On the road to Oaxaca

Here in Ixtlán de Juárez we took the day off from collecting to catch up with our processing of specimens. We collect the spiders live. When we return from the field, we sort them to species, choose ones to photograph, and preserve the rest, freeing up their vials for the next day. The photographs take a while, and when you add it to the basic note-taking and other duties (we hope to do videos!), we usually don’t quite get done the day’s tasks. Today I had a big pile of spiders that took most of the day to photograph.

So, a belated #Mexigonus2017 report on our trip down from Mexico City. The drive was smooth on the big toll highways, and of course we chose to make a few stops to look quickly for spiders. The highlight of the day for me was to find Habronattus nahuatlanus (at least, that’s what I think it is) at Santa María Tinú and to learn its habitat — in or under grass clumps, just like the recently described H. luminosus from Arizona. Here is the male, and female. The female wasn’t known before, so it’s good to see what it looks like.

Habronattus nahuatlanus, male (top row) and female (bottom row)

We’ve had many successes in subsequent days, and I’ll report on purple tomatoes, green ghosts, and blue-legged magic as soon as I can, perhaps not in chronological order.

By the way, for English speakers who don’t know Spanish, “Oaxaca” is pronounced (more or less) as the English “Wahaca”.

Expedition to Oaxaca and Chiapas

It’s been too long since I’ve been on a major field expedition, more than 3 years. Today I fly to Mexico to begin three weeks in the mountains of Oaxaca and Chiapas with salticidologists (jumping spider experts!) Uriel Garcilazo and Łukasz Trębicki and others interested in arthropods: Ricardo Paredes, José Arturo Casasola, Jorge León, and Gerardo Contreras. Uriel, Łukasz and I will be looking for new species of jumping spiders, with special focus on the genus Mexigonus. There are only a few species of Mexigonus described, but we already know that many more undescribed ones are hiding in the mountains of Mexico.

There are many poorly studied groups of spiders, so why did we choose to focus on Mexigonus? One reason is that it is an evolutionary radiation of the Mexican highlands, its species having diversified among the mountain ranges that fragment the landscape into isolated patches of habitat. Studying the diversity of Mexigonus species and their evolutionary relationships could help us understand the biological history of this region. Another attraction of Mexigonus is the red or orange courtship ornamentation that males of some species have — attractive to the females perhaps, but to us attractive because red ornamentation is not common in salticid spiders. There’s a good chance that most salticids can’t distinguish red (colour blind, in a sense), and so when we find a salticid that can, it could tell us something about the evolution of colour vision.

A species of Mexigonus new to science, from Oaxaca.

Our expedition has been supported generously by Tila Pérez, Griselda Monteil, and Ricardo Paredes of the Universidad Nacional Autónoma de México (UNAM) in Mexico City. We’ll drive first to Oaxaca, where we’ll spend about 10 days collecting, based at Universidad de la Sierra Juárez (UNSIJ) with José Arturo. After that we’ll spend about 10 days in Chiapas, where Jorge León (EcoSur) has been guiding our plans. At the end of the trip we’ll attend the meetings of the American Arachnological Society in Juriquilla being organized by Fernando Alvarez.


Quest for a tidal spider

In my last blog post I described my somewhat obsessive quest to find the mysterious green-faced Habronattus of southern Arizona. It’s not my only such quest. Another that comes to mind was spent mostly waiting — for the chance to return Sonora to look for the strange tidal spider of the Sea of Cortez.

On the northernmost shore of México’s Sea of Cortez is a little town called Puerto Peñasco. The land there is a harsh, harsh desert, with sparse vegetation barely hanging on. The sea, though, is beautiful, and rich with life. Where they meet, the land blooms. The fluctuation of the tides has eroded inlets that are called “negative estuaries”, mud flats with river-like channels where the tides drain. These mud flats are covered with plants like Salicornia that are tolerant of salt water.

In 2003 I visited one of these negative estuaries, and found a male Habronattus jumping spider that I thought was immature, because it lacked the usual fancy colourful ornaments typical for adult male Habronattus. But a closer look showed it to be adult, a rather peculiar one, unlike anything I’d seen. When I got it back to the lab, I was confused by its features. Some of its traits suggested that it belonged to one group of species; others suggested it belonged to another group. Was it a hybrid? Did it occupy a special place on the evolutionary tree?

I called it “the Peñasco beast”. My curiosity was strong, but I didn’t get a chance to get back to look for more until 10 years later. Our little 2013 expedition, consisting of Heather Proctor, Geneviève Leduc-Robert, Sam Evans and me, arrived to Puerto Peñasco after the drive from Tucson. We were staying and working at CEDO (Centro Intercultural Estudios Desiertos y Oceanos), a scientific and educational centre that plays many roles in raising knowledge and awareness about the amazing ecosystems there. The estuary was close by, so every day we went to look for the Peñasco beast.

What we found, instead, was a different species of Habronattus that was quite striking: a little yellow-orange “monkey” with green legs and a stunning red face, hopping from plant to plant. It was common, and yet it was another new species, never before collected. Exciting, but where was the Peñasco beast? We found but a single baby, and nothing more.

The morning came when we were to pack up and leave. I was pretty disappointed. My colleagues offered to pack up, and urged me to go out one last time to look. So, I went out with our local guide Abraham Meza López to a new spot, a bit of a drive away. The habitat at the other estuary was a bit different. I found a female! And another! And a male! I was beside myself with joy, but at the same time, anxious. We were already late returning to CEDO, and I still wanted to look for more. I knew that the crew would be worried as to why we were late, and might be imagining bad things happening to us in the unfamiliar estuary. But how to tell them not to worry? We were in the middle of this desolate estuary, probably a few kilometers from the nearest human. I knew that none of my colleagues would have their Canadian or American cell phones turned on. But, I knew that they had computers, and internet access at CEDO, and they were probably bored (but anxious) waiting for me. So, I turned my cell phone on — signal! — and sent a tweet that we’d found the Peñasco beast. When I got back I was greeted with congratulatory hugs, rather than cries of relief, and so I knew they’d seen the tweet. And we had the Peñasco beast again!

Habronattus aestus and its habitat in the negative estuaries of Sonora

Habronattus aestus and its habitat in the negative estuaries of Sonora

The specimens we got in 2013 helped me to prepare the publication describing it as a new species, Habronattus aestus. The specimens were also used in a genetic analysis that found it to be a cousin of some species found around my haunts here in Vancouver (Habronattus americanus and Habronattus ophrys). Even when you travel far away, you find things with genetic ties to home.

Real life cryptozoology: the green-faced Habronattus

We’ve all heard of the Yeti, the Sasquatch, the Loch Ness Monster and other such presumably-fictitious creatures that we dream (or fear) we will find someday. Biologists who study biodiversity have our own versions of these, though they aren’t fictitious — just very hard to find. We go into the woods, deserts or oceans, hoping to some day find one.

My “Yeti” was a jumping spider: the green-faced Habronattus of southern Arizona. I have been studying Habronattus for many years, and thought I knew the various species well. Then, I came across a specimen in the American Museum of Natural History that had been collected in the Chiricahua Mountains by Barbara and Vince Roth in 1977. It was unlike any I’d seen before, a male with a metallic green face.

After I moved to Arizona in 1990, I *so* much wanted to find the green-faced Habronattus, and learn more about the species. I found that there was lodging at the site where Barbara and Vince had found it, the Sunglow Ranch. I convinced my family to have a vacation there, and while they were relaxing, I stole off to look for the beast. No luck. Over the years we tried 3 or 4 such vacations at Sunglow, none with spider success. I collected all over southern Arizona over the 13 years I lived there, and never found it. I’m not sure you’d call it an obsession, but my students and friends heard about it. The tiny Yeti remained hidden. I was baffled. Normally, if a Habronattus lives in an area, I’ll find it. I’d been doing this for decades.

In 2012, nine years after I moved back to Canada, I got a query from Thomas Shahan, asking me to identify a Habronattus male found by Maddie Girard on an expedition by the Damian Elias lab. She’d found it in an area I’d collected frequently, Mt. Hopkins Road in the Santa Rita Mountains, an hour’s drive from where I’d lived for 13 years. Thomas’s photo showed a completely unfamiliar male with a blue spot on the face, surrounded by red. I had a momentary thought “Could this be the green-faced Habronattus?” — but no, its face wasn’t green. Eventually, the specimen was sent to me, and I saw that when preserved in alcohol — as the Roths’ specimen had been — the blue spot turns green. It was the green-faced beast, found at last.

We went to Arizona in 2013, and, having the latitude and longitude from Maddie, we were able to go to the exact spot she found hers. Within a couple of hours we found more, and also discovered why it had evaded me for years. The spiders live hidden in clumps of grass. Normally, one finds Habronattus simply by looking on open ground, but this species appears to spend most of its time deep inside or under the clumps. Once we understood the habitat, we discovered it at several sites. The green-faced beast was mysterious no longer.

Habronattus luminosus female, and the grass clumps in which it lives.

Habronattus luminosus female, and the grass clumps in which it lives.

And now it has a name. Last week, in the paper that described Habronattus roberti and Pellenes canadensis of my previous blog posts, I formally named the green-faced beast as Habronattus luminosus — a nod to its first known locality (Sunglow), and to its pale colour. The tiny Yeti found, studied, and catalogued. And now, available for more detailed study. In fact, the specimen I used as the reference specimen for the species (the “type specimen”) was collected by Nathan Morehouse and Daniel Zurek for studies on spider vision.

By the way, I admit it, my pride was momentarily hurt that I wasn’t the one to have rediscovered the green-faced Habronattus. But of course, what matters is that it was found. And, how wonderful it is that there are young people with sharp eyes, like Maddie, to continue to uncover the biodiversity that remains to be found.

A spider species new to science, named to honour Canada’s 150th

Much of my recent field work has been in dark tropical rainforests — literally dark, as the tall trees shade thoroughly, but also figuratively dark, obscure, as yet little known to us. There, it is not surprising to find species new to science, especially among small creatures that most people ignore — like spiders.

Our habitats here in Canada are rich in diversity, but not nearly as rich as the tropics. We’ve been studying Canadian creatures for a couple of hundred years. This might lead you to think that we’ve found almost everything there is to be found in Canada. In fact, for very small creatures, like microbes, mites, fungi, and others, there are thousands of species yet to be discovered in Canada. For slightly larger creatures, like jumping spiders, new ones don’t show up every day, but they are out there.

In a paper published just last week I described a new species of jumping spider from Canada, a black and white striped species in the genus Pellenes. One of the perks of discovering and describing a species is that you get to choose the name. In honour of the 150th anniversary of Canada’s confederation, I named the new species Pellenes canadensis.

A male (left) and a female (right) of Pellenes canadensis, and the ground on which they were found.

A male (left) and a female (right) of Pellenes canadensis, and the ground on which they were found, Mt. Baldy, British Columbia.

Pellenes canadensis, so far, is known from just three localities, two in southern British Columbia (one, Mt. Baldy, east of Oliver; the other, near Midway) and one in northwestern Montana. It lives on open ground at mid to high elevations. It was first collected 40 years ago at the Montana locality by my brother David, parents Louise and Robert, and myself. We were on a family vacation, and as was our custom, we included beetles and spiders among the scenery of interest. David and I found it again five years later in southern BC, and then in 2013, Heather Proctor and I found it at Mt. Baldy.

The name “Pellenes canadensis” is anchored to the Mt. Baldy locality, because I designated one of the specimens from there as the “type specimen”. That’s the specimen that serves as the reference point for the name. Whatever biological species we place that specimen into, the name follows it.

I knew in 1977 that the species was new to science, but it’s taken me 40 years to describe it formally. Biodiversity is so big, there’s so much to discover, there are so few of us doing it, and we get relatively little reward for doing it, that we have a big backlog of new species awaiting our attention. I know of at least four other jumping spider species in Canada that are new to science and still waiting to be described. Today, though, I am so pleased to have finally sent a postcard from a 1977 vacation, and to have had the chance to honour, simultaneously, Canada and this little jumping spider.

Our papers, our hearts

Scientific papers appear to be devoid of emotion, with just the facts, analyses, and careful (we hope) conclusions. To an author, though, a paper holds much more than this. It is woven with hidden threads of personal meaning. That co-author is a student you cherish because they persevered despite a challenging start. That data point was sampled on the day of a turning point in a loved one’s life. That field site was a place you almost got bitten by a venomous snake, saw the northern lights for the first time, or met someone who opened your eyes to the breadth of humanity.

Science, like other pursuits of passion, leaves indelible and deeply personal memories in its practitioners. We throw our whole hearts at our work, and we do it with colleagues and friends at our sides. Sharing our love of nature and discovery, sharing moments of surprise, danger, and intrigue, we build bonds that last forever. We bring young minds into science collaboratively, raising them as a village. I go to scientific conferences as if to a family reunion, embracing friends I have known for decades.

In 1998 I was at the Chamela field station along the coast of Jalisco, México, looking for diverse species of jumping spiders along with Marshal Hedin, Gita Bodner, Fernando Álvarez Padilla, and José Luis Castelo. The field station was an excellent base for our work, well equipped and comfortable, and the tropical deciduous forest within which it was embedded was rich. We woke up on our first full day there, 1 June, and promptly found two species new to science, one of which was a dark brown and cream coloured jumping spider of the genus Habronattus. We were immersed in discovery.

Habronattus roberti, and the ground on which it lives at Chamela

Habronattus roberti, and the ground on which it lives at Chamela

When we returned to the field station, its director, Ricardo Ayala Barajas, called me into his office to tell me that I had an urgent phone call from Canada. It was my mother Louise, telling me that my father Robert had died. Although he had been in poor health, there had been no reason to expect he was in immediate danger.

In my memories, images of Chamela and those spiders will always be tied to my father: the bright sun, the impressionistic forest, the spiders hopping on the litter, the compassion of Ricardo. Sixteen years later I visited Chamela again, finding more specimens of the new species. Last year, I finally wrote up the paper describing those new species. The paper, full of memories, was just published this past week.

I decided to name the brown and cream species after my father: Habronattus roberti. It’s a remarkable species. The little knees on the third pair of legs of each male are green and red-purple; his first pair of legs are elegantly fringed. Our recent genomic data suggests the species comes from a hybrid origin, and may therefore help us to understand the role that hybridization plays in the evolution of these fancy little spiders. In the paper I wrote:

Etymology. Named after my late father, Robert John Maddison, who introduced me to the small things in nature through fishing bait and saturniid cocoons. When my brother and I developed interests in beetles and spiders, he offered to take the family on long collecting trips. His gentle encouragement let me find my own love for the riches of biodiversity.

Grandfather Paul, brother David, father Robert and me, at the cottage on Lake of Bays.

Grandfather Paul, brother David, father Robert, and me, at the cottage on Lake of Bays.

[Edit: poisonous venomous]

Mesquite 3.10 released


We’ve released version 3.10 of Mesquite, which has some important bug fixes and workarounds for operating system problems.  There are also some new features including a new alignment tool, the ability to BLAST a local database, a batch processor files in a folder, and the ability to read MrBayes sumt files.  For more details, see here.

MacClade’s 30th Anniversary

MacClade1Today is MacClade’s 30th birthday! Version 1 was released 21 June 1986, with David joining me for version 2 the following year.  The last release was version 4, but it’s not commonly in use today, as it is no longer compatible with modern operating systems. Those biologists who use it need to maintain ancient machines (or emulators) to run it. There are, however, some who do use it, and we often get comments that people miss it. Some of its DNA persists in Mesquite (both conceptually and as some code translated straight from Pascal into Java).  Happy Birthday, MacClade!

A proposal for pronoun gender for AlphaGo and other AIs

Commentary on the ongoing historic Go match between Google DeepMind’s AlphaGo program and Lee Sedol has included some anxiety about whether to refer to the program by “he” or “she”. Commentators say they are tempted to use a gendered pronoun because the program’s behaviour reminds them so much of a person. The inevitable happened, of course: the choice to use “he” by at least one commentator was accompanied by a justification from sexist premises.

Our desire to use gendered pronouns will increase as we start to speak of AIs as if they have consciousness. We have an opportunity to do this right, and make a reasoned choice, rather than a thoughtless stumble. I therefore have a proposal, but it requires a change in English grammar. Our world may be turned upside down by AIs anyway, so why not change grammar while we are at it?

My proposal: That the gender of pronouns used for an AI is that of the person speaking about it. I would call AlphaGo “he”; my daughter would call AlphaGo “she”. Whatever is the third person pronoun that you prefer to be used for yourself (“he”, “she”, “they”, whatever), that is what you would use in speaking of the AI. A group of people speaking would give the AI a plural pronoun.

This solves the obvious problem of attributing a gender to the AI, but it also acknowledges that by being human, and a member of the world culture that created this AI, I am in some small way part of this AI.

That is my proposal. And while we’re at it, we can apply the same principle to God.

Thou shalt not use unbalanced parentheses for list item labels

Among the Commandments of my lab are:

Thou shalt not use unbalanced parentheses in numbered lists

I find lists like this an aesthetic and logical abomination: 1) first item, 2) second item, 3) third item.  The programmer in me cringes; the lover of symmetry cringes; and the lover of clarity cringes.  Why not include the left parenthesis, to treat the item labels as parenthetical remarks?  Why add a new meaning to the parenthesis, thus cluttering sentences with punctuational homonyms that need to be distinguished?  The aversion to this practice is shared through my family.

Now, on the website of the 2016 Evolution meetings is an example of why not to use these unbalanced parentheses:

Those interested in speaking in one of the Spotlight sessions below should submit an application to the organizer of that session (emails below in session descriptions). The application must include: 1) name, 2) institution, 3) rank (e.g., student, pdf, faculty), 4) names & institutions of co-authors, 5) a short abstract (max 300 words), and 6) which talk types you are willing to give (28, 13, or 5; the more flexible you are the more likely you are to be selected). Applications must be received by April 30, 2016. No financial support is provided to selected speakers. Additional details here.

Here, friendly paired parentheses framing side remarks, some containing numbers, are hobnobbing with their doppleganger asocial list delimiters. I find it difficult to scan.  This does not promote clarity.  The little lost parentheses are like fish bones getting stuck in my throat.

I need to go make some honeybush tea to calm down.