Mesquite 3.01 released

It’s often the case that in the course of completing a major release for a piece of software, various changes you make don’t have a chance to “settle in comfortably” by the time of release.  And so, over the next few weeks, you discover bugs or bad performance  that was introduced with the changes you made — “unanticipated consequences”.  As usual, this happened with Mesquite 3, and so we have released Mesquite 3.01.  Some of the fixes resolve performance issues in 3.0, some avoid crashes.  We also added a couple of new features.   You can get it at the Mesquite website.

Paper published: The deep phylogeny of jumping spiders (Araneae, Salticidae)

Our collaborative paper, with Daiqin Li and our respective colleagues, on the molecular phylogeny of salticids has come out! We’re thrilled to publish these data using standard Sanger sequencing before the deluge of genomic data comes out. If we had waited a year, people would have expected hundreds more genes! Nonetheless, our data from 8 genes has contributed to a firmer resolution of salticid phylogeny. There are still some areas with poor resolution, but it does seem that we are figuring this out.

I’ve prepared a version with the supplemental materials already embedded (and the tables rotated for ease of online viewing), here, but you can get the original basic version here.

The reference is this:

Maddison WP, Li D, Bodner M, Zhang JX, Xu X, Liu Q, Liu F. 2014. The deep phylogeny of jumping spiders (Araneae, Salticidae). Zookeys 440: 57–87.

Cuddling under a log; mating in a vial

Last week, my dispersal-limited self was lucky enough to hitch a ride with Catherine Scott, Sean McCann, Gwylim Blackburn, and Samantha Vibert, to hunt some spiders along Iona Beach. You can read Sean’s blog post (with much, much better photos than I took) summarizing our short evening field trip in rather gloomy, chilly conditions not conducive to salticid-wrangling, but I wanted to relay a particular tidbit that I learned from that trip.


As we explored the habitat above, Catherine and Samantha uncovered not one, but two Phidippus johnsoni residing together in what appeared to be a single little silken retreat on the underside of a log. I collected both–a male and then a female (pictured below, respectively)–harboring in mind Sean’s suggestion to film a mating trial.

Phidippus_johnsoni_male Phidippus_johnsoni_female

Five days later, I returned to the lab intending to attempt this trial, when I noticed that the female had molted, suggesting she was a sub-adult when we collected her. This lead me to hypothesize that the male had been guarding a soon-to-be mature and relatively receptive (as virgin female spiders tend to be) mate. Hastily, I cobbled together a crude “mating arena” resulting in the following video of unremarkable quality:

After mating began, I angled for a better view of the male’s expanded pedipalp, which was pumping away to deliver sperm:

IMG_0676 - Copy

Afterwards, I took to the internet to read up on the Phidippus mating game. Much has been written about Phidippus mating strategies, including those of P. johnsoni, and males’ guarding sub-adult females is well-documented. Apparently the single silken retreat we discovered at Iona Beach was in fact a two-story townhouse of sorts. In preparation for her final molt, the female built a retreat. The male, upon encountering her, likely courted her by tugging at her retreat, and subsequently built his own abode on top of hers. Interesting that courtship can take place before the female has even matured! Of course, placing our subjects together in a vial elicited a different, more visual mode of courtship, as you can observe in the first video.

A male of P. johnsoni‘s eastern North America lookalike, Phidippus clarus, will go as far as to use chemical clues from the female’s silk to infer how soon she will molt into maturity, and will preferentially search for larger females whose final molts are more imminent*. As David Hill relays in his notes on P. clarus, “Snetsinger described how male P. clarus located a female, built a nest on top of the female’s nest, guarded that female from other males, and mated by extending its pedipalps through layers of silk to reach the female, sometimes mating multiple times.”

So there you have it. Even the shortest field trips in rather unfavorable weather can yield new natural history lessons.

* Hoefler, Chad D. 2007. Male mate choice and size-assortative pairing in a jumping spider, Phidippus clarus. Animal Behaviour 73:943-954.

Look deep into a jumping spider’s spotted, moving eyes

In previous posts I’ve shown the unusual spotted pattern inside some Habronattus males’ eyes, and you’ve seen the moving eyes of the transparent yellow amycine jumping spider. Here I’ll combine the two to show you what the spotted patterns look like in a living male Habronattus aztecanus.

To remind you, here is what the eye pattern looks like:HaztecanusEyeIMGP8780closeup

And now to the video.  I managed to get this video’d just yesterday, by pulling a piece of transparent plastic film over a live male to hold him down so that I could get him under the microscope. Enjoy!


Oz’s Glass Spider

Last week my old video on moving spider eyes went fungal (that’s a bit slower than viral), following its linking from Gwen Pearson’s Wired column, then io9, then reddit. In honour of its recent fame, I repost the story that introduced the video, from my now-lost blog at the Beaty Museum.

In L. Frank Baum’s Land of Oz, there lived a glass cat who was rather proud of itself. Being glass, it was transparent. It would say “I have the handsomest brains in the world. They’re pink, and you can see ’em work.”

In Canandé we found the most remarkably transparent jumping spider I’ve ever seen. It’s an amycine, but I don’t know exactly which one. Here is a close-up of the male’s body. At the back of the carapace, you can see the muscle bands for each of the legs, separated by yellow, which may be the blood pooling.
yellowAmycine copy
You can also see the eyes quite clearly. The black patches on the head are the smaller side eyes, but the main eyes extend like cones backward from the face. In the living spider you can see these cones move as the spider is looking in one direction or the other.

Quite remarkable. “I have black eyes, and you can see ’em work.”

Video on How To Collect Jumping Spiders

I’ve posted a video of how to collect jumping spiders, to encourage you all to go out and make this group better known! The video link is below, and also below is a transcript of the video. The transcript is useful because I misspeak several times, so my sentences are a bit garbled. We did this as a single take in a brief moment when it wasn’t raining this past weekend, so that’s my excuse for my incoherence.

The Transcript:


Hi. I’m Wayne Maddison. I’ve been collecting jumping spiders for about 43 years, and I want to show you today how to do it, how to find jumping spiders in different habitats using different techniques.

I’m going to show you my equipment, and how we go about finding [spiders]. Right now I’m on the coast of British Columbia, and it’s April, so it’s a little bit cool. We are not likely to find any spiders. We’re also in an area with a lot of traffic, so you’ll hear a lot of background noise. I hope you can still follow it.


I’m in my full field gear, with my hat for the sun and rain, and my beating stick, and everything else. I’ll show you piece by piece what I go with.

The first and most vital [pieces] of equipment are the vials, to put the spiders in. I tend to prefer glass vials, because I can see through them clearly, and look at the spiders with my hand lens that I have around my neck here. This by the way, on my hand lens [lanyard] is a little bright whistle. It’s bright coloured so I don’t lose the hand lens if it comes off, and it’s a whistle for safety reasons, in case I get lost.

The glass vials I also like because I can get fairly small ones. You may prefer plastic vials, but I like glass. They are cork topped. That means that it’s really easy for me to open them. If I see a spider, I can open it up like this, or I can open it up like this, without taking my eyes off of the spider.

I have an arrangement of two pockets. I have one pocket on the right and one pocket on the left. This [on the right] is for empty vials, this [on the left] is for full vials, with the spiders. The reason I do this, two separate ones, very clearly separated is that when I see a spider, I don’t want to take my eyes off the spider. I want to just, without looking, find a vial, collect the spider, and put it [away], and be ready for the next spider. You don’t need to use these sort of pockets. You can get whatever sort of pocket or pouch that hangs on your belt that you can find. So those are the vials and the pouches.

Next, we have bits of extra equipment: GPS, to take data, and also to keep your starting waypoint so you don’t get lost. I tend to have a little headlamp for security reasons and to look for spiders in dark places. Extra batteries, etc. Pencils, things to take notes. I’ve shown you my hand lens.

I’ve got what is one of the most important pieces of equipment, the beating sheet, in here. A beating sheet is used for many things, including beating vegetation. There are ones that are sold — there are various equipment companies — but this is one that we’ve made up. I like it like this because the tent poles can be taken apart, and you can put the whole thing in your backpack. You can extend it out to make a beating sheet.

There are two types of cloth we use for the beating sheet. I’ll show you in a minute how you might make your own beating sheet. The one type is fairly rough [in] texture. It’s very strong. Its smooth, but not very smooth, and not waterproof. I like these for dry areas and beating vegetation, because then the spiders don’t roll off so quickly. But, if we are working in wet areas, like tropical areas where water is often a problem, or if you are doing things in leaf litter, it’s good to have nylon that will shed the water and dirt very quickly. I sometimes take both sorts with me.

Here is the beating sheet, all made up. It has this little pocket to receive the poles. We tend to put a short pocket on one side, a long pocket on the other side. Just in case the poles are a little bit too big or too small, or the sheet is a little bit too tense, or too loose, you can decide which side to put it on. On this side, it’s easier to get out; on this side, it stays in better. That’s the beating sheet. I will demonstrate to you, in a little bit, how it works.


To a jumping spider, a habitat like this is many habitats. They are small enough that there are ground dwellers that live in specific sorts of ground habitats. There are foliage dwellers. There are tree trunk dwellers, there are branch dwellers. As you collect, you need to be thinking about all the different types of microhabitats and look, if you can, in each.


This is my beating stick, this is my beating sheet. You can use the beating stick to whack the vegetation. When you whack it, the spiders fall on here, and you just reach in, get your vial, and there you got your spider. (I didn’t actually get a spider, so I’ll put the vial back.)

There are a couple of things to think about as you do this. One is that the first strike is important. It has to be strong, because, if you just … Oh my gosh! There’s a spider, a jumping spider. We just got one. Phanias albeolus. When you first strike, the spider (if you just do a weak strike) will probably just hang on, and the next time you hit it again, it’s already hanging on. But, if you give a really good whack the first time, the spider falls before it knows what is going on.

Sometimes it’s better to shake, sometimes to beat. You want to get well under a good clump of vegetation. And, when you go like this, you don’t want the vegetation (if you can avoid it) to hit the sheet, because as it hits the sheet, it will probably make the sheet bounce, and things will [fall] off.

As you beat, you can look for lush pieces of vegetation, with many leaves, and flowers and vines, all in a big piece. A “happy bush” I tend call them, because they tend to be full of insects, and often, many spiders. You can also look for different sorts of trees and bushes. Trees and bushes that have open branches like this, especially if there is rough bark, can have special species of jumping spiders. Beating these, or moving your hands over the bark, or a brush over the bark, can find other things.

A special habitat for some salticids, especially in warmer climates, or other places, are grass clumps. They tend to hold species that are specific to grass, or that are special sorts of litter dwellers. What you can do there is put your beating sheet quickly under the grass clump, pull it and shake it. Get your hands into the litter and pull it out, as well as lean the grasses over top and shake them, and then you pull it out and you look.

Text: Beating vegetation is the fastest way to get many specimens and species. Conifers and plants with aromatic leaves often have different species. Small trees and canopy will have different species than bushes near the ground. Plants with large leaves, like palms, will have different species.


You might wonder why I have this stick full of colours. The reason is, it’s a very special piece of wood. This wood is very dense. It’s very hard and strong. Because it’s dense, it’s heavy. When I strike, there is a lot of momentum here. Because it’s heavy and strong, it does a better job. So, I don’t want to lose this stick. That’s why it has colours. You go like this. You see a great spider. You drop the stick. You get your vial, always with your eyes on the spider. You get it, put the spider in, and then you try to find your stick. Sometimes, it can be hard to find. But, with the colours, it’s great, [you can find it]. That’s why I have colours on everything, so I don’t lose them.


Here’s the male of Phanias albeolus that I just collected. You can see him there. One of the reasons I collect in the glass vials is so that I can see what I got with a hand lens. Many people collect spiders straight into alcohol. I tend to collect them all alive for two reasons. One is that I may realize later that they are juveniles that I want to raise to adulthood, but also I want to take photographs of them alive later.

If you pay attention to them as they are alive and as you are collecting them, as to what you are finding. You say “oh, that’s something I haven’t seen before”, it allows you to focus on looking for more of that special thing. As you collect in an area, you are adapting to what you find, to focus your efforts on where you are finding good things.

For me, collecting tends to be this learning experience, as I am learning about the spiders and their habitats. I am thinking about what does it look like I’ve got, trying to identify them alive, as much as I can.


As you are looking at the male Phanias albeolus here, you’ll be noticing my gloves. I use fingerless gloves — fingerless so that I can continue to manipulate the vials, and gloves because, as I am beating, or as I am going into the leaf litter, I’m often having to go into bushes that have thorns, or I don’t know what is in there. Normally, even with these I come out, after the day, full of blood. It would be much worse if I didn’t have these gloves. These gloves are really used to me to save my hands as I go.

I find that the days that I come back the dirtiest and the bloodiest are the days that I got the most. In other words, those were the days that I was most intensely working trying to find as many spiders as I can find.


Now I will show you how to collect on open sunny ground like this, which is the favourite habitat of Habronattus, Sitticus, Aelurillus, Maratus, Phlegra, Pellenes — different things in different parts of the world. They tend to like ground that is fairly well drained, perhaps with rocks, perhaps with sticks, perhaps with [dry] leaves.

The way you go about this is simply to look. You scan the ground, but exactly how you scan the ground is quite a trick. You need to be focused all the time. You can’t let your eyes wander. You have to be thinking about the spider and imagining where it might be sitting, looking with your eyes over all the different spots. As you step, you may scare them a little bit, so your eyes can look close to your feet as you step, then further away, then close to your feet, then further away. You are constantly scanning to see what you can find. Sometimes, you see the spider simply sunbathing on top, and so it’s the form. Sometimes, it’s the motion that you see. As you practice, you’ll get good at spotting both.

It turns out that in different conditions you’ll get males or females coming out, or juveniles, at different times of the day. Males tend to come out when it’s a little bit warmer. Males tend to be easier to see than females — they tend to be dark or brightly coloured, and they move more. So, if it’s a time of the day when you’re looking for males, you’ll be able to spot them from farther, and so you can walk more quickly. If it’s a time of the day when there might be more females, or juveniles, you tend to have to spend more time looking more closely. When you are looking for females or juveniles, sometimes you find you end up [crawling] on the ground, because they can be very hard to spot.

One of the tricks in looking for things on open ground is to decide which direction you are going to move. You don’t want your shadow to fall on the specimen, not so much that it will move or get scared, but just that they are harder to see. You tend to walk into the sun, with your shadow behind. Also, it’s often easier to walk uphill rather than downhill, because as you walk uphill you get to look more closely at the ground; you’re eyes are closer.

One thing you’ll discover is that species that live on the ground, just as things that live on vegetation or tree trunks, are very specific about what type of substrate they like. Some species might prefer rocks with sand, others might prefer grassier areas, others might prefer where it’s more solid dry leaf litter. You’ll get to know which species prefer what exact microhabitat.

What do you do if you see a spider? Well, it depends a little on what species. Some things like Phlegra tend to quickly dash under things. They are a little bit hard to get. Others like many Habronattus will just sit there, continuing to sunbathe. With those, you can just slowly come like this. They won’t see the vial, perhaps, and then at the last minute like this, and then like that.

(There’s actually no spider here.) Sometimes, though, they will be crawling into things and you have to dive down. Whether you are patient and wait, or whether you dive down, is a decision you’ll just have to make. It’s not very easy [to decide] sometimes, because when you dive down, they could sneak away, and you’ll be looking here, and they’ll be far away.


Here I am, in a forest, with the leaf litter here. Leaf litter, for salticids, is a really important habitat, especially in tropical forests. In deserts, it can be, if there are trees and so forth. In temperate zones, where it’s fairly cool, there tend not to be too many salticids on forest leaf litter, shaded forest, because it’s just a bit too cold. But, in the tropics, it’s amazing. There are species that live just in this sort of habitat.

There are a couple of different ways to look. One is to look just as we did on open sunny ground, just looking. Some are very tiny, so you are often crawling. But, many of them are hard to find that way — they might be just underneath the leaves. For the ones that are just underneath the leaves, I tend to use a beating sheet — I bring this out again. A simple way, fairly crude, is just to grab a batch of litter, put it on here, shake it a bit, and I pull it aside, and look for spiders running away.

Many people who collect spiders in litter do other things like collect big pieces and put them into extraction funnels. That can work too. I tend to do it this way [on a beating sheet] because it gives me very quick feedback as to whether the spiders are here. I can then learn, moment by moment, whether it is better to go to that sort of litter, or that sort of litter. Some of the most interesting jumping spiders tend to be where the litter is fairly deep, but well drained, so if there are pockets on a slope with litter that has humidity but is not soaking wet, then that can be great.

As you are doing this, you have to be careful, of course, for snakes and scorpions and centipedes. Some of you may prefer to have either full gloves, or to do it with some tools. I tend to just use may regular [fingerless] gloves.

Text: Suspended Litter. A distinctive habitat in tropical forests is dead leaves and other litter suspended in the trees or at the base of palms, pandanus, etc.


In many places of the world, tree trunks can be a special habitat for jumping spiders. The bark has places for them to hide underneath. So one way to collect jumping spiders is to actually peel the bark, and look for the spiders underneath. Another way is to simply look to see the spider. Many on tree trunks are very cryptic; they are hard to see. And a third way to find jumping spiders on tree trunks is to use a brush, and basically brush them off.

But, when you do any of these, it’s a good idea to be prepared for the spiders falling. This is when I use the beating sheet again, by putting it under here, like this.

Whether it’s better to look or to brush depends on your eyesight, how difficult the spiders are to see. Often it’s better just to look. Brushing can be very good for small, difficult-to-see jumping spiders.

This is an example of how useful a beating sheet is. You’ve seen it with the tree trunks. You’ve seen it used with the leaf litter. You saw it used with the beating. It can be an umbrella, a picnic blanket, it can be something to keep you warm, a little bit. It’s a very useful thing to have.

Text: Tree trunks with different bark, moss, vines can have different species of salticids.


I mentioned that I take a GPS to take good locality readings. When you take the readings, you have to think “how far can I walk before it’s a new locality?”. Certainly if you go a kilometer, it’s good to treat it as a new locality. Typically if I go about 200 or 300 meters, I’ll treat it as a new locality.

You need to take those records, and you need to keep a notebook or somehow know what is the connection between this record of the latitude and longitude, and the specimens. By the way, please use decimal degrees, no minutes and seconds. Once you’ve collected in an area, you want to separate your spiders, so that when you go to the next locality, you can keep the two localities separate — you want to know who belongs to which locality. Typically after I’ve collected in an area, I will get the specimens out, put them in a ziplock bag, put a little note inside as to which ones these were, put them back, and then I can continue to collect from empty to full.

Text: Preserve 80% ethanol for morphology, 95% for DNA. Put labels on good paper inside the vials.


We are just about done showing you how to collect jumping spiders. I just wanted to say something about clothes. You can wear what clothes you are comfortable with, but it’s important that you feel comfortable crashing into bushes as thorns go by you, scrambling up rocky hills and so forth. In other words, wear things that protect you well.

I like:

  • tall boots, which I can tuck my pants into, and which give good ankle support.
  • long pants so that I can be in cactus and so forth.
  • long shirt not only for sun protection, but also against plants and so forth.
  • nice pockets here, pockets everywhere.

In summary, before we go, here are some of the key pieces of equipment to bring:

  • Vials of course, many more than this. On a good day I’ll use up about 100 vials.
  • GPS
  • Pockets of whatever sort for your vials
  • gloves
  • a brush. A secondary piece; I don’t use that too much.
  • ziplock bags for holding the vials.
  • beating stick
  • beating sheet.

And there we go. Good luck!

The End

Cinematography, Heather Proctor. © 2014 W. Maddison

From Itching to Elegance

In my last post, I showed the Anicius that moulted. In the same area I also collected a juvenile male Mexigonus. Here he is:

He looked unusual enough that I was pretty excited to see what he would look like as an adult, but even though I fed him well, he just hung out as a juvenile. Several days before we left Mexico, I noticed that he seemed a bit lethargic, and then I saw the telltale sign of an impending moult: his legs had fine stripes on them. These stripes are the new hairs all lined up under his old skin, ready to pop out and fluff up. Recalling how my skin itched when it peeled after a sunburn, I wonder: did this young male spider feel terribly itchy when he had a new skin under old?

I made sure his container was humid enough. Moulting is a dangerous time, and dryness can cause them to get stuck in the old skin and die. I waited. A couple of days later, I saw the old skin beside him, and this is what he looked like:

He’s still not quite darkened completely in this picture, but I couldn’t wait. How elegant! I’ve never seen a male jumping spider with first legs ornamented like that. Notice how there are two segments that have dark and shiny swellings, surrounded by a fringe of yellowish hairs.