The Molecular Ecologist: Tallying differences between species — across the whole genome

Muchárik bielokrký (Ficedula albicollis); Collared Flycatcher A collared flycatcher. Photo by Photo Nature.

This week at the Molecular Ecologist, I discuss a new, genome-wide study of genetic differentiation between two closely related species — the collared flycatcher and the pied flycatcher.

Equipped with the core genome sequence, the team collected still more sequence data from ten male flycatchers of each species, and aligned these additional sequences to the genome sequence, identifying millions of sites that vary within the two species, and millions of sites where they share variants. They scanned through all these sites to identify points in the genome where differences between the two small samples of flycatchers were completely fixed — that is, sites where all the collared flycatcher sequences carried one variant, and all the pied flycatcher sequences carried a different variant. The frequency of these fixed differences varied considerably across the genome, but there are dozens of spots where they’re especially concentrated, forming peaks of differentiation.

To learn what all those “islands of divergence” could tell us about how the two flycatchers came to be different species, go read the whole thing.◼

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Nothing in Biology Makes Sense: Tuning the molecular clock

Clock Photo by Earls37a.

Over at Nothing in Biology Makes Sense!, guest poster Gustavo Bravo explains why evolutionary biologists spend a lot of time thinking about how frequently DNA mutations occur.

There are two ways in which we can translate the number of substitutions between a pair of lineages into absolute dates. First, we can calibrate the clock against absolute times resulting from independent evidence such as fossil or geological dates. And secondly, we can measure directly the rate of mutation by comparing DNA or protein sequence data in present day organisms. Because the fossil record for some groups is incomplete and the dating of geological events remains controversial, some of those clocks are likely to produce inaccurate estimates of time.

To learn how re-setting the “molecular clock” has changed our thinking about human evolution, go read the whole thing.◼

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Plants are creepy, too

Christopher Martine’s web series about all things botanical, Plants are cool, too! (which I’ve mentioned before) has a new episode up just for Halloween. It’s on carnivorous plants, natch.

Elsewhere on the science-y web, Scicurious talks about real-life werewolves, and Kate Clancy offers a terrifying peek at her schedule. Happy trick-or-treat-ing, if you’re doing that sort of thing on a school night.◼

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You should watch: Cloud Atlas

MOTHs in a china shop. Image via TeeVee in DC.

So last night I saw Cloud Atlas, the big new film directed by the Wachowski siblings and Tom Tykwer. I don’t know what I was expecting, exactly, beyond that it’s based on a widely respected and reputedly un-filmable novel and that I haven’t cared much for anything the Wachowskis have directed since the original Matrix. But, well, wow.

Cloud Atlas weaves together a set of stories set hundreds of years apart, using the same core cast of actors — including Tom Hanks, Halle Berry, Jim Broadbent, Hugo Weaving, Jim Sturgess, and Ben Whishaw — in different-but-related roles. If that sounds potentially unwieldy already, consider that many of the actors switch genders and races (to widely varying degrees of effectiveness) from story to story, and that in fact each story is really a completely different genre. There’s a Merchant Ivory-style tale about a nineteenth-century lawyer voyaging home from a slave-buying expedition, a farce that might as well have been an episode of that BBC sitcom about life in a retirement home, a mystery thriller set in the 1970s, a quest across a postapocalyptic wilderness, a tragedy about a miserable old-timey homosexual who’s composing a groundbreaking symphony in prewar Britain, and a Blade Runner-style science fiction action film.

All these films are intercut so as to highlight, with varying success, the overlaps and interconnections between their stories. The melody at the core of the symphony composed in prewar Britain recurrs in a San Francisco record shop in the 1970s, in the slums of futuristic Neo-Seoul, and among the ruins of nuclear war. In the farce, a bumbling old publisher writes a memoir which is adapted into a movie that inspires revolution centuries later. People are made captive, and set free; they help and hinder each other in their various quests. Multiple characters in multiple stories muse aloud about the interconnectedness of all people and the transmigration of souls, which is mostly unnecessary given how often we can see that, if the stories don’t quite repeat themselves, they unmistakably rhyme.

Whether or not you like Cloud Atlas will boil down to how well you think it weaves all these stories together — I came away almost entirely satisfied. I’m a sucker for big and ambitious and wide-ranging, and while there’s more than a few moments of fridge logic within the individual stories that comprise Cloud Atlas, I walked out of the theater looking forward to seeing it again.


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Science online, shaky verdict edition

Pills 3 Photo by e-MagineArt.com.

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Rescued baby echidna

And, see, I did not previously know that the appropriate word for an echidna (or all monotremes?) at this stage of development is “puggle.” So this is totally an educational experience.

Via Grist.◼

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Nothing in Biology Makes Sense: Making sense of maternal mammary metagenomics

Breastfeeding symbol Breastfeeding. Image via Topinambour.

This week at Nothing in Biology Makes Sense!, Sarah Hird digs into a new study of the bacterial diversity in human breast milk.

Cabrera-Rubio et al. (2012) analyzed the bacterial composition of HBM [human breast milk] from 18 women at three time points over 6 months. The mothers in the study varied in weight and delivery method. The researchers were basically exploring what factors influence the microbial composition in breast milk, with an emphasis on weight of the mother. They used next-generation sequencing to produce a library of sequences that were analyzed for what specific bacteria were found in each sample and how the samples relate to one another as whole communities.

Some of the factors that turned out to influence bacterial diversity in HBM are pretty surprising — to find out what they are, go read the whole thing.◼

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The Molecular Ecology Online Forum

Remember the Molecular Ecologist symposium I attended as part of the 2012 Evolution meetings in Ottawa? Well, there’s going to be a sequel, launching Wednesday in convenient online format.

The Molecular Ecologist will be hosting speakers from the Ottawa symposium in a live-chat on the blog, starting at 9 a.m. US Central Time and running until noon (that’s 3-6 p.m. GMT, for those of us located outside North American). We’re trying out a live-chat service called CoverItLive, which will let readers follow the coversation and submit questions and/or comments directly from the blog — test runs have gone pretty smoothly, and I’m excited to see how this works as a medium for scientific discussion.

If you want to review the Ottawa symposium beforehand, check out the archived material at the Molecular Ecology websited. To indicate your interest and submit questions in advance, e-mail Molecular Ecology Managing Editor Tim Vines; otherwise, just join us Wednesday morning at The Molecular Ecologist.◼

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Marathon number five

2012.10.21 - Mankato Marathon 2012 finisher medal They give you a medal just for finishing — which was kind of a feat, in my case. Photo by jby.

So I’m home and more-or-less recovered from marathon number five, the Mankato Marathon. Final time: 3 hours, 33 minutes, and 32 seconds. Which, it happens, is five whole seconds better than my last marathon back in June. At two marathons a year with this kind of improvement, I’ll qualify for Boston some time before my 200th birthday.

I tried to tweet a couple images, but this one was pretty rough going, and I had other things on my mind. Like making it to the finish line. I’m sure Mankato is a lovely town, but there’s not enough of it to contain a whole 26.2-mile course, so most of the first two-thirds of the race were out in the middle of open farmland, with nothing to block a pretty persistent wind. Which wind was good for thermoregulation, but made running perceptibly harder.

Even so, I finished the first 23 miles in under three hours, setting what I’m pretty sure is a personal record for a half-marathon. That was too fast — by the last three miles, I didn’t have anything left. I ended up walking a depressing amount of the home stretch. Just like the last time around, I crossed the finish line to Cake’s cover of “I will survive,” and I felt every word.

Of course, it wasn’t just about the race this time round, and Denim and Tweed readers came through strong at the finish, donating enough to Minnestotans United for All Families to hit my $500 goal before the race even started. You folks rock!

(Of course, it’s still possible to donate if you didn’t get around to it. But this will be the last time I pester you about it here, I swear!)

And but so now I’m looking forward to spending the next three days or so unable to easily climb stairs. Also, trying to decide whether I really want to do a sixth one of these things. (Spoiler: I probably will, once I can climb stairs again.)◼

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Race day tomorrow — last chance to donate!

So, tomorrow’s the Mankato Marathon, which means I’m presently in a cheap hotel room in charming Mankato, Minnesota, winding down for an early bedtime in preparation to run 26.2 miles starting at 8 in the morning. Also, since I’m running to raise money for the campaign against an amendment to the Minnesota Constitution that would ban same-sex marriage, it’s also the home stretch for donations. D&T readers have already proven to be as generous as they are attractive and discerning, and given $350 so far — thanks! — which leaves just $150 to go to hit my goal. Update: As of 6 a.m. Sunday morning, you’ve hit $500 in donations! Many, many thanks!

So if you’ve already given (some of you, twice!) maybe pass on the donation link via your various social networks?

And if you want to track my progress tomorrow, you can look for bib number 529 on the results page; or keep an eye on my Twitter feed, in case I manage to live-tweet again. Now if you’ll excuse me, I have a race playlist to assemble.◼

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