • Paging Doctor Pangloss? Bats might be most active at night because flying is hot work.
  • Long live the queen! The specific protein in honeybee “royal jelly” that makes bee larvae develop into queens has been identified [$a], in part by giving the protein to fruitflies to make “queen” flies.