Programming Zephyr

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My brother Wayne is visiting, and we are making very good progress on Zephyr. Programming is especially appealing when the outside world is covered in quiet snow.

David (left), Wayne (right)

David (left), Wayne (right)

Zephyr is a package for Mesquite that links Mesquite to phylogeny inference programs.  For example, one can have a matrix of DNA sequences in Mesquite, and ask that GARLI finds the maximum likelihood tree.  A dialog box from Zephyr pops up with GARLI settings, you choose them, and then Zephyr starts up GARLI.  As GARLI is running, Mesquite/Zephyr is monitoring its progress, and showing you the trees live in a tree window in Mesquite.  Once GARLI is done, Mesquite harvests the trees or trees and stores them in the current project.  

Below is a view of Mesquite with GARLI running in the background (in the black terminal window at right), and the latest GARLI tree shown in the tree window.  As GARLI runs, one can watch that tree being continually adjusted. (Touch on the image below to see a larger version of it.)

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We’ve been using Zephyr for a few years in our own work, and are now putting the effort in to making it usable by others.  So far it enables one to run GARLI, RAxML, TNT, and PAUP from within Mesquite, although the options for TNT and PAUP are limited.

We’re very pleased with the progress we’ve made, and hopefully will have something available for folks in the spring sometime.

(By the way, the image on the Zephyr banner is a closeup of the elytron of Bembidion zephyrum, one of my favorite beetles.  It lives on the sandy beaches of the Pacific Ocean in western North America.)

Posted in Mesquite, Software Development | 2 Comments

Dreaming of Saint Helena

Saint Helena is a small island in the Atlantic Ocean that is a very long way from any continent. It is approximately 1850 km from Africa, and about 3290 km from South America.  It is only 16 km by 8 km in size, and the highest peak is 818 m above sea level. It is the place where Napoleon was exiled, and where he lived the last five and a half years of his life.  It currently has a population of about 5,000 people, and is a British Overseas Territory.

And it is a place with an endemic radiation of extremely odd bembidiine carabids. I have dreamed of going there to collect some for DNA studies, to find out where they belong in the bembidiine evolutionary tree.  They are currently classified as genera separate from Bembidion.

Here is where Saint Helena lies:

I’ve looked into traveling to Saint Helena, and it is not a trivial undertaking.  There is no airport in Saint Helena (although one is under construction with a scheduled opening in 2016), and the typical route is to fly to Capetown, South Africa, and from there take a Royal Mail Ship to the island, a sea journey of five days (one way).

The flora and fauna of Saint Helena has many endemics, including all but one of the bembidiines.  In addition to the widespread Bembidion mixtum, the bembidiine fauna consists of only 12 described species, but these are fantastically diverse.  Here are three of the species:

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From left to right, Pseudophilochthus nubigena, P. rufosuffusus, and Apteromimus platyderoides,
all to the same scale. Scale bar is 1 mm.

Some of these simply don’t look like bembidiines.  The oddest one isn’t shown here – it is Endosomatium megalops, whose huge head is vastly out of proportion to the rest of its body.

Unfortunately, some or all of these may now be extinct.  The introduction of  invasive plants and animals, including goats and Homo sapiens, has destroyed much of the habitat in which these beetles lived – the special forests on the island.  Howard Mendel, as part of his month-long survey in 2005-2006, sought these beetles, and only found a single specimen of an undescribed species.  As Mendel, Ashmole, and Ashmole note in their survey report (available here), “we failed to find any of the twelve known species in these three endemic genera. They are of ancient lineage and closely associated with the cabbage tree / Tree Fern cloud forest on the Peaks. Their survival is of grave concern and in serious doubt. ”

This has made me rethink going to Saint Helena, in part because I think more work needs to be done re-establishing the beetles’  forest habitat before any more collecting is attempted.  Instead, I have focused my attention on seeing if I can extract and sequence DNA from some of the pinned specimens already in museums.   To that end, I borrowed specimens of three species from the Royal Museum for Central Africa in Tervuren, Belgium. I’ve extracted DNA from one of each of these.  The DNA from one of them, a Pseudophilochthus nubigena, looks as if it will be of high-enough quality to allow us to obtain sequences using next-generation sequencing.  And, in fact, we have PCR products for 500 bases of 28S and 450 bases of the wingless gene.

In advance of the next-generation sequencing, we will be sending the PCR products off to be sequenced, and hope to have results within a week.  We should have the first information then about where at least that one species falls.

And so, I will make the following prediction: the Saint Helena species are simply highly derived Bembidion, and should not be treated as separate genera.  They form a single, endemic clade (to test this, sequences from more than one species will be required).  My first guess is that they belong to the Bembidion Series (Maddison 2012), perhaps near the Antiperyphanes Complex of South America or the Ananotaphus Complex of Australia, New Zealand, and Hawaii.  My second guess is that they are in the Philochthus Complex.  These guesses are based more on gestalt than a careful character analyses;  the dominance of the Bembidion Series in the southern hemisphere fauna also sways me.

Posted in Tree of Life | Tagged , , , , | 7 Comments

The Group Photo

One of the required products of a weekend field trip is a group photo.

On our Big Loop Trip this summer, we joined up with the Essig Museum group for one weekend in the southern Sierras, and had a very fun time with them.  Just before Kip, John, and I departed for New Mexico, we took a group photo.  Here it is. and I would claim that, while nice, it is relatively boring.  We are all standing up nice and straight, which is good, but it just doesn’t have much compelling about it.

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Much more interesting is the progression toward that point.  Instead of a group photo, why not a group stop-motion animation, frame by frame?  It might start with this picture

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and then one of the players might move to the side, making room for other folks,

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and there can be a dash as one of the photographers (Joyce Gross) runs into view after setting up her camera

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and then the other photographer (me) steps in

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and we are almost ready

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and now that we have established our boring poses, the default group photo:

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If I hadn’t had the camera going earlier, I wouldn’t have realized how much I prefer one of the less static images.  The one I like the best is one of the middle ones, after we were all in view, but with just enough dynamism in it to be interesting, and to give a sense of spontaneity. This one:

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Much better.  We look much more lively.  By maybe all of us should be running around?  We should have taken a picture while we were all pretending to be scurrying insects.

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My favorite phylogeny

In a previous post, I showed my second-favorite phylogeny. Well, here’s my favorite one, posted on the wall outside my lab.

bembTreeNot that you can really see any details in this picture, but you get the idea:  it’s big.  It has about 600 species of Bembidion and related genera.  That’s also a maximum likelihood bootstrap tree based on seven genes, and you can see that it is pretty well resolved – there are very few polytomies.  This tree gives me so much pleasure because it tells me so much about the history of this group of beetles, and because there are so many things that make sense in light of it.

I’ll share some details about the tree later, but for now I would direct your attention to the caption under the tree.  I didn’t add that caption; it mysteriously appeared one day, like a gift-wrapped present under a sparkling tree.  I really, really like it.  Here’s what it says:

bembTreeCaption

I have no idea who wrote it.

It would be very amusing to have that as the caption in the journal article when the phylogeny gets published.

Posted in fun stuff, Tree of Life | 2 Comments

Art.Science: Shedding a Scenic Tear

Last week I had what I hope will be a life-changing experience.

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Art by (from left to right) Matt Norris, Mindy Lighthipe, Marjorie Moore and Cornelia Hesse-Honegger;
layout by Tuan Tang.

This fall I had the honor of being a juror for an exhibit of insect-inspired art, called ECLOSION, hosted by  Art.Science.Gallery. in Austin, Texas.  The event was organized by Hayley Gillespie (Art.Science.Gallery. founder) and Barrett Klein, both biologists/artists.   I’ve known Barrett for quite a few years, ever since he was a graduate student in one of my classes in Arizona; his brilliant melding of art and science was one of the reasons I was so pleased to help out with ECLOSION.  (If you haven’t seen it yet, you must look at the Damselflies of Texas field guide which Barrett illustrated – it’s gorgeous.)

[Note: all images in this post are courtesy of Art.Science.Gallery.]

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A portion of ECLOSION at Art.Science.Gallery.

The opening of ECLOSION coincided with the 61st annual meeting of the Entomological Society of America (ESA) in Austin. I have been going to these meetings intermittently since my first one in 1981 in San Diego.  I have always enjoying catching up with old friends, and seeing what cool research folks were doing, especially that being done by graduate students and junior faculty members. But the ESA meeting last week was special for me because of two talks in a “Broader Impacts” symposium.  The first was by Hayley on “Using art to enhance your science” and the second was by Barrett called “Entomoart: the power of esthetically communicating entomology”.

I had a very strong emotional reaction to these two talks, and at one point I am sure the smallest tear might have been visible in my eyes to anyone who looked closely. I sat there, as Hayley was talking, thinking, “What have I done with my life? Why am I not doing my artwork anymore?”  I suppose in part the answer is the hectic pace of my biological work, which seems to leave little time for me to re-enter the world of art.  But as I was sitting in the audience I realized that I must return to my art, and I have vowed to do so.  This is just too important to me not to.  Hayley’s and Barrett’s talks also made me realize how important art can be not only to inspire scientists in their work and inspire people to be scientists, but also to inspire artists to appreciate the wonders of science and the natural world.

Re-energized, the next day I took the bus over to Art.Science.Gallery., and saw the exhibit in person.  It was fantastic.  There were some gorgeous pieces there, in both two and three dimensions. Some of these were art that conveyed scientific knowledge about insects, others presented in a dramatic fashion messages about conservation biology or invasive species, and others celebrated the striking form and beauty of insects.

Although there were many pieces that appealed to me, I’ll mention only a few.

Barrett Klein’s “Biodiversity” is a pie-chart showing the relative diversity of various groups of organisms, with a representative of that group used to “label” that slice of the pie:

Biodiversity by Barrett Klein

Biodiversity by Barrett Klein

I really liked the sparseness of “Differential Grasshopper 3 (Melanoplus differentialis)”, created by Inked Animal by painting parts of dead grasshoppers with inks and pressing those against the paper; it is thus like classical Japanese fish prints but done with insects.

Differential Grasshopper 3 (Melanoplus differentialis) by Inked Animal

Differential Grasshopper 3 (Melanoplus differentialis)
by Inked Animal

Pen Brady’s beautifully composed images of animals, drawn in a style reminiscent of northwestern First Nations cultures, were very inspiring:

Returns the 5th of Fibonacci by Pen Brady

Returns the 5th of Fibonacci by Pen Brady

This bronze bowl by Jessee Smith, inspired by galleries made by bark beetles, captivated me by its design, texture, and weight; it was so comforting to look at and touch:

Galleries by Jessee Smith

Galleries by Jessee Smith

In addition to static art, the exhibit featured video art, including this beautiful one by Barrett:

The importance of melding art and science came to me not only through Hayley and Barrett’s talk and the ECLOSION exhibit, but also through a chance encounter with a former student, Bruce Noll.  Bruce took my Systematic Entomology class when I was but a wee junior faculty member, 19 years ago.  Bruce is a poet who does dramatic interpretations of Walt Whitman, and who is fascinated by insects.  After all of these years it was delightful to see Bruce, with his quiet and gentle passion.  Bruce intermingles entomology or phylogenetics into his poems, which appear regularly in American Entomologist.  I realized, as I was talking to Bruce at the airport on my way home, that he too was part of this message I was receiving in Austin to return to my artistic roots.

Posted in Musings, Scientific Illustrations | Tagged , | 4 Comments

(Almost) my favorite phylogeny

I recently reported on my favorite beetle illustration.  In the same collection as that illustration was a favorite phylogeny of mine:

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This drawing was also done by my daughter Julia at age 3 or 4; perhaps she was depicting what her father did at work.  (I think I need to add smiling hearts to my published phylogenies from now on. And happy faces on the beetles.)

The title of this post has the word “almost” in it because, as wonderful as this phylogeny is, my favorite has got to be our growing phylogenetic tree of the subtribe Bembidiina – 600 species and counting.

Posted in fun stuff | 3 Comments

BotW: Thinopinus pictus

In honor of Margaret Thayer and Al Newton’s visit to the PNW this week, the Beetle of the Week is a staphylinid.  It’s Thinopinus pictus, a large rove beetle (family Staphylinidae) that lives on the sandy beaches of the Pacific Ocean.  It is common in Oregon, but one only tends to see it at night.

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Thinopinus were common on the beaches near the mouth of the Salmon River, north of Lincoln City, Oregon, in early October.

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Posted in Beetle of the Week | Tagged , | 2 Comments

Examining name-bearers at the USNM

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I’m at the Smithsonian Institution for the next three days, working in the United States Museum of Natural History (the “USNM”).  My main goal is to look at type specimens, especially Casey types, so that I can figure out what to call some of the species we are recognizing from the morphological and molecular work we are doing.  I thought it would be interesting to do a bit of a diary while I am here, reporting on what I find as I find it.  Because Internet access here requires me to leave the area with the microscopes, I’ll do updates only on occasion, rather than “live”.

Here’s the cabinet with Casey types:

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And here is one of the drawers:

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For those who are unfamiliar with the concepts of type specimens, here’s how it works.   When someone discovers what they think is a new species, and publishes an article to give it a name, they designate a “type specimen” that is the “name bearer”.  If someone ever wants to see a specimen that goes by that name, that’s the specimen they would have to look at.  There are different sorts of type specimens; a species discovered in 2013 would have a “holotype” as its name bearers, in general; for many of the older names there are different sorts of types (for reasons I needn’t get into here) such as lectotypes and neotypes.  Holotypes, lectotypes, and neotypes are all the name bearers for their names; as such they are called “primary types”.

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Posted in Revising Bembidiina, Taxonomic Process | Tagged , , , , , , , , | 1 Comment

Lindrochthus at Mount Tamalpais

In an earlier post, I wrote about how the distinctive subgenus Lindrochthus, viewed in the literature as consisting of the single species Bembidion wickhami, was actually at least two species.  And those two species live together at Mount Tamalpais, just north of San Francisco; Peter Hammond collected them at a single site on Barths Creek on “Mt Tam”.

In early September Dave Kavanaugh and I went to Mt Tam, and looked for Lindrochthus along the banks of Cataract Creek and Barths Creek.  We knew the exact localities where Peter Hammond and Kip Will had collected the beetles I had previously sequenced, and we went to those spots.  We couldn’t find the beetles there.  Mind you, it is very dry in September (the winter rains had not yet started), and so we thought that perhaps the beetles were in hiding.  But we had hope that in the moister, more humid areas near the creek we could find them.   We looked in perhaps 20 or so places, and found them in only one small patch.

This patch was only about 2 square meters, and consisted mostly of a moss-covered small cliff face, about 3 meters from the water of Cataract Creek.  The area with beetles is outlined in yellow on the image below, and extended a small bit to the right, outside the view of the photograph.

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We got a total of 31 specimens of Bembidion subgenus Lindrochthus, all by dumping buckets of water on that patch.  The beetles appeared after the water wet the moss and soil.  In addition to the Lindrochthus, some Bembidion iridescens lived there.

Here’s one of the beetles from that patch:

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We were hoping that our 31 specimens would be a mixture of both species of Lindrochthus known from Mt Tam, but I wouldn’t find out until I got back, sequenced seven, and looked at all of them more carefully.  These new specimens also gave me enough material to enable me to find definitive morphological characters to tell the species apart.  As it turned out, they are easier to distinguish than I expected.

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Posted in Fieldwork, Revising Bembidiina, Taxonomic Process | Tagged , , , | 3 Comments

It was fifty years ago today…

Fifty years ago today, Carl Hildebrand Lindroth’s revision of the Bembidion of Canada and Alaska was published; this was part 3 of his opus on the ground beetles of Canada and Alaska. This work is the basis of all that has been done in Bembidion systematics in North America since then. It is astounding to think how far Lindroth took a speciose group that, before he entered the scene, was a complex chaos of confusion, and how quickly he did so, for he was coming in to the fauna as a European, someone who had not worked long with North American Bembidion.

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Not only is it a study that is beyond thorough (for he covers many species outside of the stated geographic range), it is also elegant in its simplicity.  I think one of the most amazing things about this revision is how he conveys, in a few sentences, the essence of each species.  There are no lengthy descriptions to sift through, just the diagnostic details and illustrations one needs.

For example, he describes Bembidion nudipenne as follows:

“102. Bembidion nudipenne n.sp. (type loc. Brandon, Manit., DAO!).
Smaller, slenderer, and darker than constricticolle. Dull; piceous to almost black, elytra with a usually well defined yellow subapical spot laterally, also shoulder and suture slightly paler; legs dark reddish, antennae piceous with indistinctly paler base. Head narrower than in constricticolle, prothorax (fig. 171b) with sides less rounded; both without setiferous punctures. Elytral striae with somewhat finer punctures, intervals only with a row of extremely small, non-setiferous punctulae (easily overlooked). Microsculpture strong and perfectly isodiametric over entire upper surface, except ± effaced on disc of prothorax. Wings constantly full. Penis, fig. 172. L. 3.5—4.0 mm.”

And, yes, that’s B. nudipenne in a nutshell.  I wish I had the ability to so succinctly communicate the means to recognize a beetle species.

The work is also art.  Lindroth’s drawings are beautiful, and extraordinarily informative. They were far ahead of most other illustrations from the 1960s of carabids.  Just as his text captured the essence of the beetles in a few words, his habitus drawings gave an accurate sense of the organisms through pencil and ink.

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And his genitalic figures are so much better than others at the time, and most if not all that have been done since.

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I don’t think I can fully convey how much I love Lindroth (1963).  I have five copies of it, and these are scattered around my life, which means I am never far from its pages.

Tonight I will raise a glass in honor of this remarkable achievement, 50 years later.

I might also note that my first contact with this work was when I received it from Carl Lindroth a few weeks after my 17th birthday.  George Ball had contacted Carl, asked him to send me the faunal work, and had paid for it – all shortly after I had first contacted George expressing my interest in carabid beetles, when I was 16.  Tonight I will raise a second glass in honor of George – thank you so much, George, for helping me fall in love with these little beetles.

Posted in Revising Bembidiina, Scientific Illustrations, Taxonomic Process | Tagged , , | 8 Comments