Mesquite version 3.0 and Zephyr 1.0 released

Wayne and I have been working hard over the last few weeks to release Mesquite version 3.0, and today we released it!

The main changes in this version of Mesquite are architectural, both in how the user interface is organized, and in how we build and distribute Mesquite.  The changes to how we make and distribute Mesquite were done in part to make it much easier to do future releases, and in part to make the code and documentation more open so that others can be involved more easily.  We have done this by moving the source code to GitHub, and the documentation to a wiki (http://mesquiteproject.wikispaces.com).  In addition, there have been some changes to the files distributed with Mesquite that will make it easier to manage and update.

There are a number of new and useful features in this version of Mesquite, the most important of which is support for a new package called Zephyr.

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Zephyr is a package that allows Mesquite to interact with phylogeny inference programs.  To begin with we have added support for RAxML, GARLI, and PAUP*, but we will be adding other programs in the future. We released version 1.0 of Zephyr today as well.

Here we are at Pender Harbour, BC, doing the last major push.  It was great to do it in such a beautiful location, and it was nice to have our mom there providing support.

PenderHarbourHackathon2Small

 

 

 

Posted in Software Development | 1 Comment

42 years between golden buprestids

In the summer of 1972, I was doing what I did every summer around then, which was to spend a few glorious weeks at a cottage my family rented around Lake of Bays, in the Muskoka district of Ontario. At the time I was 14 years old, and interested in jumping spiders, along with my brother Wayne.  But then one fateful day I found a beetle on the wood siding of the cottage, just to the left of the sunporch door.  The wood siding was a dark reddish color, and the trim around it was white.  The beetle was vivid against the dark red.  It was the most beautiful beetle I had ever seen, and I with a shaking hand quickly grabbed it.  I didn’t know much about it at the time, but eventually I learned that it was a Buprestis, possibly Buprestis aurulenta (I haven’t tried to identify it, but I do know it is close to that species, at least).

That beetle is the oldest specimen I have in my collection.  Sometime during my teenage years the beetle fell apart, and the elytra became detached.  Even though it is now in pieces, it is still one of my treasures, because of my memory of the awe I felt in seeing its beauty as it rested on the side of the cottage.

I’m not sure if that beetle played a role in my becoming a coleopterist, but it wouldn’t surprise me if it did.  It was about a year later that I started collecting beetles in earnest.

On Saturday I was near a small tributary of the Winchuck River in southwestern Oregon.  I was on a delightful trip with my mother; we were exploring northern California and southwestern Oregon, seeing the sights, collecting beetles, eating good food, and staying in nice places.  The Winchuck River stop was one of our lunch & collecting spots, along a gravel road in a beautiful forest.  There, beside the road, was a little patch of daisies.  On one of the daisies was the Buprestis pictured below It was the first time I had seen a Buprestis like this alive since that day in 1972, and I must say my thrill at seeing one in 2014 was almost as great.  They are wonderful animals.

Buprestis

Posted in Fieldwork | 2 Comments

Map of unrecognized species in Bembidiina

Here’s an addendum to the post about Unrecognized species in Bembidiina.  The map below shows the known distribution of most (but not all) of the unrecognized taxa of Bembidiina in America north of Mexico.  Notably absent are some of the coastal Notaphus, as well as some widespread forms such as “Bembidion kuprianovi” which consist of multiple species but I don’t know which ones are the recognized ones and which ones are unrecognized.  I should also note that the distribution of these species have not been mapped in detail; for the most part, the distributions shown below are of specimens whose DNA we have sequenced, and the full distributions of some of the species is broader.

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Approximate distributions of some of the unrecognized species of Bembidiina in America north of Mexico.

As you can see, the vast majority of unrecognized taxa are in the west, especially in California.

Update: for comparison, here is the distribution of all species.  The pattern for recognized species has some similar properties to unrecognized species in that there are many more species in the west.  The primary reason that there are many recognized species in Canada (including British Columbia) but relatively few unrecognized ones is the excellent work of Lindroth (1963).

SpeciesDistribution

Posted in Revising Bembidiina | 9 Comments

Unrecognized species of Bembidiina in the USA and Canada

I’ve been mentioning in this blog several unrecognized species which we have been finding in the fauna of Bembidiina in America north of México. By “unrecognized” I mean both undescribed species (those without a name), and species that have already been described, but that are currently and incorrectly considered in the literature to be a synonym of another species.

For my amusement, I decided to tally up how many species we now know about that are unrecognized in the literature, and I present the following list. The number of unrecognized species in the genus or subgenus or species group is listed in parentheses. A “+” after the number means we have hints of additional species, and ++ means that there are surely many more species, but we haven’t worked as much on that group yet and so we don’t understand how many more there are. I have not included the genus Amerizus, as Dave Kavanaugh is working on that group and is more familiar with it.

This list will continue to grow as we focus on various groups, but for now it gives a sense that we already know of a lot of undocumented species.  For context, I should mentioned that there are about 250 recognized species in Canada and the continental USA.

Unrecognized species of  Bembidiina (excluding Amerizus) in Canada and the continental USA

  • Lionepha (2+)
  • Bembidion (40++)
    Subgenera of Bembidion:

    • Lindrochthus (1+)
    • Furcacampa (2+)
    • Notaphus (5++)
    • Trepanedoris (2++)
    • Ocydromus (1)
    • Peryphus (2)
    • “Nearctic Clade” (5+)
    • Hydriomicrus (1)
    • Plataphus (16+)
      • breve group (4+)
      • arcticum group (1)
      • kuprianovi group (2)
      • gebleri group (2+)
      • prasinum (i.e., rusticum/sulcipenne/hyperboraeorum) group (1+)
      • curtulatum group (4)
      • planiusculum group (2)
    • Hydrium (1)
    • Trechonepha (1)
    • Liocosmius (3+)

This totals to 42 unrecognized species.  Immediately evident is the unrecognized diversity within the subgenus Plataphus; at least 16 species unrecognized, and there are likely more.  This high number is partly because we have done a lot of DNA sequencing on that group.  It would not surprise me if subgenus Notaphus might rival that once we study them more.  Subgenus Trepanedoris might not hold as many new ones, but it clearly has quite a few. Subgenus Hirmoplataphus is very complex, and may have many undetected species.

Update: see my follow-up post about showing the geographic distribution of these species.

Posted in Revising Bembidiina, Taxonomic Process | 1 Comment

The legacy of a taxonomist

I have recently been looking through the notes of Kenneth W. Cooper, a renaissance entomologist who wore many hats, one of which was as someone passionate about the same beetles I love, the genus Bembidion.  Kenneth and I began corresponding about these beetles when I was a graduate student, and in later years we discovered a mutual interest in the subgenus Liocosmius, and began a collaboration on that group.  Kenneth gave me his notes in 2005, so that I might use them to finish our joint project.  Kenneth died in 2007, at age 94.

Kenneth’s notes are a treasure trove of detailed information, and a perusal of them led me to ponder the legacy of taxonomists, and our struggles to make those legacies last.

Kenneth Cooper (right) and me.  Riverside, California, January 2005.

Kenneth Cooper (right) and me. Riverside, California, January 2005.

Those of us who are explorers in the land of biodiversity are continually gathering new data, even when we don’t intend to.   As we follow the backwaters and trails laid down by our predecessors,  and then strike out through the bush on our own, we are continually noting patterns in biodiversity’s tapestry.  Through the years, we construct in our brains a detailed map of whatever group we are fascinated in.  For me it is Bembidion and other carabids; for you it might be a clade of spiders, or a group of fungi.

Much of that map of life, including the patterns of morphological and ecological variation, is housed in the delicate folds of tissue inside our skulls.  We also occasionally write down into our notebooks (paper in the past, now digital) observations about the variation in one subgenus, or an unusual series of specimens from a recently sampled locality, or the details of some morphological structure.  Even more rarely some subset of these discoveries gets synthesized into a paper that is published, for the rest of the world to see.  As frequently, our knowledge dies with us.

The nature of the taxonomy is such that it is perhaps particularly prone to such losses.  The pattern recognition engines and data storage in our brains makes us all natural taxonomists; we are continually building maps of the world around us, although of course most humans don’t build maps of small beetles.  When taxonomists go into the field or museum, they are continually adding to this map, including in areas they had not meant to explore.  When I go into the field and look for a particular Bembidion, I will find other Bembidion, notice new species, observe previously unknown microhabitat associations, and see geographic patterns I hadn’t noticed before.  I store that information in my brain (and notebooks), with the intention that the newly discovered territory in my map will be published, someday, but, if you please, after I finish the last ten or fifty discoveries I serendipitously uncovered as I explored.

It is both one of the joys and burdens of taxonomy that we have this vast territory to map (at least in groups like insects), and discoveries are so easy to come by that we are continually, often unintentionally,  uncovering nuggets worthy of record.  In other fields of  science one might plan an experiment, execute it, and gather the data, with the rhythm of the work leading to natural breakpoints for writeup and publication.  This is less the case with taxonomy, where we are bombarded, willy-nilly, by the revealing of small new puzzle pieces in our enormous maps.

Kenneth’s notes illustrate the burden. I have papers and notebooks of his that would fill two filing-cabinet drawers.  About a quarter of this is on the subgenus Liocosmius, a group of delicate, pretty Bembidion in western North America.

An undescribed species of Bembidion (Liocosmius) from California

An undescribed species of Bembidion (Liocosmius) from California

Kenneth had become interested in this group in the 1960s, and his notes indicate an ever-expanding fascination with them.  He delved into the detailed structure of their genitalia, and made excellent sketches of his dissections.

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He made hundreds of slide mounts of genitalic preps, and filled notebooks with standardized drawings of every specimen.

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He took copious measurements, and made table after table containing data.

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He was puzzled over the variation in the number of setae on the eltyra of these beetles, and started to explore the literature on fluctuating asymmetry. He filled pages with speculation about species boundaries as he tackled this difficult group.  He marveled at  Laboulbeniales (a group of very cool fungi – more about those later) on the beetles’ bodies, and carefully collected data on those, too.

His notes are a treasure map, but only he could unlock some of the secrets: these notes were meant for his eyes, not mine.  The parts I can interpret show a very careful, thoughtful, thorough mind; the drawings are beautiful. However, there is so much information he gathered, and so many paths that Kenneth’s exploration led him, that he never managed to rein it all in and publish.

Kenneth was not alone in this by any means.  The shelves, filing cabinets, and museum drawers of any taxonomist of his generation (or mine, for that matter) are filled with knowledge of which the world at large is unaware.  I remember visiting Henry Dybas (a world expert in featherwing beetles) in 1980, not long before his death, and heard many tales and saw many drawings of amazingly cool things about ptiliids.  Some of that knowledge died with Henry, and some is now only in his notebooks, or in the brains of the very few other people who have seen his notebooks.  I am sure that when I die many things I have learned will not be passed via paper, bits, or human brains, and will have to be discovered anew by future generations.

Also at play here is the nature of those who choose to be taxonomists.  I suspect we in general are people who like everything neat and tidy, organized, and complete.  It is rare that we sense that we have fully understood a group, and so we are perhaps prone to wait for that never-to-be-achieved enlightenment before we publish, and yet we continue to accumulate knowledge.

One of the goals of my current revision of North American Bembidiina is to participate in the development of tools to capture some of this information before it is lost, via quantum publication.  But it will require more than just tools – it will require a rethinking of how taxonomists view their work.  How we can use the pattern-recognition engines and memory banks of our brains to our best advantage, in the context of the administrative structure of modern science, is something I struggle with; a blog post on this is in my near future.

Posted in Academia, Taxonomic Process | Tagged , , , | 6 Comments

Sheep Creek in the Cascades of Oregon

Here’s a lovely creek in the Cascades of Oregon.   This part of Sheep Creek is at 795m elevation.  It has a rich bembidiine fauna living in the gravel patches along the shoreline.  In addition to two species of Lionepha (L. casta and L. sequoiae), there are six species of Bembidion.  Five of the species belonging to the Plataphus Complex of Bembidion: B. turbatum, B. curtulatum, B. haruspex, B. nigrocoeruleum, and an undescribed species related to B. sierricolaB. iridescens, a widespread species in the Pacific Northwest, also lives here.

13.270b

Posted in Collecting Site of the Day | Tagged , , | Leave a comment

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.)

Screen Shot 2013-12-11 at 10.41.18 AM

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:

Habitus

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 , , , , | 4 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.

Posted in Fieldwork, Musings | Leave a comment