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.


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.


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.


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, 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.  🙂


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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:


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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:


They have edible gold stars on them!


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.


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.


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.


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.


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.


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.


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.


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.


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


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.



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