phylogeny

Insulin, sugar, and evolution

sporte — Tue, 23 Dec 2014 03:29:55 +0000

Insulin, sugar, and evolution

In my last post, I wrote about insulin and interesting features of the insulin structure. Some of the things I learned were really surprising. For example, I was surprised to learn how similar pig and human insulin are. I hadn't considered this before, but this made me wonder about the human insulin we used to give to one of our cats. How do cat and human insulin compare?

It turns out, that all vertebrates produce insulin, even frogs and zebra fish. Human preproinsulin is only 110 amino acids long and even human and fish insulin are pretty similar. Of course, this observation only leads to more questions. Like why? Why would fish insulin and human insulin be similar at all?

One clue comes from insulin's function. Many cells require insulin for growth. Another clue comes from the insulin structure. A key feature of the insulin protein is a pair of disulfide bonds that hold the two chains (A and B) together.

Disulfide bonds between chains A and B in human insulin, PDB ID 1TRZ

When insulin is made, it's made as one long protein (preproinsulin). Afterwards, a small part gets cut off at the amino end when it gets transported through the membrane. Later, another chunk gets cut out of the middle (C peptide) leaving the two disulfide bonds between cysteine residues holding everything (Chains A and B) together.

Those four cysteines look like they must play a pretty important role since they're charged with the task of holding it all together. This made me wonder: Do all the creatures that make insulin have cysteine bonds in the same positions?

To test this idea, I needed a way to identify those four cysteines within the insulin protein.

I opened 1TRZ (the human insulin monomer) in Molecule World* and applied molecule coloring to identify chains A and B. Then, I hid all the protein chains, and one by one, touched the C's in the two sequences to highlight the cysteines.

Once I found all the cysteines, I touched some of the C's again to deselect the ones that formed disulfide bonds within a chain and used the "Hide unselected" button to hide them. Now, we only see the cysteines that hold the A (pink) and B (blue) chains together.

The protein sequences are a little dim, but I can see the one letter abbreviations for the amino acids around each cysteine. These sequences help me spot where these cysteines were located in each chain of the protein.

Assembling the data set

The next step was to put together a set of sequences. I picked protein sequences since I wanted to include some distant relatives (worm & fly). To find the protein sequence for the human insulin gene (INS), I searched the gene database at the NCBI. The INS gene record contained a link to Homologene, a database that I used to get similar insulin protein sequences from other organisms. Curiously, I found that that mice and rats have two insulin genes! That was a surprise! Do rodents really consume that much sugar? I decided to include both rat insulin 1 and rat insulin 2 genes, since I didn't know which one was most important. As it turned out they're pretty similar to each other.

I also used the NCBI Gene database to get sequences from C. elegans (a nematode, a type of small worm) and Drosophila ananassae (a type of fly, related to Drosophila melanogaster).

Time to BLAST!

After compiling my list of accession numbers, it was time to run blast. I chose blastp from the BLAST home page at the NCBI and checked the "Align two or more sequences" box to compare my human insulin sequence to a set of other sequences.

Then, I pasted the accession numbers for my data set in the subject field and clicked BLAST.

BLAST results

All the sequences matched and had significant E values, even those from the fly and worm proteins.

But what about the cysteines?

Curiously, NCBI protein blast has this new feature and a new algorithm (to me anyway) for multiple alignments, called Cobalt.

To create a multiple alignment, you just click the "Multiple Alignment" link on the blastp results page.

Voila! You get a multiple alignment from Cobalt!

I think this alignment could be improved by a bit of editing, but the general idea is pretty clear. Even flies and worms keep those cysteines in the right place.

NCBI's Cobalt results will even let you make a phylogenetic tree. Those, this was a little bit flaky. Sometimes, I would click the link and see an error message saying the page wasn't there.

Nevertheless, sometimes, I could click the Phylogenetic Tree link, and sometimes, get a tree. And, it even makes sense.

I can see that the cysteines that participate in our key disulfide bonds are conserved through evolution from fish to humans. This was true for the cysteines in both the A and B chains.Students might like to investigate how far this goes. How many organisms have genes for insulin? Are they found in insects or starfish, or worms? Are insulin proteins from all organisms held together by disulfide bonds?

Check out While visions of sugar plums danced through their heads to see other interesting features of insulin molecular models.In the meantime, have a sweet holiday! And give thanks for insulin. This holiday, when many of us are consuming too much sucrose, it's nice to remember that insulin is busy handling the consequences.

Images & Bioinformatics software: All the images in this article were made from the new version of the Molecule World™ iPad app (Digital World Biology). Many of things we do with Molecule World can also be done with Cn3D, it's just a bit more complicated.

The 1TRZ structure was obtained from the NCBI's Molecular Modeling Database. The protein sequences, from the NCBI, and the blastp algorithm and Cobalt were used at the NCBI.

sporte Mon, 12/22/2014 - 22:29

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Hanging Upside-Down in the Tree of Life

milhayser — Wed, 11 May 2011 08:05:36 +0000

Hanging Upside-Down in the Tree of Life

On Tetrapod Zoology, Darren Naish acquaints us with all manner of vesper bats, a group which comprises 410 of the 1110 bat species worldwide. In Part I, Darren provides an overview of the group as a whole, including their snub-nosed morphology, invertebrate eating habits, echolocation frequencies, and migratory tactics, which may have "evolved at least six times independently." In part III, he looks at a sister group to vesper bats called bent-wing bats, which "have the smallest reported genome of any mammal: it's about half average size." And in part VII, Darren explains that desert long-eared bats "drop right on to their scorpion prey and may be repeatedly stung on the body and face while subduing them: amazingly, this seems to have no effect." In all parts, Darren shows us fantastic pictures of the species at hand, and explains their physical attributes and their position in the phylogenetic tree. There are now XX parts in the complete series.

Introducing the second largest mammalian 'family': vesper bats, or vespertilionids on Tetrapod Zoology
Bent-winged bats: wide ranges, very weird wings (vesper bats part III on Tetrapod Zoology
Desert long-eared bats - snarling winged gremlins that take scorpion stings to the face and just don't care (vesper bats part VII) on Tetrapod Zoology

milhayser Wed, 05/11/2011 - 04:05

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bats

biology

phylogeny

A Phylogeny for the Dolichoderine Ants

awild — Wed, 31 Mar 2010 12:37:25 +0000

A Phylogeny for the Dolichoderine Ants

Leptomyrmex darlingtoni, Australia

A big day for ant evolution! The Ant Tree of Life research group (AToL) has published their dolichoderine phylogeny in the journal Systematic Biology.

Dolichoderines are one of the big ant subfamilies, comprising just under ten percent of the world's ant species. These are dominant, conspicuous ants noted for having ditched the heavy ancestral ant sting and armor in favor of speed, agility, and refined chemical weaponry. Most dolichoderines live in large colonies with extensive trail networks, and they fuel their frenetic lifestyle through copious consumption of hemipteran honeydew.

The paper is unfortunately behind a subscription barrier, but I've reproduced the primary finding below.

A cladogram of dolichoderine ant genera based on 10 loci and 48 taxa, simplified from Ward et al 2010.

The study is typical Phil Ward: exceedingly thorough from the first field collection to the last detail of the final analysis. The team employed 10 nuclear loci (without any missing data!) amplified from 48 specimens, using multiple species for the larger genera. The analyses took years to finish, not because the data set was large but because they meticulously tested numerous models, data partitions, and outgroups to probe the robustness of their trees.

Dolichoderus bispinosus, Panama

A few thoughts:

Kudos to Steve Shattuck. Big kudos. The guy performed an exhaustive taxonomic reworking of the genera in the early nineties for his dissertation, based on morphology.Â And we see here all of Steve's genus-level taxonomic decisions reflected in the molecules. As far as AToL could discern, the existing genera are monophyletic.
Back in the day, Bill Brown speculated based on the ubiquity of fossil Dolichoderines that this was an older group slowly succumbing to myrmicine domination, surviving as relicts in isolated places like Australia. But the AToL team provides little support for Brown's thesis. The enormous diversity of an Australian clade (there must be about 100 species of Iridomyrmex alone!) is young, 25 million years old, and apparently radiating quite actively.
The relationships deep in the tree hinge on a number of factors, most disturbing of which is the inclusion of Aneuretus as an outgroup. Aneuretus simoni is the single surviving representative of an ancient subfamily, it is found only on Sri Lanka, it is not common, and it may well become extinct within our lifetimes. Yet our ability to reconstruct its sister group's evolutionary past depends on access to rare Aneuretus DNA. Conservation of our biological resources is imperative for research, too.

Tapinoma sessile, USA

source: P. S. Ward, S. G. Brady, B. L. Fisher , and T. R. Schultz. 2010. Phylogeny and Biogeography of Dolichoderine Ants: Effects of Data Partitioning and Relict Taxa on Historical Inference. Systematic Zoology Advance Access published on March 31, 2010, DOI 10.1093/sysbio/syq012.

awild Wed, 03/31/2010 - 08:37

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Phooey. Hate it when I can't download or even read an interesting paper. But it sounds so exciting!

I would have expected Tapinoma and Technomyrmex to come out as sister genera given their nearly identical and peculiar "non-scaled" petiole, among other things. Oh well.

BTW, "Systematic Zoology Advance Access", that's very nostalgic on your part Alex ;)

Very nice, especially the congruence with Steve's morphological genera (although the tree doesn't seem to be fully resolved, so ...). I hope you are studying his key to Aussie ants while considering your book - illustrating every key character and having the illustrations next to the couplets made even ant genera accessible to acarologists.

About half the Australian Myrmozercon species (i.e. 2) are known from Iridomyrmex ants - clearly a highly evolved and discriminating genus.

Thanks, especially to Alex, for the very kind words. When I suggested looking at the dolichoderines for my thesis project people said I was crazy, and they were almost right - it took 18 months to crack the "Iridomyrmex problem" and split it into the 5 genera we have today. I was reassured it was OK when Bede Lowery, by far the best collector of Australian ants, said that what I was proposing made sense to him based on his field observations. And now to have an independent dataset confirm it is exciting (and a bit of a relief!).

For the Australian Ants book, I rewrote it three times before I was happy: the first was too technical, the second was too casual and the third finally got the balance about right. And I have Natalie Barnett to thank for the excellent "cartoon" drawings. I had the vision but she mastered an early version of Freehand (before the days of Illustrator) to create hundreds of drawings within a very short period of time. It would have been impossible with pen-and-ink, the standard in those days.

As Alex suggested, Brian Heterick and I are putting the finishing touches on a species-level revision of Iridomyrmex. It's proven exceptionally complex given that the group contains some 80 species and yet is so young (having split from its sister genus approx. 8mya). Several "species" show complex patterns of morphological variation and yet minimal genetic divergence (based on COI) while at least one other clade shows similar morphological variation but has deep branches based on this same gene. Clearly there's a huge amount of evolution going on here and our paper certainly won't be the last word on these fascinating ants. Australia is the place to be if you're interested in ants.

The phylogenetic position of the "primitive" Myrmecia

awild — Thu, 04 Feb 2010 13:23:37 +0000

The phylogenetic position of the "primitive" Myrmecia

A clarification, relevant the discussion below:

Tree from Brady et al 2006.

awild Thu, 02/04/2010 - 08:23

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So does your clarification mean that Myrmecia is not primitive, but you would entertain the notion for the h-lineage (or is this just an outgroup?) or the b-lineage?

Looks like (my eyes aren't so good) that Prot- and Pro- show up in several of the genera there, implying someone once thought them first on the scene.

Dave- not at all. I don't think the term "primitive" has much meaning in a phylogenetic context, so it wouldn't correctly refer to any of the branches. As a case in point, one might naturally think of the Leptanillines (the "h-group") as primitive from their position, but Leptanilla is also on a rather long branch. That means they've undergone more molecular evolution than most ants. So it's while it's a remarkably old lineage, it is also one of the most evolved.

What I mean to demonstrate here is that Myrmecia is a relatively young lineage.

Young? How does one determine age from the cladogram?

Apart from fossil-calibrated dating analyses (which were also done for this study), one can determine relative age from the patterns of nestedness.

We know, for example, that Myrmecia must be younger than the early formicoids, as it is contained within the formicoid clade.

I checked the article you linked and they cite one of their earlier works (Geiner et al. 2007 Curr Biol 17) in support, but that paper just declares Myrmecia primitive:

"Here we report striking correlations between the timing of foraging bouts and the modification of eye structure in four species of ants belonging to the primitive genus Myrmecia." (p. R879, second sentence)

So, you clearly have a point that this is a gratuitous and apparently ignorant use of 'primitive'.

I think my point is that you can't have primitive without also having 'advanced' and this is one of many dichotomies we use when telling stories. I've started to see these rhetorical tools as limiting, because you become trapped by the implications. Whether or not we can do away with them and still communicate effectively, I'm not sure. In any case, most people seem to need to divide things into two groups when discussing them.

They say there are two kinds of people in the world. Those that divide things into two groups, and those that don't...

By the same token, it does not seem very yuong within the formicoids.

And you're right: it's a pretty old formicoid. But age is also relative to expectation, and I think there was a fair expectation after the chatter about Nothomyrmecia being the "most primitive living ant" that the myrmeciines were a potential sister to the remaining extant ants. When they turn up instead as nested higher in the phylogeny and close to "higher" ants like Dolichoderines, that wasn't what a lot of people expected.

If anything, I'd not mind referring to myrmiciines as relictual. After all, that group was once found worldwide but for whatever reason is now extinct everywhere but Australia.

Aha! Relictual, got you right where I wanted!..

Why Study the Tree of Life?

grrlscientist — Tue, 06 Oct 2009 03:59:55 +0000

Why Study the Tree of Life?

tags: Tree of Life, conservation, biodiversity, ecology, evolution, biology, statistics, teaching, streaming video

grrlscientist Mon, 10/05/2009 - 23:59

Discovering the Great Tree of Life

grrlscientist — Mon, 05 Oct 2009 03:59:08 +0000

Discovering the Great Tree of Life

tags: Tree of Life, conservation, biodiversity, ecology, evolution, biology, statistics, teaching, streaming video

This video presents a very brief glimpse into what I do as a professional researcher studying "my birds" -- the parrots of the South Pacific Ocean (during those rare and beautiful times when I actually have a job!!). It features interviews with one of the scientists whom I worked with when I was in grad school at the University of Washington: Scott Edwards, who now is at Harvard University. To say the least, this video fills me with intense longing to reclaim my long lost life.

Did you notice that the "bacteria" they showed on this video were not bacteria at all, but rather, were actually Paramecia? I am absolutely surprised that error made it past all those scientists who made this film.

grrlscientist Sun, 10/04/2009 - 23:59

TimeTree of Life

awild — Thu, 11 Jun 2009 11:05:12 +0000

TimeTree of Life

I see that the TimeTree of Life project is now public.Â This collaborative project draws on the research of dozens of biologists to estimate the timing of past evolutionary divergences.Â The work is available as a book, but the online version has an interactive section that allows the user to name two organisms and get back the date the two last shared an ancestor.

For instance,

Ants vs. Bees: 163.5 million years ago

A word of caution, though.Â While the output is extremely precise (i.e., it gives exact dates with decimal places), precision is not necessarily accuracy.Â The given dates are really the midpoints across a range of estimates, and for appropriate scientific caution you're still best off consulting the referenced papers themselves. In our insect example, the work was done by the Smithsonian Institution's SeÃ¡n Brady.

Still, it's a fun little tool.

awild Thu, 06/11/2009 - 07:05

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Science

evolution

phylogeny

Srsly, I should know better by now than peek at the basal details of trees not done by certified protistologists...

One of the editors seems to be a bioinformatics dude, the other guy seems to be more metazoan-oriented (anyone who uses "higher eukaryotes" and worships "complexity" is almost guaranteed not to be a certified protistologist ), so while they obviously know their stuff, the branching of glaucophytes between reds and greens makes me cringe a little. The tree also makes protists seem basal, rather than extremely paraphyletic and scattered all over the place (rather, animals plants and fungi are little islands in a sea of protists). Also, microbial life tends to get grossly underrepresented in those things...

But, my nitpicking aside, the project looks pretty awesome! (I just wish my favourite organisms got more representation out there =( )

(Oh and when I first read Time Tree of Life, I thought that meant Time as in the magazine. "Time made a tree of life? WTF? This is gonna be fun to decimate... wait, why the hell would they make a tree of life in the first place?!")

This is very cool. Useful tool for people just wanting a quick estimate of divergence times without trawling through all available literature.

However one should be careful what you use as search terms.

I was confused at the date it was giving me for monotreme/marsupial divergence -- then I realised Echidna may not mean what I think it means.

Sunday Night Movie: Watching Arachnids Evolve

awild — Sun, 07 Jun 2009 16:25:19 +0000

Sunday Night Movie: Watching Arachnids Evolve

I saw this short video at a conference last year and was entranced. The clip shows how the ancestral arachnid body plan changed as it evolved through various descendant lineages.

awild Sun, 06/07/2009 - 12:25

Tags

Science

evolution

phylogeny

Wot? No harvestmen?

Yeah, I noticed that. Where should they go in the tree?

Oh, um, yeah, there is that... The latest major study (Shultz, 2007) placed harvestmen (with underwhelming support) as the sister taxon to scorpions, but I wouldn't be surprised if this changed again in the future.

Thanks! This was AWESOME =D

Hmmm... someone should do these for as much of the tree of life as possible! Some place where you can just click and watch your favourite lineage evolve through time!

Pyramica vs Strumigenys: why does it matter?

awild — Sat, 06 Jun 2009 18:15:50 +0000

Pyramica vs Strumigenys: why does it matter?

Pyramica (or is it Strumigenys?) rostrata, Illinois

I've been thinking today about the Wikipedia edits to the Pyramica page, and my curiosity about the controversy prodded me to attempt a quick phylogenetic analysis.Â Before I get to the analysis, though, here is some background.

The Ants.Â Forests in warmer regions around the world hold a great number of tiny, sluggish ants covered with bizarre hairs of unknown function.Â These oddly ornate little insects are predators of other arthropods.Â Mites, springtails, and the like.Â Because of their size, their preference for below-ground prey, and their habit of freezing when disturbed, these are not easy ants to find even where they are abundant.Â Most belong to the genera Pyramica and Strumigenys.

While all species are stealth predators, approaching prey by edging almost imperceptibly slowly towards it, species show either of two distinct ways to subdue prey once they get within striking range.Â Pyramica use their mandibles like pliers, holding fast while they swing their abdomen around to sting.Â They are slow but grippy.Â Strumigenys are trap-jaw ants, stunning their prey with a sudden blow when their mandibular trap slams shut.Â They are fast but lack a powerful grip.

The photos below show the two mandible types.Â However different their jaws may be, the ants are otherwise quite similar.

Pyramica reflexa

Strumigenys louisianae

I'll also point out that while mandible length alone often indicates the hunting strategy a particular ant uses, the trait isn't absolute.Â Some Pyramica slow-grip with long mandibles, rather more like needle-nose pliers, while a few Strumigenys sport surprisingly stubby trap-jaws.Â If you wish to peruse the diversity, Antweb hosts extensive specimen galleries of Pyramica here and Strumigenys here.

The Taxonomy. The taxonomic issue is more substantive than the usual nomenclatural squabbling that systematists frequently engage in.Â It's not just about what to call the ants, but a deeper disagreement about how they evolved.Â Because the ants have different mandible shapes and hunting strategies, the phylogenetic arrangement of the various species will have profound implications for how we infer traits to evolve.

For instance, if Pyramica turns out to be an ancestral radiation from which Strumigenys later emerged, then the trap-jaw must have arisen as a special case of the slow-grip mandibles, and the evolutionary trend over time in some lineages is towards longer mandibles and prey capture by shock-and-awe.Â In the converse situation, Strumigenys birthing the slow-grip Pyramica, then the trend is instead towards shorter mandibles, and with the slow-grip being a subsequent modification of a trap-jaw.Â Finally, it could also be that both groups are independent, each having created its specialized form by modifying the generalized mouthparts of a common ancestor.

At the moment, myrmecologists hold conflicting views on which scenario they prefer.Â E. O. Wilson and Bill Brown famously raised what I call the Incredible Shrinking Mandible hypothesis, preferring trap-jaws to be ancestral to the slow-grippers.Â This view is shared by Barry Bolton, who revised the larger tribe Dacetini in 2003.Â Cesare Baroni-Urbani prefers the opposite, postulating that trap-jaws emerged second, and that the groups are so blurred in places that they ought to all be placed in a single genus, Strumigenys.Â Apparently, adherents of both views have taken to alternating edits of Wikipedia.

My Half-Baked Analysis. This morning, my interest piqued by controversy, I visited Genbank to see if I could find species with enough overlapping gene fragments to generate a phylogeny.Â Turns out that 5 species from each genus had sequences posted from the same 2 genes: the 28S ribosomal gene and the COI mitochondrial gene.Â Considering the hundreds of species distributed across the two genera, this is certainly a paltry representation.Â But it's enough for a preliminary look.

I took about an hour to align the sequences and prepare a file for analysis, and another hour for my computer to run it.Â (If you'd like the details, email me).Â Here's the result:

A phylogeny of Pyramica (red) and Strumigenys (blue) based on DNA sequence data from the genes 28S & COI. Generated using the freeware program MrBayes; numbers are the Bayesian posterior probabilities supporting the indicated relationships.

What does this tell us?

To be honest, not as much as I'd hoped.Â Support values are low throughout the tree, undercutting the confidence we may have in the depicted relationships.Â But it does show that, for these species and for these genes, there is no immediately clear-cut distinction between Strumigenys and Pyramica. Contra Baroni-Urbani, we do get a hint that the trap-jaw came first.Â But contra Bolton, the two groups may be intermingled to an uncomfortable degree. It might be that everyone is wrong!

A proper resolution to the Pyramica problem will require sampling hundreds more species than I did here, using more genes and a more exhaustive set of analyses.Â More that just a couple hours' work on a Saturday.Â But this is exactly the kind of approach we need.Â In an ideal world, the genetic research would be accompanied by behavioral assays to determine what each species eats and how each uses its mandibles, as well as a careful biomechanical assessment of the mouthparts themselves.Â Only then will a clear picture emerge about how these ants came to acquire such strange jaws.

footnote:Â The DNA data I used is publicly available, and the software programs I used (Mesquite and MrBayes) are both freeware.Â A surprising amount of evolutionary biology can be done without spending a dime.

awild Sat, 06/06/2009 - 14:15

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Great post. I've been pondering how one might get a handle on the ecology-morphology aspect of this story for a while. It's hard not to think about such gorgeous ants!

Great little article Alex.

Thanks guys. What we need is some wealthy philanthropist willing to toss us the $100,000 or so it'd take to do the job right.

Well, Iâm not very good in phylogenetic things but, if your tree has some meaning, two things result clearly from it:

1. Separation of Pyramica from Strumigenys is wrong.

2. Wilsonâs, Brownâs and Boltonâs idea, apparently supported also in your blog, for which âPyramica turns out to be an ancestral radiation from which Strumigenys later emergedâ is also wrong.

The taxonomy underlining this conclusion was already published 150 years ago by Roger, the discoverer of Pyramica.

Is it necessary that they form two separate lineages? Could not different species switched from one strategy to another over time as they evolved in response to changing environments?

Alex, I'm not sure whether to applaud or show concern for the amount of scientific ponderings on your blog. I think it's good for science, but not the proprietor of the blog.

I wouldn't be so bold as to publish so many evaluations of ideas without the backing of formal peer review. I wouldn't be as concerned about the validity of my criticisms, but rather the perceived validity. Perhaps I'm hypersensitive to alienating other scientists. I just wouldn't want to be responsible for airing other people's dirty laundry.

I'm not saying that you're unfair. But I think most people whose work is being reviewed on your site feel that it won't stand up to rigorous review.

Colleague:

Alex and any other scientist reader knows it wonât stand up to rigorous review. That's why it's in a blog, not an online journal or other formal outlet. Pondering of this sort, followed by discussion with colleagues leads to good research. This post clearly points to the need for further scientific research and eventual peer-reviewed publication of the results, and is not a substitute for these.

An excellent show of how anyone with a computer can go have a play with bioinformatics!

Everyone should do it.

Blogging on published research is part of the process that used to be carried on in hallways, on the telephone, and in the bar at conferences. It's actually part of the post-publication peer review process in which professionals noodle on published research, thinking about its meaning, teasing out implications, wondering about extensions.

The issue is not whether it will stand up to "rigorous review," it's whether it's an interesting take on the research. Admittedly, some professionals don't appreciate those takes being published for the world to see, but then, that's the way the world is nowadays.

From a research point of view, I'd agree with RBH - blogs can be the new tea room/pubs (well maybe not the latter - I'm too familiar with how I spout off after a few beers to let myself blog then, but Coopers & Cladistics does come to mind).

From an ex-lecturer's point of view, I'd say that blogs can be like classrooms too. I think that one of the better ways to teach science is to present (blog) two or more contrasting explanations for a hypothesis and let the class (readers) ponder their interpretations (0 comments) or disagree. I know blogs (and professors) are infamous for their political ranting, but there is no reason why every blog or classroom should be a political pulpit. Presenting an alternative to an established scientific hypothesis is science and political in only the most abstract sense.

However, as RBH notes, blogs are really different from watercoolers and classrooms in one critical way - they are potentially in everyone's face. I'm not sure how I'm going to respond if and when someone starts rubbishing one of my favourite hypotheses, but I imagine waking up at 3 am with the perfect response and then heading for the computer in my pajamas and without my usual collegial facade.

I would applaud Alex for doing so. Why should he, or anyone else, be shy about proposing and debating ideas? If someone gets their toes or favorite theory stepped on and doesn't like it, then they are either in the wrong business or should come up with a reply or defense. They are free to comment here or elsewhere. The "Blog" is simply another way for the scientific method to poke and prod hypotheses. That's what the whole game is about. This new medium is no different in spirit from the numerous public letters, journals, and even layman's newspapers of past years. Some of the best and most animated debates on evolution, for example, were carried out this way.

I say carry on the ideas, rebuttals and debate.

Colleague:

If you or somebody else thinks that the logic or the information of a comment is wrong, he should simply point to and explain the weak points of the comment in the same blog.

I fear understanding that comments that you dislike and you are unable to contradict should be prevented from publication in the blog. Please reassure me, possibly with facts and not with dialectic exercises.

In this spirit, thank you Pdiff.

I don't know Alex. First you dare to post your expert opinion on some parts of HÃ¶lldobler and Wilson's latest book. Now you provide a succinct review on a topic of your specialty while actually doing your homework and throwing in some original results. What's next, an insightful view on soon-to-be-published high end research?

Let me tell you something. This "critical scientist" attitude of yours, using this novel digital medium, won't let you anywhere young man.

When we thought that the earth was the center of the universe nobody could dare doubting the ideas of the Vatican. Are we confronted with an ant Vatican?

(channeling Uguthecrow) - Aren't Alex's opinions/hypotheses/etc. being peer reviewed right here, right now, in the comments? And doesn't Alex refer to this as a "half-baked analysis" that requires more resources "to do the job right"? I agree that Alex would get more academic "credit" (i.e., a notch on his CV) with a more detailed, peer-reviewed critique, but that might not be the best use of his time and resources right now (in this particular case).

At least he provoked, perhaps, someone else to take up the reigns to solve this taxonomic and evolutionary conundrum. My postdoc and I are posterchildren for how the free flow of scientific ideas can motivate research on important topics. One of you science bloggers (not Alex) made a statement recently on your blog about something that sent me and my postdoc on a wild and crazy mission. Now we have a MS to be submitted in August-ish that I think a certain group of you will find quite compelling. This research never would have happened without your science blogging - THIS "just throwing that out there" kind of science blogging. We simply wouldn't have thought of addressing this question.

Keep up the good work, bro.

Great blog!!!

This question has been on my mind quite a bit lately because I have some species lists up on my site of southern US ants and am wondering when or if I should be changing some names. Also, we have a new species of Pyramica from Mississippi, but should I call it Strumigenys or Pyramica? I have corresponded about this matter with both Bolton and Baroni-Urbani, both of whom I greatly respect for their obvious dedication and love of myrmecology and their many contributions to the ant world. But, obviously, they have radically different viewpoints about this issue. I suppose for me, at least right now, the question is are people following Baroni-Urbani's recent treatment of the group? I noticed that the names on Antbase.org have been changed to reflect his synonymy. Are most people following this now?

I went through a few weeks ago and found the same species that you used in your phylogeny on the Barcode of Life Data Systems site, probably from the same projects. Although I don't really know much about phylogenies, it looked to me (from the small sample anyway) that it would be hard to separate these species from one another. I certainly don't have any problem calling them all Strumigenys, although the ones here in North America are easy enough to separate.

Great post, and the comments about blogging are just as interesting. I've written a short note about this edit war on iPhylo, partly as an excuse to show another history flow visualisation of the edits to a Wikipedia page. It would be interesting to see whether other taxon pages in Wikipedia pages that have been the subject of edit wars will also generate analyses of the kind you've undertaken here.

More flu follies: comparing sequences and making trees, activity 4

sporte — Wed, 29 Apr 2009 09:21:54 +0000

More flu follies: comparing sequences and making trees, activity 4

What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu?

If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer.

Activity 4. Picking influenza sequences and comparing them with phylogenetic trees

We can get the genome sequences, piece by piece, as I described in earlier, but the NCBI has other tools that are useful, too.

The Influenza Virus Resource will let us pick sequences, align them, and make trees so we can quickly compare the sequences to each other.

This is how I got the sequences that I wrote about yesterday. I think the more people we have looking at sequences, the better off we are.

I'll show you how this works by getting and comparing sequences from the hemagglutinin (HA) protein from the recent cases of H1N1 swine flu and comparing those sequences to the HA protein from other cases of H1N1 swine flu that happened last year.

1. Go to the NCBI Influenza Virus Resource (this will open a new window).

2. Start out by getting the sequences from the recent swine flu cases in California and Texas.

To do this, we will pick Influenza A as the virus species, human as the host, North America as the region, and HA as the segment. Protein sequences are selected by default and those are just fine.

Then, we set the date range from 2009, 03, 01, to 2009, 04, 29.

Last, we click the Add to Query Builder button to get the sequences.

I forgot to put this in the image, but I also used a filter to select for H1. I typed "H1" in the really long text box. Also, note, I was looking at the protein sequences. (We should look at nucleotides, too, but that's a later experiment.)

3. This query finds 7 sequences. If we click the Get Sequences button, we can see that that these are the California and Texas isolates.

Now, we have to decide which groups we'd like to compare. I decided to compare these to other H1N1 flu sequences and to some sequences from pigs.

4. To get other flu sequences for comparison, I used the same queries (1-2) with some changes.

a. For one set of sequences, I changed the host to "Swine."

b. For the other set of sequences, I changed the date range so that I could get older sequences.

c. Each time I changed the settings, I clicked the Add to Query Builder button.

Now, the Query Builder contains the H1 sequences from the seven US cases, 272 sequences from people who've been infected with H1N1 over the past year in North America, and 5 H1 sequences from pigs.

5. Then, I click the Get Sequences button.

This gives me a long list with far more sequences than I want to use. I click the check box at the top to deselect everything, then I use the check boxes to select the sequences I want to compare.

I sorted by year to make my 2009 cases easier to find. Then, it's time to decide which sequences to pick.

Hmmm, of course I picked the seven swine flu cases, then I picked some sequences that were isolated from actual swine, then some other human cases of H1N1 that happened in different parts of North America last year.

At this point, I could download sequences and work on my own computer or I can use some of the analysis tools at the NCBI. I decided to let the NCBI's computers do the work, so I clicked the Multiple Alignment button to see the amino acid similarities, then, I clicked the Build a tree button, and a lot of Next step buttons.

Here's my tree:

After making the tree, I decided to look at all the sequences in my set. Here's what I get from that analysis:

What do I conclude from this? Well, first, it looks reasonable to say that the people in Texas and California were probably infected with the same strain since those sequences cluster pretty closely together.

Second, it looks like the HA protein from the California and Texas strains is most similar to the HA protein from a strain that infected some pigs in Ohio a couple of years ago and it is not as closely related to the 200 some strains of H1N1 that infected other people in 2008.

You guys can play amateur epidemiologist, too, and look at other strains or look at the New York strains. I think the more eyes we have looking at these, the better off we are.

Nucleotide sequences should be looked at and other tree methods would be good to try as well. And, of course as if things weren't complicated enough, there are 8 different segments of the flu genome.

Have fun!

sporte Wed, 04/29/2009 - 05:21

Tags

bioinformatics

classroom activities

databases

Genetics & Molecular Biology

NCBI influenza resources

Hi, if you Fasta search the sequences for this current North american H1N1 outbreak, it can be seen that in fact a closer maych fopr the HA gene is a kansas strain: (A/Swine/Indiana/P12439/00 (H1N2) but given the dates on all of the isolates, all that really can be said is that the HA gene seems to have come from pig viruses already circulating in the USA.

I think you meant a BLAST search. And Indiana.

But the real problem here is sampling bias. If we sample 200 swine a year from the USA, and 100 from Asia, and ZERO from central America or South America, of course the "best hit" in a BLAST search will be a USA or Asian swine.

What you are looking for, is a swine (or bird, or human) sequence that is 98% to 100% identical to the California 2009 human sequences. 92% to 95% identity indicates a rather distantly related strain.

Sampling bias is our biggest problem here. We have not been sampling hundreds of swine each year in central and south America for the past 20 years. Nor Sand Hill Cranes and other wild migratory birds.

Hi Brian, No i meant a FASTA search which is more sensitive than a BLAST search.. try the, both and you will see. And what you say is obvious, you need a sequence in order to get any kind of aligment.. but the practical issue is we only have the sequences which have been sequenced. And of course the % identity would ideally be as close to 100% as possible, but out of the 1000's of sequences in the database, the A/Swine/Indiana/P12439/00 (H1N2) HA sequence gives the closest match.. so i dont understand why ohio has been labelled as the closest match (well i do as the sample only consisted of HA sequences from 2005 onewards.

I'm trying to develop this as an exercise in my Genetics course. I chose some sequences and aligned them, but for some reason the 'Build a Tree' button in the alignment window is grayed/dimmed out (and thus not available for use).

Wonder what I'm doing wrong?

Hi Russell,

I'll take a look this weekend and see if I can figure out what's going on. In the meantime, you might also want to take a look at a different activity that I wrote that uses Scenario Based Learning to investigate flu and build phylogenetic trees.

You can find this one here: http://elc.fhda.edu/bioinfo/index.html