Port and Roses

Posted on 21 April 2013 by David Maddison

In late January 2012, my daughter, Julia, and I were dining at Luc, having a typically excellent meal. At one point, Julia went to the restroom, and then returned to the table. The following conversation ensued.

Julia: “David, I think you should go to the bathroom. The first one.”

David, skeptical: “Okaaay…” (He goes to the bathroom, then comes back)

Julia: “Did you notice the glass cabinet?”

David: “I did notice.”

Julia: “Well. It’s unlocked, and quite empty, don’t you think?”

David: “Yes indeed. How interesting…”

Julia: “We need to put something in it! Something artistic!”

We brainstormed about it, one thing led to another, and the next thing you know we had decided to put on a multi-act play in the glass cabinet in the washroom.  We named the play “Port and Roses”.

Julia wrote the screen play, and made wire sculptured figures, and props.  The next time we went in, Julia snuck into the washroom with a full backpack, set up Act I, Scene I, and so began the adventure.

Act I, Scene I

Act I, Scene I

That first scene was simple, with a man (holding a large rose) descending down a ladder attached to a bottle of Kopke port, and a woman sitting on top of her Grand Marnier bottle.

For the next several months, whenever one of us went to Luc, we would sneak into the washroom and set up the next scene.  We felt like criminals doing this, as we never told them what we were doing.

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What should I name this beetle?

Posted on 18 April 2013 by David Maddison

Along some creek and pond shores in the Sierra Nevada of California there lives a pretty, spotted Bembidion, and this Bembidion has no name.  It belongs to the subgenus Liocosmius, a group of Bembidion that range from BC to Baja California, east to New Mexico.  There are three described species in the subgenus (B. mundum, B. horni, and B. festivum), and three undescribed (one species in western California, one in Arizona and New Mexico, and the one in the Sierra Nevadas).  I have names figured out for two of the undescribed species, but the third one (the one that lives in the Sierra Nevada) eludes me.  Here’s what a male of that one looks like.  The spots look brighter when it is alive.

DNA3104Larger

This species is restricted to the Sierra Nevada of California, and it is unusual within the subgenus in its restriction to mountainous areas.   Below is a picture of one of its habitats in the Sierras.  At this site it was found along with Bembidion iridescens, B. wickhami, Lionepha pseudoerasa, L. osculans, L. sequoiae, L. erasa, and other species of Bembidiina.

Strawberry Creek at Sciots Camp, El Dorado Co., California

Strawberry Creek at Sciots Camp, El Dorado Co., California

What should I call this species?  I’ve thought about several possibilities.

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Posted in Revising Bembidiina, Taxonomic Process | Tagged , , | 9 Comments

Changing of the guard

Posted on 16 April 2013 by David Maddison

In 1985, my brother Wayne wrote the first version of MacClade, a graphical program for studying branches of a phylogeny (“clades”) and phylogenies more generally.  It was a very small program, that did just a few things, but was notable in introducing graphic manipulations of phylogenies on the screen.  I started working on the MacClade code a few months later, when I acquired my first Macintosh Plus computer.

MacClade's icon

MacClade’s icon

By about 1989 I had more or less taken over MacClade development; version 3.0 came out in 1992, and the last release was version 4.08 in 2005.   MacClade celebrated its 25 anniversary in 2010, and was still being widely used and cited.  However, in July of 2011, Apple released a new operating system, and removed from it compatibility with older code such as that contained in MacClade, and MacClade could no longer function.

In 1997, while I was working on version 4 of MacClade, Wayne started a rewrite of the whole program, and Mesquite was born.  We have been developing Mesquite ever since.  Mesquite is modular, and very flexible, and it now does much more than MacClade ever did.  That comes with a downside, however – Mesquite’s interface is much more complex than MacClade’s, and so it has taken people a bit longer to get used to it.

Mesquite's icon

Mesquite’s icon

Wayne and I abandoned MacClade for our own empirical work quite a few years ago, but the community has continued to use it.  Even though MacClade’s development stopped in 2005, as late as 2008 there were twice as many citations that year for MacClade as for Mesquite.

Yesterday, as I was looking up some statistics for a report, I realized that the changing of the guard had been completed: for the first time, Mesquite’s citations for a year topped MacClade’s.  In fact, in 2012 Mesquite was cited more times than MacClade had ever been cited:

Number of citations each year

Number of citations each year

This is both good, and a bit sad… sometimes I miss MacClade.

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Names approved!

Posted on 15 April 2013 by David Maddison

In two earlier posts, I wrote about the dangers of naming species after the name of the first peoples of an area, as well as the concerns about using a word from a native language.

In the first of those posts, I mentioned that I was hoping to name a species “Bembidion mimbres”, after the Mimbres people who lived in that area and made pottery depicting many insects.  The Mimbres represent an extinct culture, but apparently the Hopi include their descendants.  Last week I received word from a legal representative of the Hopi, and he said there would be no objections to my using that name.  He pointed out that “mimbres” was not a native word – and, in fact, it is a Spanish word that means “willows”.  It couldn’t be more ideal, as this species lives under willow trees along the banks of rivers; in the picture below, the beetles can be found at night up under the willows walking on willow leaf litter.  I am delighted both by the permission to use the name, and by this added meaning.

Gila River at Billings Vista, NM

Gila River at Billings Vista, NM

In the second post, I talked about wanting to name a Lionepha from Marys Peak, Oregon, which lives along the edges of waterfalls and seeps, “Lionepha tuulukwa”, as “tuulukwa” means “waterfall” in the local (now extinct) native language.  The habitat of this species is shown below; one night, 12 specimens were found in moss in the circled area.  I’ve been talking to some friendly people associated with the local tribes, and they have generously given me permission to use that name; they also provided more detailed linguistic information about the word, which is very helpful.

Alder Creek Falls, Marys Peak, OR

Alder Creek Falls, Marys Peak, OR

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

How to collect beetles for DNA studies

Posted on 12 April 2013 by David Maddison

Preserving beetles for DNA studies is easy, but a few rules need to be followed.

You will first need to decide which specimens to preserve. It is ideal to have two or more specimens of a species preserved, so that the extra specimens can serve as backups in case the first specimen fails to yield good DNA.  Also, because the specimen from which DNA sequences will be obtained serves as the voucher, it is important to choose the gender that contains the key morphological characters for distinguishing species.  This will allow the DNA data to be properly associated with the morphological data, type specimens, etc. For Bembidion, males contain the most diagnostic characters, and so males should be preferentially preserved for DNA. The general rule of thumb is that whatever gender is best for a holotype is the gender you should choose for DNA preservation.

Exactly how a specimen should be preserved depends upon the materials you have available.  I use one of two preservation methods:  in 95-100% ethanol, or in silica gel.  One of the most important things that both of these do is to remove water from the beetle’s tissue, which prevents nasty enzymes from destroying the DNA.  Here are some procedures I use to ensure high-quality DNA.

Ethanol preservation
95-100% ethanol is ideal; lower concentration doesn’t work as well.  Drop the live beetles into ethanol.  Make sure there aren’t too many beetles in the vial; ideally there is at least four times as much ethanol as there is beetle mass.  The vial on the left below will have well-preserved DNA; the vial on the right is too tightly packed with beetles, and the DNA won’t be as high quality.

vials

Once the beetles have all died, it is ideal to pour off the ethanol and replace it with fresh ethanol.  If you can’t do that right away, that’s OK; but you should change the ethanol in the next day or two.  If you can change the ethanol again a few weeks later, that would be even better.

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Posted in Revising Bembidiina, Taxonomic Process | Tagged | 7 Comments

More hidden species in Bembidion: a multiplicity of “Bembidion kuprianovi”

Posted on 6 April 2013 by David Maddison

In Lindroth’s magnificent 1963 treatment of Bembidion of Canada and Alaska (and the northern contiguous States), he notes the extent of structural variation within species. Some species he notes to be relatively uniform, others more variable. As I delve into bembidiines of North America more thoroughly, I find that just about any species he notes to be rather variable I will find (using more detailed morphological or molecular data) to be multiple species.  For example, he starts his description of “Bembidion chalceum” with “An extremely variable species: in size, impression and punctuation of elytral striae, convexity of intervals (including the 9., with seeming variation of its width, as a consequence), &c. ”  My 2012 paper on subgenus Pseudoperyphus shows that his “Bembidion chalceum” consists of at least four species, now named Bembidion chalceum, B. rothfelsi, B. bellorum, and B. louisella.

For this reason, I was suspicious of Bembidion kuprianovi, as Lindroth begins the description of that species with the statement: “Varying in size more than perhaps any other species of Bembidion, also in color, form of prothorax (figs. 133a, b), &c.”  Some are small and brown (as in the specimen on the left, below), some are large and black (as the specimen on the right), but there seem to be lots of in-betweens.

"Bembidion kuprianovi"

“Bembidion kuprianovi”

I had become convinced that this was a complex of species in 1981, when I was on a collecting trip to the Yukon with George Ball and Nigel Stork.  One day I found a population of B. kuprianovi on damp soil under leaf litter under small willow bushes on the upper bank of a slowly-moving river.  All specimens there were the small, pale form of B. kuprianovi.

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Why I spend my time with carabid beetles

Posted on 1 April 2013 by David Maddison
Dicaelus purpuratus

Dicaelus purpuratus

Omophron

Omophron

Bembidion zephyrum

A closeup of part of an elytron of Bembidion zephyrum

A closeup of part of an Elaphrus elytron

A closeup of part of an Elaphrus elytron

 

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Four?

Posted on 23 March 2013 by David Maddison

In western North America small, dark Bembidion (Plataphus) are common on gravel river shores.  Most of these are called Bembidion curtulatum.   They are the smallest members of subgenus Plataphus (sensu Lindroth) in North America, at about 3.5 mm long. As I noted in a previous post, DNA sequences of 28S ribosomal DNA suggests that “B. curtulatum” may be as many as 3 or more species.  This week we got some more sequence data, and it looks as if there may be at least 4 species.

Here is one of the specimens from which we have sequence data:

"B. curtulatum" specimen DNA3207

“B. curtulatum” specimen DNA3207

Here’s a section of the 28S gene; each row is a different specimen:

Screen shot 2013-03-23 at 5.07.17 PM

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BotW: Two species of Lachnophorini

Posted on 21 March 2013 by David Maddison

Because I have been remiss at blogging about beetles recently, today I’ll post two Beetles of the Week.  Both are members of the carabid tribe Lachnophorini. The first is a member of the genus Calybe, which are elegant, ant-like species that live on sand or silt shores of bodies of water (rivers, lakes). I found the Calybe sallei, below, in Texas.

Calybe sallei

Calybe sallei

The second is Lachnophorus elegantulus, a common species on gravel river shores in the Southwestern USA and neighboring Mexico.

Lachnophorus elegantulus

Lachnophorus elegantulus

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Where have all the left parentheses gone?

Posted on 15 March 2013 by David Maddison

Today is another day in which I am curmudgeon regarding grammar.

Why, oh why, is it deemed acceptable by so many to have forlorn, partnerless right parentheses?  I am referring in particular to the common practice of presenting a numbered list in which each number is followed by a “)”, as follows:

The items are: 1) first item, 2) another item, and 3) a third item.

Argh!  If the numbers are parenthetical remarks (as they often are), then they should be treated like parenthetical remarks in other contexts, i.e., with two parentheses:

The items are: (1) first item, (2) another item, and (3) a third item.

One could use commas, although that gets a bit confusing:

The items are: 1, first item, 2, another item, and, 3,  a third item.

There are some contexts in which one might want only one punctuation mark following the number, and none before.  There are punctuation marks designed for being singletons, and punctuation marks that are intended to be used alone should be used when only one is desired.  For example, instead of

The items are:
1) first item
2) another item
3) a third item

one could simply use colons or periods:

The items are:
1. first item
2. another item
3. a third item

Why one would want to use one half of a pair of parentheses in this context is beyond me.  Why force a new and rather different use on a punctuation mark when there are other perfectly good punctuation marks that are built for the job?  Whenever I encounter unmatched right parentheses I feel as if I somehow neglected to notice the left parentheses that preceded them. Parentheses are meant to be in pairs.

As you might expect, paired parentheses is another one of those language requirements I inflict upon my graduate students.

I am reminded of this relevant xkcd comic.

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