Please, don’t use CO1 barcodes alone for spider phylogeny

We systematists seeking to understand phylogenetic relationships of spiders need all the data we can get, and as easily as possible. There are few of us doing this work, and we have so many species to consider, that we could use a lot of help. It’s therefore tempting to look at the growing hoard of data from CO1 barcoding as a ready solution. But don’t, please don’t, use CO1 alone to reconstruct spider phylogenetic relationships.

CO1 (“cytochrome oxidase one”) is a mitochondrial gene that was chosen as the standard gene in animals to provide a natural “barcode” for identifying species. I won’t comment on how well it fulfills that task, except to say that I think it provides useful data, and that sometimes it works to distinguish species, sometimes it doesn’t. I will comment instead on how well it can be adapted to a different task: figuring out how species are genealogically related, looking back in time along the evolutionary tree. In the jumping spiders I have studied, CO1 is frequently highly misleading.

I’m provoked to say this because CO1 came into my consciousness, coincidentally, from four different directions this last week. Two colleagues independently mentioned they are planning or had planned to focus on CO1 for spider phylogenetics projects. I learned of a published paper that uses database-mined CO1 data, alone, to reconstruct phylogeny of some spiders. Finally, I was pulling together a phylogenetic analysis and looked to Genbank for additional data — where I found many sequences of CO1 from barcoding efforts. I will use those, but only because I have enough other data (both other genes and morphology) to overwhelm CO1’s flaws and provide the primary signal of evolutionary history.

What’s the problem with CO1? It frequently yields phylogenetic trees that are so bonkers, crazy, goofy that it can’t be trusted to stand on its own. How do I know that? By comparison with all other genes and morphology. Other genes we’ve studied well, 16SND1 (also mitochondrial!), 28S, Actin 5C, and wingless, produce phylogenetic trees on their own that largely make sense morphologically and that largely agree with one another.

CO1, on the other hand, is psychedelic. You can see that in Fig. 26 of Maddison et al. 2014 (ZooKeys 440: 57–87) shown below: the scattered pale blue lineages are all euophryines, clearly, by morphology and all other genes. Yes, there are moments of sanity (the purple hasariines hold together), but then CO1 simply loses it. You might rightly criticize this as a very sparse taxon sample for such a big group (shown in that figure is the major clade of >5000 species), but we’ve seen it in denser samples, the other genes do not suffer so, and the clade is probably rather young (<50 million years). We cite previous results from 2003 and 2012 showing that “CO1 struggles through both shallow and deep levels”. With a much denser taxon sample in the tribe Euophryini, Junxia Zhang and I (2013, Molec. Phyl. & Evol. 68: 81–92) found the CO1 tree to have regions of sanity but then some wildly broken parts, not only with members of other tribes and subfamilies jumping scattered into the midst of euophryines (Plexippus, Aelurillus, Heliophanus, Neon, Philaeus, spartaeines), but with members of a single genus (clearly, by all other data and geography) split far apart in the tree (Popcornella, Thyenula).

Salticinae portion of tree from CO1 (from Maddison et al. 2014)

I could focus my criticism on the sole use of a single gene, being way behind the times that we are now in, with phylogenomics giving us 500-gene results. Yes, we should have more data than just from a single gene, but it’s a matter of acceptable errors. With CO1, all signs are that its errors go beyond acceptable. CO1 is peculiarly misleading. Its mitochondrial colleague 16SND1 is not so bad, and while I’d still hesitate to base conclusions solely on it, from my experience it would make only small mistakes, not huge ones. And, as difficult as it may be to interpret, morphology alone is more reliable than CO1, as its basis is distributed throughout the genome. If one has only a single gene, morphological support for the results should be sought to improve their credibility. If that gene is CO1, I’d want to see a lot of morphological support.

Oh, had the barcoders only chosen a different gene!

Edits: hordes to hoard; through to throughout.


To the Heroes of Brazil’s National Museum

To the curators, collections managers, researchers, students, assistants and volunteers of the MNRJ: Thank you for working tirelessly to build, organize, research, and conserve the collections, fulfilling a duty and a trust that you and your predecessors have kept over the last 200 years. You knew the promise held by every artifact: to tell the stories of our people, to reveal the secrets of nature. Against ignorance, against a lack of appreciation, against a lack of investment, you persisted. You must have felt alone, candles in the dark.

You may feel today that it was all for nothing. I cannot know how deep is your grief. Even from such a distance I have felt bereft, lost, all of today. My friends, though, have reminded me that the world’s reaction of despair shows us there is hope. Your artifacts and specimens are gone; there is no hope for them. But, the cries that have sounded around the world may help save other museums. There would be no cries if you hadn’t succeeded in bringing the collection to the 21st century as such a valuable resource. And now, each one of us who makes choices to support or not to support a museum must today consider: what would be lost forever if “my” museum burned to the ground? Should I light the match by neglecting it?

The burning of your museum has been characterized as “history lost”. What burned last night wasn’t just the past; it was the future. Every cultural artifact or natural history specimen is a gift to the future: “This unique artifact will teach you about a person, a culture, a species, the natural world. Learn from it.” Every artifact represents an act of forethought, an investment in future knowledge, and a commitment to tangible truth.

The fact that we as a society neglect the specimens and artifacts so readily shows how distracted we are by immediate gratification, by a focus on short-term return on investment. Brazil’s inferno may have happened last night, but quiet fires are smouldering all around the world as we invest so little in these places that safeguard the tangible evidence of our past and of nature.

It’s difficult to describe to someone outside the museum community what our work means to us. We feel as if we are bound to a sacred trust for which we are merely custodians. We do not see the artifacts as belonging to us, or even to the institution. They belong to humanity. Most importantly, they belong to the future. The shock waves of the loss in Brazil will ripple though our species’ knowledge for centuries.

Not all of your efforts are lost. You managed to extract stories from many of the artifacts to publish papers, to build our understanding and to establish your careers. That knowledge remains. However, my guess is that your career is secondary to many of you. My guess is that if you could have chosen between a fire that destroyed every one of your publications and all memory of them, but preserved all of the artifacts you gathered and cared for, or a fire that destroyed all of the artifacts but left your life’s research intact, you would have chosen to sacrifice your research and career to save the specimens. We do see ourselves as merely temporary custodians of artifacts and specimens that are more important than we are, because they are for our great great grandchildren. Our great great grandchildren, we hope, will be wiser than we are, and will learn more from the artifacts than we could ever dream.

The artifacts are tangible truths, the anchors of our memory, treasures for our species’ future. We humans proudly say that our ability to understand the past and contemplate the future sets us apart from other animals. Shall we be human?

Edit: Added a tag. And here is a related Twitter thread:

It’s hard not to worry that the stunning loss of Brazil’s National Museum is being repeated in slower motion all around the world as we invest so little in these places that safeguard artifacts — tangible evidence — of our past and of nature.

In these institutions we hold objects of our cultures and of nature that remind us, that teach us, about how we and our world came to be.

Our failure represents a lack of respect for the future, for the past, and for our species thoughtfully contemplating its path.

and another:

The burning of Brazil’s National Museum has been characterized as “history lost”. What burned last night in Brazil wasn’t just the past; it was the future.

Every natural history specimen is a gift to the future: “This unique artifact of the natural world will teach you about biodiversity, about nature. Learn from it.”

Natural history specimens represent forethought and a commitment to tangible truth. The fact that we neglect them so readily shows how distracted we are by immediate gratification.

The museum’s loss is just another sign of how fragile is our wisdom and our civilization. I don’t feel grief so much as fear.


Habitat, Habitat, Habitat: Using Google Street View for scientific documentation

The old adage about the value of properties depending on “location, location, location” translates to non-humans as “habitat, habitat, habitat”. When we biodiversity scientists go out into to the world studying obscure species, one of the first things we want to learn is “what habitat does it live in?”. Our search for Pellenes logunovi focused on finding the right habitat.  When we finally find a species, we want to document its habitat, so that others may find it again later, and also to begin the long process of understanding its ecology. We can write simple descriptions like “on rock”, but better is to include photographs and other data. My brother religiously photographs the habitats in which he collects beetles, and I’m starting to follow his lead.

Now, to document a habitat (as place and time), scientists can use a wonderful new photographic tool: 360 degree photographs in Google Street View. Here’s one at the spot where we found the nearly-mythical Pellenes pulcher. You can see details of the microhabitat (the little rocks on the ground) and macrohabitat (Nanophyton steppe along the shores of Uvs Nuur). When you contribute a 360 degree view to Google Street View, it’s as if you’ve given the viewer a little time and space machine to take them to the exact spot and time where you found an interesting species.

Not exactly a street, but a Street View: habitat of Pellenes pulcher at Uvs Nuur, Tuva.

The value of 360 Street Views for scientific documentation would be considerably increased by two “minor” enhancements. The first would be to have some way to attach a searchable comment: my notes about what was found there, a collecting code to link to my databases, etc. I can’t figure out any way to attach a comment. The second would be to have some assurance that the view would remain accessible on Google Maps for at least 10 years or so. That assurance, of course, seems unlikely.

Even still, I’m glad to have the ability to post Street Views of a habitat, even limited as they are for now. To have them listed in one public place, here are some of our spider hunting locations in southern Siberia. The codes like WPM#18-009 are my standard codes referring to a collecting place and time (which I have been using since 1975!).

A Bounty of Sitticini

My trip to Siberia was designed to find special species of Pellenes jumping spiders, but I paid attention to other species also, for my other studies of jumping spiders. One of my projects is on a group called the Sitticini, which includes species familiar on houses in some areas (e.g., Sitticus fasciger, Sittipub pubescens), as well as species in many other habitats. Sitticines originated in South America and spread into Eurasia, where they diversified into many species, and, it turns out, evolved interesting chromosomes (but that story will be for another day).

Almost all of the sitticines we saw in Siberia were new to me. Most have muted colours, but one, Sitticus mirandus, has males with a blue and purple sheen on the face:

Sitticus mirandus, male.

For the jumping spider geeks, here are the 7 species of sitticines we found. In each set of photos, the male is on the left, the female on the right.

Attulus ammophilus
I’ve known this species for many years, as it was introduced into North America in the 20th century. It’s good to see it in its native continent.

Attulus ammophilus, male and female, from the shores of Uvs Nuur.

Attulus avocator
Very similar to A. ammophilus, but more solidly black first leg.

Attulus avocator, male and female, from the Irbitey River in Tuva

Attulus burjaticus
This cute species I called “clown”. It was pretty common in isolated grass clumps in dry areas of Tuva.

Attulus burjaticus, male and female, from Tuva.

Attulus mirandus
This is the purple-sheened guy shown above. I found just one male and one female of this marvellous species.

Attulus mirandus, male and female, from the Tes-Khem River, Tuva.

Sittiflor inexpectus
From the marshy shores of lakes in Tuva.

Sittiflor inexpectus, male at left, from Uvs Nuur Lake. I’m haven’t confirmed that the female shown at right is the same species.

Sittiflor zimmermani
A sweet little species from leaf litter and dead trees near Karasuk.

Sittiflor zimmermani, male and female, from Karasuk.

Sitticus terebratus
On buildings; taxonomically important as the type species of Sitticus.

Sitticus terebratus, male and female, from Karasuk and Novosibirsk.

Success in Siberia

I’m back (not that you noticed I wasn’t posting), and can give you the final summary of my field work in Siberia to look for Pellenes jumping spiders: success. It was a challenge. July is past the typical breeding season, and with most males gone to the next trophic level, we were left to look for the harder-to-find females and juveniles. In the end, we found every one of our targets.

I’ve already posted about our finding Pellenes logunovi, P. limbatus, and P. sibiricus, as well as P. gobiensis and P. stepposus. Those we found on the first major trip out from Novosibirsk, to the Altai. For the second major trip, to Tuva, there was one big target left: Pellenes pulcher.

Pellenes pulcher, a member of a distinctive group of species important for my studies, was known from only a few specimens from Mongolia, Kazakhstan, and Russia. The only Russian locality was in the Uvs Nuur basin, a unique area of special steppes and salt lakes that is primarily in Mongolia, but just reaches north into Tuva, a republic in the Russian Federation. The precise locality from which Dmitri Logunov had collected it more than 20 years ago was right along the Mongolian border where Uvs Nuur Lake peeks into Russia.

Pellenes pulcher, male, from the north shore of Uvs Nuur.

As happened with P. logunovi and P. gobiensis, Galina Azarkina saved the day by finding the first female of P. pulcher, thereby figuring out that they live on the rocks of their strange steppe habitat: the tiny round woody “bushes” of Nanophyton, only a centimetre or two tall, dot the landscape, making it look like a bonsai savannah. In the end we got one male and four females. As its name suggests, P. pulcher is beautiful both in appearance (striped!) and personality (vivacious! — they hop a lot). Above is the male; here is the female and other views of the male. Notice the elegantly long first legs of the male, and his reddish jaws.

Pellenes pulcher, female and male, from Tuva.

And so, in the end, we got 7 species of Pellenes. Here are the other 6, in retrospect.

P. logunovi
We got only females and juveniles. Here are two females to show variation in colours.

Pellenes logunovi females, from the Altai.

P. sibiricus
Closely related to the well-known European P. tripunctatus, we got only a few, but both males and females.

Pellenes sibiricus, female and male. We found it at Karasuk and in Tuva.

P. limbatus
We found just three, two old decrepit males, and a juvenile female. I kept the female alive, and am feeding it in hopes it will mature.

Pellenes limbatus, male, from the Altai.

P. gobiensis
We got only females and babies.

Pellenes gobiensis, females, from the Altai.

P. stepposus
Although this is currently considered a Pellenes, I suspect this isn’t a Pellenes, but rather a Sibianor. It was common on bushes in the drier steppes.

Pellenes stepposus, female and male. We found it in the Altai and Tuva.

P. epularis?
I’m not sure about the identity of this. We found four juveniles, including this one, in the Altai. They look similar to P. epularis that Galina found recently in Kazakhstan. I am trying to raise them to maturity to figure out what they are.

Juvenile Pellenes, possibly P. epularis. From the Altai.

Fieldwork: a game of chance, a test of will

As we are driving back from the Altai toward Novosibirsk, I’m thinking about how lucky we were to have found two of my important target spider species, Pellenes gobiensis and Pellenes stepposus. In both cases what seemed like bad luck turned into good luck.

We’d stopped along the Buguzun River because we suspected Pellenes gobiensis might live there, but as the rain fell, I thought we’d missed our chance to find them. I was surprised when Galina came to my tent to say, “I found a Pellenes!”. Galina had figured out how to find them in the rain, nestled in little camouflaged retreats under rocks out on the steppe. Here is a female:

Pellenes gobiensis, female. The dark markings under her eyes, “tears”, are seen in females of various other species of Pellenes and Habronattus.

Here’s the twist of luck: rain not only didn’t prevent us from finding this species, but it likely helped us. Our subsequent searches turned up many specimens, but all were adult females in nests with babies. This means that they likely wouldn’t have come out onto the rocks even if it had been sunny. And, if it had been sunny, Galina and I probably would have simply walked along, scanning the ground. Not seeing anything, we might have assumed it was the wrong habitat, and not bothered to turn over rocks, which is normally a low-success activity. The rain changed that: if we were going to look, we had no choice but to take the laborious route, and it worked.

In the case of Pellenes stepposus it wasn’t rain, but a delay, that led to their discovery. On the Kuray steppe we had pretty much finished our search for Pellenes and aelurillines, and were ready to move on to another site. But, one of the tasks of this expedition is to set up pitfall traps for an ecological study, and that task was taking longer than planned. I wasn’t involved in setting up the traps, but it meant I couldn’t leave yet. I looked around, exhausted, took a deep breath, and looked for something new to try. I saw some Artemesia along a stream and thought I might as well start looking on those, not expecting to find Pellenes (but perhaps some other interesting jumping spiders). Lo and behold, specimens of Pellenes stepposus started falling on my sheet.

Pellenes stepposus, female.

(By the way, P. stepposus is probably not actually a Pellenes, but most likely belongs in another genus like Sibianor. That doesn’t diminish its importance to me, as Sibianor specimens are useful as a more distant point of comparison with Pellenes and Habronattus.)

I think of both of these successes as due to a twist of luck, though you could argue in both cases the “bad luck” simply provoked us to work harder. I am reminded of the old saying: “I am a great believer in luck, and I find the harder I work, the more I have of it.”

Raising spiders on a diet of human

Rain brings most jumping spider hunting to a halt, at least in temperate areas. Perhaps they need the sun to bring their body temperatures up for their needed activities (hunting, developing, mating); perhaps the water itself is a threat. The spiders don’t come out, and it’s awfully difficult to find them in their little retreats. I imagine them sitting by the fire drinking hot chocolate. As I write this (14 July) I am, like the spiders, sitting in my little retreat (tent) by the Buguzun river in the Altai, waiting for the rain to stop and the sun to come out. This is a good time to feed spiders.

I am waiting for the mosquitoes to bite. In fact, I have my tent flaps open, to help them find me. You see, I need to feed the spiders that we hope to rear to adulthood, the most important of which for me are the subadult males of Pellenes logunovi we got at Tekelyu. The problem is that the mosquitoes are rather skinny, and I’d like the P. logunovi to have a big meal. But, mosquitoes can be quickly fattened up from the richest source of animal material nearby, namely, me.

When a mosquito bites me, I wait for it to start to fill up with my blood, then I gently put a vial over top of it. When it’s done, it tries to fly away but it’s trapped by the vial. Here’s one finished its meal of me, about to become a meal of a Pellenes logunovi:

Mosquito fat with my blood.

What a nice juicy snack for a spider! A few minutes later, the spider was feasting on my blood:

Spider eating mosquito and me.

It’s somehow pleasing to be lower on the food chain than my spiders, at least occasionally.

By the way, there are jumping spiders that appear naturally specialized on this sort of diet… Evarcha culicivora.


I’ve looked forward to this Siberia trip for many reasons, one of which is the chance to learn about aelurilline jumping spiders from the world expert. Aelurillines have been the primary focus of study by my host in Siberia, Galina Azarkina, for almost 20 years. In North America we see them rarely, as only one native species lives there: the striped Phlegra hentzi, whose males have a pale blue face. It lives alongside the much more common and diverse Habronattus, on open sunny ground with dry leaf litter. In Eurasia and Africa, however, aelurillines are diverse and common, occupying habitats very similar to those of my familiar Habronattus back home.

In just a few days of collecting I’ve now seen 7 species of aelurillines: Phlegra fasciata and two Asianellus at Karasuk, three species of Aelurillus at Kuray, and an Asianellus at Kokorya. I must say, aelurillines are charming. Here is the most dramatic, a beautiful male Aelurillus from the Kuray steppe:

Striped Aelurillus species from Kuray, male.

He has especially long, spiny legs:

Striped Aelurillus species from Kuray, male.

I look forward to seeing more aelurilline diversity as we continue our explorations here in Siberia.

Sunbathing spiders

Pellenes, the target of my spider field work in Siberia, is somewhat of an exception among jumping spiders for its choice of habitat. Most jumping spider species wander about on plants, from grasses to trees, using their special abilities to see and jump to navigate and hunt in this 3 dimensional habitat. Not all inhabit the cool greenery, however. Some, including Pellenes and Galina’s aelurillines, hunt regularly on sun-baked ground. Here is Pellenes peninsularis sunbathing on a rock outcrop in Ontario, and an Aelurillus on the Kuray steppe of Siberia:

Pellenes peninsularis (left) and Aelurillus sp. (right) sunbathing on rocks.

They don’t sunbathe on rocks to get a tan. It probably helps raise the spider’s body temperature to develop, hunt, escape and court more quickly, but it may come with the risk of heat stress, dessication and visibility to predators.

Only a few evolutionary lineages of jumping spiders have braved a lifestyle on hot sunny ground. Five have done it and diversified in a big way. The sitticines of South America did it, and did it with enough success to spread all the way to Eurasia and diversify into many species there — although the Eurasian lineage has shifted to many other habitats, not just open ground. The harmochirines of Africa and Eurasia returned the favour, starting on sunny ground in the Old World before some “Pellenes” went to the Americas to diversify there as the paradise spiders, Habronattus. The peacock spiders of Australia (Maratus) similarly live on sunny ground, as do Yllenus and relatives of Eurasia, and the aelurillines of Africa and Eurasia.

How have these five lineages come to be similar, as they have adapted this new habitat? Apart from the females typically being quite cryptic — the same colours as the rocks they are on, for example — we don’t yet know the answer to that question. Here are some suspicions:

  1. They are probably more heat tolerant than their relatives.
  2. At least some members of each group have unusually long jumping legs (3rd legs in the case of Pellenes and relatives; 4th legs in the case of Sitticus and Yllenus).
  3. Three of these groups bear male courtship ornaments that are spectacularly detailed and colourful (Maratus, Habronattus, and Stenaelurillus) — perhaps encouraged by easier vision in the high-light environment.

Given that Galina and I both study sunny-ground lovers, it’s not surprising that we make a good collecting team. In fact, the synergy that helped us get Pellenes logunovi has worked frequently: each of us has played a key role in the others’ successes on this trip. She was the first to find Pellenes logunovi and later, P. gobiensis (more on that species in another post). I was the first to find several of her species: two Aelurillus at Kuray and an Asianellus at Kokorya.

Diverse eyes: the nonlinear effects of collaboration

You might think that having two scientists makes discovery go twice as fast as one, that three makes it three times as fast, and so on. But, if there is a diversity of talents and inclinations, it’s far better than that. At Tekelyu Valley, our diverse eyes led us to the most important target of my trip to Siberia: Pellenes logunovi.

After our chilly first night camping on the alpine steppe of Tekelyu Valley, we greeted sunrise with anticipation. Once it was warm enough to hope the spiders would be out, Galina set off in one direction, I in another, to seek Pellenes logunovi. I had a particular image of the habitat I was looking for, short bushes with patches of rock between. At a nice south-facing slope I found two male Pellenes, to my great excitement. The spiders seemed too small, but otherwise from what I could see, they might be P. logunovi. I headed back to camp and took a look at one under a microscope — no, wrong Pellenes (P. limbatus). Still important scientifically, but not my dreamed-off P. logunovi. So I set out again to a slightly different habitat. Another male Pellenes, but P. sibiricus. By this time it’s after 11:00 am and getting hot. I’m getting discouraged, because soon it will be too hot and the spiders will be taking their siestas. It seemed we might miss our chance here to find P. logunovi.

And then Galina radioed — she’d found a female she thought might be P. logunovi. She was on the other side of the hill. Off I went on the long trek, and when I finally reached her, I saw that she was on a dry grassy hillside with small rocks, a rather different habitat from the ones where I’d been. She handed me the specimen and instantly I was 90% sure it was P. logunovi (and later, I confirmed it under the microscope). I was so excited.

More important than anything else, she had found the type of micro-habitat that Pellenes logunovi likes. A place like Tekelyu has dozens of different types of ground — with dry grass, or green grass, or moss, or Artemesia, or rocks, or wetter soil, or on a slope, or south-facing, or near pine trees, or some combination. A spider species might prefer a precise combination for its micro-habitat. The diversity of micro-habitats at Tekelyu was too great to survey completely in the time we had, so we had to focus on some best guesses. My inclinations led me to the wrong combination; Galina’s to the right combination.

On Galina’s hillside we didn’t find as many specimens as needed, but that wasn’t as important as knowing that they were at Tekelyu, and learning the habitat. If she hadn’t discovered them, we might have decided to leave that afternoon to look for another site to camp, and might have failed to find the species at all. Instead, we stayed through the afternoon and discovered that they were ridiculously common on rocks of a grassy gravel bar of the river below our camp. We now have enough specimens to do the research we want to do.

The exploration phase of science depends on diverse ideas and creativity, which can unlock hidden doors to progress. Having two searchers had a compound effect on our spider gathering: it doubled our chances of finding their habitat, and once that was found, we could put double effort into gathering specimens. Because both of us could follow leads that either one of us found, our productivity as a team was well more than twice what either would achieve solo. Galina and I have made a great team for several other species as well, though those stories are for later.

As I explained in a previous post, P. logunovi was my highest priority because it seems unique among Eurasian Pellenes in its similarities to the common group of species native to North America. That was judged based on pickled specimens in museums. Now, seeing them alive, I see how much they look like North American species. Here are photos, of P. logunovi at left, and the American P. longimanus at right.

Pellenes logunovi from Siberia and Pellenes longimanus from Texas.

We didn’t find any adult males of P. logunovi (it seems they aren’t in season), but we have many almost-adult (“subadult”) males that we will try to raise to adulthood. After only a few days, my 5 week long trip to Siberia is already a success.