Ten years later: the Lionepha paper is out

In September of 2009, I arrived in Oregon, excited to begin my new position at Oregon State University. I was also excited to live near Marys Peak, as the top of Marys Peak was the locality of capture of the only known specimen of what was then called Bembidion chintimini. (I’ve since moved that and related species out of the genus Bembidion, and as the genus Lionepha.) A few days after I arrived in Corvallis, I drove up to the top of that mountain to see if I could find the species again. I found some little beetles that might or might not be Bembidion chintimini, but I was a novice with that group of bembidiines, and so I wasn’t sure. I also found a larger, related specimen lower down the slopes of Marys Peak, near Alder Creek Falls, which confused me as well. My efforts to discover the identity of those specimens took a long time, and the threads I was tugging on as I explored caused an unravelling in my understanding of that group of beetles, which I would eventually re-weave into a new tapestry. In the end, this path led to the discovery of a total of four new species, as well as a merging of three others.

A specimen from Marys Peak of the same species I found in September 2009

In many ways this project was the heart and soul of my first decade in Oregon. I spent many hundreds of hours on this project, traveling and collecting specimens, extracting and sequencing their DNA, making genitalic preparations, studying their structures, photographing them, examining their chromosomes, doing phylogenetic analyses, and, eventually, creating the figures for the paper and writing the text. Perhaps more emotionally compelling was the discovery and solving of many puzzles along the way, especially that revolving around “Bembidion chintimini”. That some of these puzzles were solved by a combination of old-fashioned morphological studies as well as next-generation genomic sequencing of old type specimens, including a 159-year-old LeConte lectotype, made the tale all the more compelling to me.

John Sproul, a former graduate student of mine, helped by sequencing the DNA I extracted from some pinned type specimens (including that LeConte lectotype), as well as by doing important collecting in the Sierra Nevadas of California; for these efforts, he is a co-author of the paper that has finally resulted.

This paper, titled “Species delimitation, classical taxonomy and genome skimming: a review of the ground beetle genus Lionepha (Coleoptera: Carabidae)“, came out recently in the Zoological Journal of the Linnean Society. The paper can be found at https://doi.org/10.1093/zoolinnean/zlz167; if you would like a PDF, email me.

It turns out that I did find a female of “Bembidion chintimini” on Marys Peak that first trip in 2009. It took until the following summer for me to realize that. It took even longer to eventually come to the realization that this species was widespread, and had a much older name (Lionepha erasa LeConte). Here’s a condensed version of the story, as told in the paper:

Investigation of the rarer species, the one here called Lionepha erasa, began in 2010. Dissection of the first recognized males from Marys Peak, Oregon (type locality of Bembidion chintimini) revealed an aedeagus indistinguishable from those from San Juan Island, Washington (type locality of Bembidion lummi). The female holotype of B. chintimini is wingless and has slightly rounded shoulders. However, the Marys Peak population is wing-dimorphic, and winged individuals are in body form no different from the type series of Bembidion lummi. The elytral microsculpture of the holotype of B. chintimini is perfectly isodiametric (against Erwin & Kavanaugh, 1981), thus matching that of B. lummi. Other characters mentioned by Erwin & Kavanaugh as distinguishing the two populations are not consistent with available specimens. The lack of evident morphological differences, combined with effectively identical DNA sequences in specimens from Oregon, British Columbia and Alaska suggested that the Marys Peak populations are the same species as populations further north, and for this reason, Bembidion chintimini and B. lummi were synonymized by Maddison in Kanda et al. (2015).


This left in question the specimens considered to be Bembidion lindrothellus by Erwin & Kavanaugh, which are at first glance similar to the Marys Peak and other populations of ‘Bembidion chintimini’. Specimens classified as Bembidion lindrothellus are reported to be paler, but all specimens mentioned in Erwin & Kavanaugh (1981) are teneral. The unsclerotized aedeagus of the holotype of Bembidion lindrothellus made comparison of internal sac sclerites difficult. However, the internal sac membrane that rests in the left-most position has a species-specific microsculpture in Lionepha, and the microsculpture scales of the holotype of Bembidion lindrothellus from Alaska match those of Marys Peak specimens. A non-teneral male was also collected by Lindroth at the type locality of B. lindrothellus, but was not included in the type series, perhaps as the specimen was housed in Lindroth’s collection in Lund, Sweden. This specimen is presumably the one whose genitalia Lindroth figured as Bembidion brumale (1963: fig. 127f). We have examined that specimen, and it is indistinguishable from specimens of ‘Bembidion chintimini’ from Alaska, British Columbia, Washington and Oregon, including details of the internal sac. Most critically, DNA sequences of the holotype of Bembidion lindrothellus are identical in eight studied genes to those of other specimens from throughout the range (Figs 5–7). It is thus evident that the holotypes of Bembidion chintimini, B. lindrothellus and B. lummi belong to a single species.


However, there is an older name. The type series of Bembidium erasum consists of four females. These specimens have traditionally been considered to belong to the common, widespread species here called Lionepha probata. Females of these two isodiametrically microsculptured species are difficult to tell apart, especially those with less-extreme prothoracic proportions (neither wide nor narrow). Although there are distinctions in the lobe of the female bursa of fully sclerotized individuals, interpretation of tenerals is more tenuous. Specimens in the type series of Bembidium erasum are all teneral, with prothoraces of moderate width, and thus there is no clear morphological evidence to place them to species. The type series was provided by George Suckley (LeConte, 1859), presumably captured during his travels as naturalist for the governor of Washington Territory during 1853–57 (Cooper & Suckley, 1859). The type series is from ‘Oregon’, which at the time encompassed the current area of Oregon, the southern half of what is now Idaho and some parts of Wyoming and Montana (Barry, 1932). Suckley’s travels in Oregon included areas within the range of both species (Cooper & Suckley, 1859), and thus geography provides no clues about species membership. However, DNA data from the lectotype (and two of the paralectotypes; Sproul & Maddison, 2017) makes it clear that these specimens belong to the current species (Figs 5–7; Supporting Information, Fig. S1). Thus, the valid name of this species is Lionepha erasa, with Bembidion chintimini, B. lindrothellus and B. lummi as junior synonyms.

Maddison and Sproul (2020)

That description of the history does not adequately capture all the many mysteries, proposed and rejected explanations, and confirmed hypotheses along my multi-year path, and the eventual pleasure as the hypotheses became confirmed through the emergence of consistent, repeated patterns. It was one of the more pleasing journeys of discovery I have been on. I’ve previously mentioned a few of the turns and twists in the story, in my posts on Rainy-season beetles and surprises in Lionepha.

In addition to solving the mystery of the small beetles on top of Marys Peak, four new species were discovered along the way and described in the paper:

  • The larger specimen I discovered on my first trip up Marys Peak belongs to a species that lives along the sides of Alder Creek Falls and on rock seeps in the area, as well as along a creek west of Eugene, Oregon, and in the Trinity Alps of California, is now officially named Lionepha tuulukwa Maddison. I’ve talked about the naming of this beetle here and here.
  • A species I first became aware of through a single male along Bishop Creek that John Sproul found, is now called Lionepha lindrothi Maddison & Sproul.
  • The species I found in the central Sierra Nevada of California, and which provided another surprise in the group, is now called Lionepha australerasa Maddison.
  • A species from western Montana and Wyoming, as well as eastern Oregon and Washington, came to light from specimens collected by my good friend David Kavanaugh. This species is now called Lionepha kavanaughi Maddison.

This paper on Lionepha implicitly tells a love story between me and my beetles. When I look at the final product, I see it as a celebration of the process and fruits of discovery. I also see it as a history of my embracing the Pacific Northwest, and the abundant and diverse life that lives here.

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The Tree of Life Web Project: 25 years online

On 16 November 1994, we first made public the prototype version of the Tree of Life Web Project. At that time, it was a series of static web pages, with trees made out of text characters, created by a special version of MacClade.

This was more than three years before Google existed, and more than a year before the research project that led to Google began. In November 1994, Wikipedia was still more than six years away, Facebook was nine years in the future, and YouTube more than 10 years away.

In the years that followed, the Tree of Life Web Project was nurtured by a host of people on the home team (both deeper in the past and more recent), along with hundreds of biologists from around the world who contributed content.

Although the project is still alive (it still gets over a million separate visitors a year, from many countries), it has been relatively dormant, awaiting someone with a passion to take it over and reinvigorate it.

It’s been a good 25 years; it’s hard to believe it’s been that long.

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In Memory of George

As the ship rolls gently upon the waves,
I look east toward the Tasman Sea,
The relentless surges swallowing time,
As they have for millions of years,
Through turn after turn of the Milky Way,

Beneath and beyond the waves,
The tree of life has grown,
Both struggling for life
Against harsh forces,
And exploding in exuberant replication.

And within our small leaf,
The courage and strength of the principled
Inspires and uplifts,
Giving us strength to seek a brighter future,
And explore this world which has given us birth,
And to which we will return.

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George Eugene Ball

25 September 1926 – 12 January 2019

There are those amongst us who, through their words and actions, radiate strength, courage, compassion, and generosity, causing a positive ripple to spread across the communities they touch, increasing the good in the world, and casting light against the darkness. George Eugene Ball was such a man.

When I was a teenager, my parents would visit our grandparents, and on the way would drop my brother and me off at the University of Guelph library, where we would happily spend a Saturday or Sunday pouring through the shelves of beetle and spider books, photocopying as many of them as we could.  It was in this library that I discovered Ross Arnett’s Beetles of the United States, and, inspired, purchased a copy of that tome.  One chapter in particular captured my attention, about Carabidae, written by George E. Ball of the University of Alberta. As a 16-year-old, on 13 December 1974, I decided to reach out to Dr. Ball, in case he might be able to answer my queries about some of the ground beetles I was finding in southern Ontario. I wrote him a four-page letter, but did not expect a response – a famous professor would surely have more important things to do than write a teenager far across the country.  To my great surprise and delight, a few weeks later I received an eight-page letter in response, answering my questions in detail, and providing me with the names and addresses of many other carabid systematists to whom I could write.

Decades later, when I wrote a letter telling George how profoundly his letter affected me, and how much it inspired me, and thanking him for it, he replied that the best way to thank him would be to respond similarly when a 16-year-old wrote me asking me questions about her or his favorite beetles.

This typified George. He was a man of principle, duty-bound to serve the causes he believed in, including the people who were part of his community.   He would have viewed helping me as a necessity, as he was committed to educating youth and encouraging those who might engage in the honourable cause of discovering and documenting our planet’s biodiversity.

George sought to deflect attention away from himself.  He did not want to be viewed as a grand master, separate and above the rest of us. In later years he reluctantly allowed us to celebrate his achievements, not because he wanted to bask in the glory, but rather because it allowed him to see old friends and hear about their discoveries.

George was virtually egoless when it came to science.  I remember once sitting with some fellow graduate students as George was explaining some entomological knowledge or systematic principles (I don’t remember which), and at one point he just stopped, looked thoughtful for few seconds, and said, “Wait, why did I just say that?  That isn’t true at all”, and he then proceeded to correct himself.  This was a profound message to those of us concerned about social standing: it told us that science required us to focus on honesty and the pursuit of knowledge, even if that meant proving ourselves wrong in public.  We learned that science was not about us; our pursuit was bigger than any of us.

One of George’s most important traits was his positivity toward others.  He was almost always generous regarding others, and emphasized their better traits.  He would not say anything negative about anyone in frustration or in spite, an inspiring demonstration for those of us not always so kind.  Even in situations where it would be better to be honest about the negative traits about someone, he struggled to express them.  To be at fault in this direction is vastly more preferable than the alternative.

One might think a man such as this would set such a daunting example that he would not inspire others, as he would be viewed as so distinct from the rest of us that we could not possibly follow his path.  But George was humble, and that gave us a sense that we, too, could live by those principles.  He was also not perfect, and did not hide his imperfections, and through those we could see his struggle, and what he had achieved by force of will; this led us to believe that we too could achieve our goals with honesty and hard work.

You will be missed, George, but the ripple of goodness and light that you created will continue to spread and amplify.

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Zephyr 2.0 and Mesquite 3.3 released

Yesterday, after about three years in gestation, we released Zephyr 2.0.  Zephyr is a Mesquite package that manages interactions with phylogeny inference packages including RAxML, GARLI, PAUP, and TNT.

zephyrBanner

The most notable additions to Zephyr 2 include implementation of the SOWH test, CIPRes support, much better interapplication communication, and more extensive support for PAUP.   Many bugs were also fixed, and other improvements made.

SOWH Test

The Swofford-Olsen-Waddell-Hillis test allows one to test particular aspects of phylogenetic structure, such as the presence of a hypothesized clade. Given a Mesquite file containing:

  • the data matrix
  • a constraint tree showing just the phylogenetic structure to be tested (e.g., a tree showing just the one clade with everything else as polytomies)
  • the model tree: the best tree with branch lengths that fits that constraint (inferred in a constrained analysis)
  • models of evolution (e.g., GTR+I+G) with parameter values inferred from the matrix,

then the SOWH feature in Mesquite will automatically find the observed value of the test statistic using whatever tree inference program you choose among those Zephyr supports, and simulate data many times on the model tree, calculating the test statistic for each simulated matrix.  It will show you the p-value as the analyses goes along, and gives a report once you have decided you have done enough replicates.

SOWHCompleted

In the figure above, the model tree on which data are simulated is shown in the middle, with the results from the SOWH test on the right.  (In this example, only four replicates were conducted; to get an accurate estimation of the p-value, many more would need to be done.)

More details are in Zephyr’s SOWH test documentation.

CIPRes connectivity

CIPRes (CyberInfrastructure for Phylogenetic Research, http://phylo.org) provides a gateway for doing phylogenetic inference on a fast cluster of computers.  Zephyr 2 allows one to run analyses on CIPRes from within a Mesquite session, and will harvest the results once done and move the trees into the Mesquite file.

Interapplication communication

Zephyr 2 has many improvements under the hood, including much better communication mechanisms between Mesquite and the external program.  Among the improvements are the option to have Mesquite directly start the external program (as opposed to asking the operating system’s shell to do that), which gives Mesquite more control over the process.

Better PAUP support

Zephyr 2 now provides a means to do likelihood, distance, and SVD quartets analyses using PAUP from within Mesquite.

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Happiness is a Big Tree on the Wall

 

In the hallway outside my lab, about 800 species of Bembidiina, together in one tree.  🙂

davidandthebigtreedecember2016small

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A Stained Trepanedoris

I started learning how to do stained glass pieces over the summer, and for my first piece I decided to honor our Discovering Insect Species class by doing the head of an undescribed species of Bembidion (Trepanedoris) that we discovered.  I finished the piece on Tuesday; here it is:

BembEndecaStainedGlassSmall

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Flavor 100

Today we reached a milestone:  our 100th flavor in our approximately weekly Guess the Potato Chip Flavor event in my lab.  Today we decided to celebrate the event not only with our 100th flavor, but also with five other flavors to round out the meal.  Those five other flavors were some current Lay’s flavors:  West Coast Truffle Fries, Southern Biscuits and Gravy, Greektown Gyro, New York Reuben, and Pico de Gallo.  Over the last couple of years we have had quite the variety: Happiness Butter (from Japan, by a South Korean company), Butter Chicken (Lay’s, from Canada), Slow-cooked Ribs (Old Dutch, from Canada), and many others.  Some were excellent, some.. not so.  The two that stayed in the bowl the longest, by far, were Sea Salt Pomegranate and Cappuccino.  We try to stick to potato chips, but we do occasionally branch out into other types (such as corn chips) if there are compelling flavors or if we have no novel potato chip flavors.

But the 100th flavor… now that was a fantastic one.  My graduate student James Pflug acquired it online, from the UK, and, well, here are two pictures:

StarChips

They have edible gold stars on them!

JamesWithChips1200

The flavor:  Winter Berries and Prosecco with Edible Gold Stars and a touch of Fizz, by Marks and Spencer.  Berries and sparkling wine with gold stars.  Wow.  I can’t imagine how we can top that.

Here’s the full list of what we have tried.

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Discovering Insect Species: the Trepaneleven Awards!

In the Discovering Insect Species course, the eleven of us (students Alex, Ana, Danielle, Elle, Julia, Mamo, Shannon, Tom, and Trevin, plus John and me) formed a great team, and we learned a lot together.  Over the course of the term, we became… the Trepaneleven!

TShirt1 small

Design by Julia Amerongen Maddison.

As with any group of superheroes, talents vary from hero to hero.  In order to recognize the amazing abilities and achievements of the Trepaneleven, we held an award ceremony, at which awards were awarded.

And the winners are:


Leaves Analysis Champion: Julia

Julia excelled at finding the best species delimitation using a pre-release version of the Mesquite package Leaves (which attempts to delimit species using gene trees).  Her award was a Leaves Champion trophy.

JuliaLeaves


Most Unusual, Pleasing, and Course-appropriate Career Ambition Award: Elle

Elle’s interest in insect taxonomy and illustration made her the obvious choice for this award.  Her award consisted of a magnifying glass (with built in vial!), some watercolor paper, and some Pigma pens.

ElleAward


Best Dry Sauté and Best Ice Cream Proponent Awards: Danielle

Danielle taught us the wonders of sautéing without oil during our Malheur field trip (as, well, the oil was inadvertently left in Corvallis).  She was also excellent at leading us to ice cream, which the judges very much appreciated.  Her award was a trophy topped with crossing items: a skillet and an ice cream cone.

DanielleAward


Most Ambitious Taxonomist Award: Ana

As someone who has described new species in her native Brazil, the country that probably contains more undescribed species than any other, Ana was a natural for this award.  Her project (an interactive key to Bembidion (Trepanedoris)) also swayed the judges. Her award was a copy of E.O. Wilson’s book, The Diversity of Life.

AnaAward


Most Unexpected Comments Award: Alex

Let’s just say you had to be there, in multiple places at multiple times.  With Alex’s interest in forensic entomology, a zombie survival guide and a bug collecting kit seemed the appropriate items to honor his achievement.

AlexAward


Best Habitat Discovery and Best Car Snack Awards: Mamo

Mamo discovered, at Malheur NWR, the habitat of the undescribed species that we first found at Klamath Marsh NWR.  This allowed us to collect what will become the type series of the species.  It was the most significant habitat discovery during the course, and for this the judges will always be thankful.  As important, though, was Mamo’s evangelism for the wonders of Spam sushi, of which we became rather fond on our road trips.  Her award consisted of a book on the history of Spam.

MamoAward


Awards for Solo Discoverer of a New Species, Best Harpalinophile, Best Lover of Words, Best Reaction to a Tick:  Shannon

Shannon not only discovered a new species in her parents’ backyard (it is still the only known locality), she was also overly adept at collecting little harpalines (thinking they might be Bembidion).  She loves words and their histories, and so one way we honored her contributions was with a copy of Brown’s Composition of Scientific Words.  On the Malheur trip, her neck decoration one day, a tick, caused such a reaction that we immortalized that tick in a very small clear box, and presented that to her as well.

ShannonTick


Best Knowledge of All Things Aquatic and Best Walkie-Talkie Personality Awards: Tom

Tom knew everything about aquatic invertebrates (at least, that was part of the class myth).  He also was excellent at manning a walkie-talkie so that we could communicate between vehicles as we drove our convoy to and from the field sites; his British accent and humor (or, rather, humour) were a real plus.

TomAward

Tom was also adept at spreading parts of our aspirators around the countryside, and so his trophy was affixed with one such piece.

IMG_4735


Best Effort to Follow Instructions and Not Screw Up Award:  Trevin

Trevin did an excellent job of following instructions.  He also coveted a National Wildlife Refuge sign (containing instructions) that we were given by one of the wildlife refuge managers. In hopes that Trevin would continue to follow instructions, the judges were pleased to give him this award.

TrevinAward

 

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