Infer all the branches!!!!!

I’ve already sent this image out into the Twitterverse, but I thought I should record the thought here as well.  Sometimes us phylogeneticists are rather obsessed about having a complete phylogeny. In one moment when I was dreaming of having all Bembidion species incorporated into a phylogenetic hypothesis, I thought of Allie Brosh’s iconic Clean All the Things image, and recombination between those thoughts yielded the following image.

inferAllTheBranches

Posted in Tree of Life | Tagged | Leave a comment

Return of the Taxa

Those who might follow my blog may have noticed a rather long lull in my posts.  For this I apologize, but life happens, and my attentions were elsewhere.  I hope to make up for that in the coming months.  In the meantime, here are some sequels to two stories previously posted, in case you are hanging on the edge of your seats to find how our heroes and heroines are doing.

Delectable Bembidion wickhami

In two previous posts (here and here), I outlined how subgenus Lindrochthus consisted of two species, both hiding under “Bembidion wickhami“.  One of those species was known only from Mount Tamalpais just north of San Francisco (this species is indicated in pink in the map below), the other from Mount Tamalpais and the Sierra Nevadas (shown in orange, below).  I have one specimen from the Cascades of Oregon, from the pale blue dot below, that I thought might belong to the widespread species, but I was not sure.  I didn’t know which of the species was the true Bembidion wickhami, and whether the other one might have a name, and so I named them “Bembidion wickhami #1″ and Bembidion wickhami #2″.

wickhamiDNA2

Since my posts, I have added DNA data from one important specimen, a female from Berry Summit in northwestern California. I had figured this would be a member of the widespread species, but to my surprise, this specimen belongs to the “Mount Tamalpais” species (that is, Bembidion wickhami #2 from my earlier post) indicating that that species is more widespread than I had originally thought.

I’ve also looked more at the specimen from Oregon, and I think that is probably the widespread species.   So here’s where we were at:

wickhamiNoTypes

In order to determine what the names of these species might be, I borrowed the primary type specimens of the three names within this subgenus.  Those three names are:

  • Bembidium wickhami Hayward, 1897
  • Bembidion delectum Casey, 1918
  • Bembidion carlhi Erwin and Kavanaugh, 1981

The type localities and details about the primary type specimens are as follows:

  • Bembidium wickhami Hayward. Type locality: Dunsmuir, Siskiyou County, California.  Lectotype male in the Museum of Comparative Zoology, Harvard University (MCZ)
  • Bembidion delectum Casey. Type locality: Gilroy Hot Springs, Santa Clara County, California.  Lectotype male in the National Museum of Natural History, Smithsonian Institution (USNM)
  • Bembidion carlhi Erwin and Kavanaugh. Type locality: Steamboat Falls, Douglas County, Oregon. Holotype female in the California Academy of Sciences (CAS)

I’ve looked at these primary types, and done the work to determine the species to which each belongs. Whatever species the lectotype of Bembidium wickhami Hayward belongs will be called Bembidion wickhami.  If any of the other types belong to that same species, then those names will be junior synonyms of Bembidion wickhami.  The name of the other species will depend upon what type specimens fall within it; the name of the species will be the oldest name whose type belongs in the species.  If no types belong in that second species, then the species will be unnamed, and I would need to describe the species and give it a new name.  (For more explanation about this process, see my earlier post about name-bearers.)

Here’s a map showing the localities of the type specimens, with the type specimen’s dots shown in white, indicating that I didn’t know before I looked at them in detail to which species they belonged:

wickhamiBlankTypes

Because the holotype of the name Bembidion carlhi is a female, it will be difficult to place that to species.  If DNA work is done on the holotype, or more specimens are collected from near the type locality, then it may be possible to place it with certainty.  For the moment, let’s leave that name aside.

However, the lectotypes of the names Bembidium wickhami Hayward and Bembidion delectum Casey are males, and their genitalia would allow certain placement of the specimens to species.   I borrowed the specimens from the MCZ and USNM, did genitalic dissections, and to my surprise the lectotype of Bembidium wickhami belongs to the rarer species (“Bembidion wickhami #2″) and the lectotype of Bembidion delectum belongs to the widespread species. Thus, the name of the widespread species (orange dots on the map) is Bembidion delectum, and the name of the species from Mount Tamalpais, Berry Summit, and Dunsmuir (the locality where the type specimen of Bembidion wickhami was collected), shown with pink dots, is Bembidion wickhami.  The revised distribution map is shown below, with Bembidion wickhami in pink and B. delectum in orange.

wickhamiMarch2015Distribution

The specimen I have sequenced from the Cascades of Oregon, and the holotype of Bembidion carlhi, are likely both members of Bembidion delectum.  I hope to do more collecting in that area to confirm this.  I have shown their localities in orange in the above map. (I’ve changed to color from pale blue to orange to indicate they are likely just members of B. delectum.)

And now there are six…

In three previous posts I have talked about the complexity of what is called “Bembidion curtulatum”.  At first I thought it consisted of three species, then four, then five.   The last post in the series gives a summary of the story.  Since then we have sequenced DNA of more specimens, and better understand the distribution of the species.

The two most significant recent specimens were sent to me via Foster Purrington.  These specimens were collected by Dick Maxey from Whitewater Creek in western New Mexico, near the town of Glenwood.  I had never seen Bembidion curtulatum-like specimens from anywhere near there, and was quite surprised to see them.   Genitalic dissection suggested they were extremely close (maybe identical to) to an eastern member of the B. curtulatum species group, Bembidion basicorne, which suggested to me that the specimens may have been mislabelled as to their localities.  But as Dick specifically remembers collecting the (now dried and pointed) specimens, I decided to see if I could sequence DNA from them.  I managed to get 28S rDNA sequences from both specimens, and the sequences made it very clear that these are not B. basicorne, but a separate, surely undescribed species.  This is thus the six species that would be hiding within “Bembidion curtulatum“.  It is marked with a yellow dot in the map below.

B. curtulatum group Distribution

Now I am pondering when I might go to Whitewater Creek, and find the “yellow dot” species in nature!  I’ve been in touch with the Forest Service folks down there (in particular Pat Morrison, recently retired), and they are excited about an expedition to find it.

I’ve also looked at the type specimens of more of the names, and I now suspect that species 3, 5, and 6 are undescribed.  Species 4 might also be undescribed, but it might have a name from specimens described in the Russian far east (although I don’t yet know if the species lives there).

 

Posted in Fieldwork, Revising Bembidiina, Taxonomic Process | Tagged , , , , , , | 4 Comments

A Love of Leptoferonia

For many years I had wondered who Hilary A. Hacker was.  In the carabidological literature she appeared on the scene in 1968 with the publication of one of the best revisions of a carabid group that had been done to date, and then she just as quickly disappeared.

Hacker1968 Her work “The Species of the Subgenus Leptoferonia Casey (Coleoptera: Carabidae: Pterostichus)”, published in the Proceedings of the United States National Museum, is a very thorough work.  It is concisely written, but full of details, with excellent genitalic and habitus illustrations, and maps. Her revision is based upon her very extensive collecting efforts – she studied about 2400 specimens, most of which she collected herself throughout western North America. It is one of those revisionary works that is satisfying to open and use because of its quality.

My curiosity about Ms Hacker was not just a result of her single, unusually good publication, but also because the Oregon State Arthropod Collection was fortunate to receive, some time ago, much of Hilary’s collection.  I had been curating and looking at the Bembidion she collected, and found some important specimens from throughout the western USA, and down into Mexico.  This piqued my curiosity more: who was this excellent collector who travelled seemingly alone for many thousands of miles?

Kip Will, I suspect, had been even more curious about Hilary, as Leptoferonia are some of his core study organisms; her 1968 publication is the groundwork for all that he has done on the group.

Until recently, I had thought that perhaps Hilary Hacker was no longer alive – but then Kip did some sleuthing and tracked her down, to the hills near Redway, California. A few letters and phone calls later, and an expedition to meet Hilary was in the works.

This past February, Kip, Christopher Marshall, and I drove from Kip’s house in the Bay Area north to Redway.  And there she was, stepping out of a blue pickup truck.  Her short hair, red flannel shirt, plaid jacket, jeans, and tennis shoes revealed a no-fuss, practical person.  Now in her late 70s, her lively eyes spoke of a still razor-sharp intellect. We ate lunch with Hilary, and she then led us west into the hills to her off-the-grid house, which she built, and now shares with Betty.

Hilary's house

We had a wonderful time.  The best part for me, by far, was to see Hilary and Kip together, the two people in the world who most understand and love Leptoferonia.

Hilary and Kip

We talked to Hilary about her history, and how she came to do her Leptoferonia work.  Her family is from Seattle.  She noted that her grandfather collected butterflies, which was an inspiration to her; her father was a fish biologist.  She went to Reed College for one year, and then graduated from San Francisco State.  She was a lab technician, at least in part in soil science at Oregon State University.

She said that when Hatch’s series on the Beetles of the Pacific Northwest came out, she became interested in Leptoferonia, and began working on them.  As she travelled the logging roads of the west in a VW bus in the late 1950s and into the 1960s, collecting Leptoferonia and other carabids, her only companion was her dog.

Kip Hilary Sitting

In the stories she told us, there was no mention of a mentor, of someone from whom she learned the trade.  Her answer to my queries about this yielded the most astounding response:  she had no direct mentor. She learned from the literature, correspondence with others (including George Ball), and had some help from Kenneth Fender.  But she did not have a mentor under whom she studied, and so in that sense she was self-taught.   That she managed to accomplish such excellent work with Leptoferonia on her own speaks to her focus and abilities.

During our visit, Betty brought out some old pictures and newspaper clippings about Hilary.  Included in these was the following gem of a picture, of Hilary when she was 13 years old, in 1951.  The accompanying newspaper is titled “Hilary Hacker Prefers Beetles to Beethoven”, and states “She loves beetles.  All kinds of beetles. And she has more than 400 of them.” How wonderful for our community that her passion lasted for a couple of decades, allowing her to produce her Leptoferonia revision.

Hilary Hacker 1951

While visiting her, we collected some Leptoferonia around her house, and Kip put them in a tray.  I sat back and watch the animated conversation as Kip and Hilary talked about the little beetles scurrying around.

Kip and Hilary

It was a magical moment.  I watched two kindred spirits, and felt a very deep bond with these people who are so enthralled by the organisms with which we share this Earth.

Posted in Fieldwork, Taxonomic Process | Tagged , , , , | 8 Comments

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.

zephyrBanner

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 | 3 Comments

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.

newTaxa

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