Taxonomist envy and the importance of names

Imagine: seeking, finding, watching, sampling, measuring, comparing, analyzing, imaging and… naming.

These goodies are all part of taxonomy. As Wikipedia defines it, taxonomy “is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups.”

Taxonomists are the true explorers at the foundation of biodiversity science: they are to be appreciated, and I’m envious of their discoveries.

I’ve always been a collector and sorter and feel some kinship towards taxonomists: although when I was young I engaged more in the process of categorizing ‘non-living’ things such as sticks, stamps, coins or rocks. But there were comparisons of shared characteristics: some rocks were pink, with lightening-strikes of white crystal; some rocks were angular and sharp, some were smooth, shaped by time and oceans. Perhaps it’s not surprising that during my PhD I thoroughly enjoyed sorting and identifying almost 30,000 spiders from Canada’s boreal forest. It brought back good memories from my childhood: it felt right.

It matters that this is Arctosa hirtipes instead of "Wolf spider species X"

It matters that this is Alopecosa hirtipes instead of “Wolf spider species X”

I think my experiences are shared with some of my ecology colleagues, especially those who also call themselves ornithologists, mammalogists, or entomologists: many of us like ‘species’, and their names. We think about interesting species in our study systems, and think about similarities and differences, about a place’s history with its species, and the relationship to other species or spaces nearby, upstream of downstream.

But I, like most of my ecology colleagues, are not taxonomists. Instead we exploit and repurpose the good work done by taxonomists (and often not citing their work – oops!). For a concrete example from my own experience: without the taxonomic expertise of great Canadian arachnologists such as Charles Dondale, and colleagues, who described species and then wrote accessible taxonomic keys, my work would be of much lower value. The keys allowed me to get names on things. These names increase the value of the work tremendously.

Despite being retired for many years, Charles Dondale still has an office at the Canadian National Collection of Insects

Despite being retired for many years, Charles Dondale still has an office at the Canadian National Collection of Insects

Let’s look closely at this value: Surely it would be possible have the same main results from my ecological work without having the actual species names? Surely I could have called everything by my own pretend name – a secret code that I could develop – a series of ‘morphospecies’. And, these days, I could have a long code to represent a barcode. Isn’t that enough? In truth, the broad community patterns that I sometimes publish about don’t depend on the names. Rather, these community patterns depend on recognition of different types of things, but the names themselves don’t drive the patterns.

While it’s true that names are only one part of my ecological research, they are a very important part. They provide an important common ground for understanding our biodiversity – they allow us to compare apples to apples in all the right ways. The names are a doorway into a rich history, a life story that perhaps goes back hundreds of years in the literature. It means more to know that Alopecosa hirtipes is running around the Arctic tundra than it does to know it is ‘Wolf spider species X’.

But the name comes at a cost: it means that someone spent their time searching, watching, measuring and comparing; looking at shared characteristics, and putting the species in an evolutionary framework, and perhaps producing a valuable taxonomic key so free-loading ecologists like me can stick a name on ‘Wolf spider species X’. The cost is worth it: taxonomists are as valuable to science as are ecologists, molecular biologists, or physicists.

A glimpse at the grad students hard at work, using microscopes, in my lab. As ecologists, we need taxonomists.

A glimpse at the grad students hard at work, using microscopes, in my lab. As ecologists, we need taxonomists.

Taxonomy is a science that is relevant and important, and despite increased availability of molecular tools, names still matter. We need taxonomists to be our quality control, and bring sense and order to strings of code in GenBank, and help us compare and connect across systems, or among similar habitats. We need the full package figured out for a species: specimens, meta-data, barcodes and names. After that, we need to go further and assess evolutionary history and test hypotheses about relationships among species.

Today is Taxonomist Appreciation Day, but let’s make sure it’s more than one day. Let’s make it something we think about every day: every time we see a Corvus corax fly by, or see a Chelifer cancroides on the wall of our bathroom, let’s remember that every name has a story, and the narrative is brought to life because of taxonomists.

An indoor field trip: visiting Canada’s national spider collection

Last week I traveled up to Ottawa with two of my students – our goal was to visit the Arachnid collection at the Canadian National Collection of Insects (CNCI) (and Arachnids and Nematodes). The spider collection is housed on the fourth floor of the Neatby building, in a room that seldom has its lights turned on.  Canada’s National Spider collection has been without a curator since the 1990s, when Dr. Charles Dondale retired. In fact, his name is still on the door.

Dr. Dondale

The spider collection has historically been one of the finest, world-wide. It contains numerous type specimens, and houses thousands upon thousands of vials, all within stand-up cabinets. These vials contain rich biological information – they contain a spider with a species name, where it was found, who collected it, and when. These kinds of museum data are absolutely vital as we try to understand our biodiversity, and how it might be changing in the face of environmental stresses. Museum data form the basis of taxonomic revisions, and museum specimens (identified to species, by experts) are an important way for someone to learn taxonomy (that is how I did it!).

Our goal in the spider collection was to data-base some specimens – this means taking what is written on (old) labels, and entering data into a data-base (one that will eventually go on-line). On this trip, we were looking for some records of purse-web spiders in North America, and for northern black widow spider records. We also worked to database the jumping spiders (Salticidae), with a particular focus on those species occurring in Canada.

The task of data-basing.

The task of data-basing.

You might wonder why we would take time away from our own (busy) laboratory in Montreal to drive up to Ottawa to enter data; surely there are better uses of that precious resource of time (and money)?  Nope: A visit to the CNCI is always worth it.  Here’s why:

1. Label data are useful data! I have quite a few projects ongoing this summer, including a better understanding of the distribution of jumping spiders in Quebec. There’s no better way to find certain species than going to where they have been found before.  How do you know where they have been found before? Although much can be gleaned from publications, there are hundreds of specimens that have been collected and stored at the CNCI, but whose data has never been used in a publication. Looking at vials and reading labels is a good place to start, and while doing this, it only makes sense to enter the information into a data-base. It’s not exciting work, but having data digitally accessible allows my own research interests to move forward more effectively.

Treasures in the cabinet.

Treasures in the cabinet.

2. I’m an Arachnologist in Canada, and as such, I feel a responsibility to use the collection in Ottawa. The spider room at the CNCI is where (historically) Canada become a global leader in spider taxonomy. Charlie Dondale and others (notably James Redner) wrote some of the most important papers and books about spiders in North America, and their (free!) books remain a critical resource for Arachnologists throughout North America.  The hallowed grounds of the spider room are where much of this work occurred. It’s a special place, and one that is worth visiting.

3. If you don’t use it, you’ll lose it. The future is not bright for this spider collection. Surprisingly, a replacement for Charlie has not be hired. We need an Arachnologist in Ottawa (I’ve written about this before). I worry deeply for this collection, and even a few visits per year are better than none at all – it shows there is still broader interest in the spider collection, and that it remains an important resource for people from other regions of Canada. Showing continual use and interest in the collection is a great way to show its value.

4. If it’s lost, let’s hope the data are not. Time for thinking about ‘worst case scenarios‘:  every time I am at the CNCI I see evidence of further degradation of the spider collection. Spiders are stored in ethanol, long-term, and without  curation the ethanol degrades, discolours, the specimens get brittle or break apart, the labels fade or become unreadable, or perhaps a vial or two break.  The spider collection has not receive high consistent curation for a very long time. At the very least, we better have the data from those specimens, and that requires data-basing.

Trouble in the collection: A vial with a cracked glass lip.

Trouble in the collection: A vial with a cracked glass lip.

In sum, the spider room at the CNCI is a national treasure and it was really great to be there. We didn’t get much done (only about a hundred specimens databased – and, truthfully, I did very little of the hard work – my students did all the heavy lifting).  But it was a start, and means that we’ll need to come back. I sincerely look forward to the next visit!

Expiscor (19 April 2013)

Here’s  Expiscor -some discoveries I stumbled upon this week… (past versions can be found here)

  • World’s Biggest Butterfly Collection.  This video explores the amazing collection at London’s Natural History Museum.
  • Spiders, spiders, lovely spiders.  How about this image of a spitting spider by Chris Ruijter – STUNNING (thanks Alex Wild for directing me to Chris’ photos…)
A spitting spider, photo by Chris Ruijter (reproduced here, with permission)

A spitting spider, photo by Chris Ruijter (reproduced here, with permission)

  • The trees are speakingthis story describes how scientists listen to ultrasonic noise made by bubbles forming inside water-stressed trees (thanks Carly Ziter for that link)
  • More on the links between Art and Science.  The debate about “E.O. Wilson versus Math” inspired a discussion in my ecology class, but coincidentally, a friend of mine also pointed me to this truly lovely writing about Mathematics and the Arts (starts on page 55), written by Marston Morse in1959. Here is a quote from that piece:

            “…mathematics is the sister as well as the servant of the arts and is touched by the same madness and genius. This must be known.”

  • A passion for beetles: a retired researcher from Germany’s Federal Center for Meat Research in Bavaria has a lovely collection of Coleoptera, 6,000 species at over 30,000 individuals. Now that’s a hobby! (thanks Bug Girl for the tweet about that story)
  • To finish, glad to see that Entomologists are out there correcting bad taxonomy.  Here, Ainsley Seago (aka @AmericanBeetles) does some fine work (and it was given a stamp of approval by Taxonomy Hulk – yes, we do need him, too!)

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We need the Taxonomy Hulk

The Taxonomy Hulk burst onto twitter yesterday. We need superheroes like Taxonomy Hulk. As his/her alter ego, s/he surfs the internet, working away as a taxonomist, doing things that taxonomists do – describing species, inferring their evolutionary relationships, discovering their natural history. However, if s/he spots a taxonomic mistake on a website, news story, scientific article, or blog – LOOK OUT. The Hulk goes through an impressive metamophosis. S/he gets mad and gets even. If you make a taxonomic mistake, you will be shamed. Message: DON’T MAKE A #TAXONOMYFAIL. Taxonomy Hulk points out misidentifications in images (e.g., see this website with a Harvestmen instead of a spider.. oops [although a common mistake]).

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Taxonomy Hulk reminds us to use Latin names, not common names.

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Taxonomy Hulk is also funny. We need humour – every day.

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On a slightly more serious note: correct taxonomy is critically important. Other posts (e.g., see here or here) have pointed out taxonomic failures – and I especially like Bug Girl’s Flickr set!. One letter difference in Miridae (a family of plant bugs) gets you to Muridae (rodents and their relatives) – yeah those two are just a bit different. As an ecologist (although one with envy of taxonomists, and one in awe of the work taxonomists do!), I admit that I am perhaps not as careful as I should be when it comes to checking nomenclature, or ensuring spelling is always correct. I try – but given that my training is not in taxonomy, I surely make mistakes. I fear that some ecologists appreciate the importance of sound taxonomy even less than I do, and we need a watchdog. Reminders about correct taxonomy are a good idea. Taxonomy Hulk reminds us that we must be clear in what we are saying, whether it be in science journalism, writing a blog post, or working on a scientific paper.

Taxonomy Hulk is a concept not a person and this is a good thing: the humour and fun and ‘alter ego’ perspective is non-threatening, and allows taxonomic issues to be brought into the open easily and effectively. We can fix our mistakes, smile about it, and move forward.

Thank you Taxonomy Hulk. (and yes, you should follow Taxonomy Hulk on twitter)

I finish by stating that Taxonomy Hulk’s ‘regular’ persona (the Bruce Banner) is known to some of us (and s/he’s an incredibly competent taxonomist!, and a super-nice person).

But I’ll keep it quiet – it’s better that way.

Natural History: unknown.

I sometimes see this statement in taxonomic papers that describe a new species:

Natural History: Unknown

Think about this… specimens have been collected, somewhere, sometime. Perhaps these specimens sat in an Entomology museum for decades until a MSc student took them out and started a revision. Perhaps the specimen was recently sorted from a bulk malaise trap sample from the Amazon basin, and sent to a taxonomic expert for identification. S/he recognized it was something different and later, while doing a taxonomic revision, included it, measured it, did a line drawing, extracted some DNA, wrote a description, gave it a name. However, when writing what is known about its natural history and biology had to write “unknown“. (by the way, discussions about defining natural history can be found here and here).

An unknown weevil with unknown natural history.

I recognize why nothing is known, but when trying to get some sense of why a particular species might be found in a particular habitat, having no information about natural history and biology can be frustrating. This is especially true for ecologists, whose research might benefit immensely from ANY natural history information. In my own work, after I key out a species of wolf spider, for example, I immediately flip to the description, and scan down to the notes about the biology of the species – these notes can confirm details about the species (hey look, I found it under rocks on a shoreline, and that is where it is reported, also!; or, indeed, it makes sense that I found that egg sac in late summer – that species is known to mate in mid-summer).

Natural history is important, as is so elegantly stated in many papers (e.g., see Greene’s 2005 paper) and the impending extinction of natural history was written about over 10 years ago by Wilcove & Eisner.  The world needs natural history information, and although I recognize that having a name is clearly very important, it is also essential to have some natural history information. Such information can lead to additional research on the species, or allow others to document the species in new locations around the globe. Having some information will help future graduate students figure out when during the growing season they should find specimens, and perhaps what host plants they should look on.

So, I ask these questions, and I look forward to responses, especially from taxonomists:

Should taxonomists wait to describe a species until there are some details known about its natural history? (this will, of course, take more specimens and more time…)

and,

Under what conditions is it acceptable to state “Natural History: unknown”?

Caveats:  I am coming from this question as an ecologist with an appreciation for taxonomy, but not as someone trained in taxonomy.  I am, therefore, biased in my views.  I also recognize that in many cases, taxonomists only have one specimen and a label to work with, and data on the label itself may be lacking, hence the need to state “natural history: unknown”.  My questions are meant to be more general, and I am hoping to gain insights into whether seeking additional natural history information about species (when it is described) is a losing battle… and whether this task should be in the hands of the individuals who describe species.

References

Greene, H.W. (2005). Organisms in nature as a central focus for biology Trends in Ecology and Evolution, 20 (1), 23-27 DOI: 10.1016/j.tree.2004.11.005

Wilcove, D. and Eisner, T. (2000) The impending extinction of natural history. Chron. Higher Ed. Sept. 15, B24. Available here.

Taxonomic sufficiency in biodiversity research: Is it always necessary to identify species?

It’s been a successful few weeks in the lab!  Two weeks ago I promoted an exciting paper about spider silk and herbivory and just after that paper come out, another publication from our lab was published, titled: “Does species-level resolution matter? Taxonomic sufficiency in terrestrial arthropod biodiversity studies“.  This paper evolved out of a past graduate-level class in Forest Entomology at McGill, and was re-worked and re-written by post-doc Laura Timms, former Phd student Joseph Bowden, and my colleague Keith Summerville.

Let me provide a plain language summary of this work and I will also touch upon some of the controversy that has arisen because of this paper:

Biodiversity science is about the discovery and description of all the different kinds (species) of organisms living on our planet.  It is a vitally important area of research because different species play important roles in our ecosystems, and as a consequence, are important to us.  The different number of species in an area can also inform us about how we might be harming or helping ecosystems.  This is an active area of study in the context of forestry, since some forest practices (for example, cutting all the trees down in an area) can cause changes in the number of species (and whether they are rare or common) and these changes can inform us about whether our forestry practices are harming our ecosystems.  All of this kind of work, however, depends on the ability of scientists to collect, sort, and identify different kinds of species.  Since most described species on the planet are Arthropods (e.g., spiders, insects, and their relatives), these animals are often used as a way to indicate how biodiversity might be affected by environmental change.  However, there is a problem: it takes a very long time to identify different arthropods, and it is costly and difficult – requiring highly specialized training, by people known as taxonomists.  In our research project, we asked whether not you always need to know the exact differences between insects and spiders  in order to tell if a disturbance is affecting biodiversity.  We did this by looking at a series of data-sets about beetles (Coleoptera), moths & butterflies (Lepidoptera), and spiders (Araneae). These data-sets were from past research projects about how forest disturbance affects biodiversity.

Here is how we did the work: Different kinds of organisms are classified using a two-part name:  the genus and the species.  There can be many different species within one genus.  You can then classify different genera (the plural of genus) into grouping called Families.  For example, all wolf spiders are in the Family Lycosidae.  A common genus within this family is Pardosa – there are dozens of species of Pardosa in Canada; Pardosa mackenziana, Pardosa moesta, Pardosa hyperborea, etc.  We first took our big data-sets and using the lowest level of naming (the species) we asked whether forest disturbance affected biodiversity.  We then grouped all our species into their respective genera -this meant that the data-sets got smaller (i.e., there are necessarily fewer genera than species).  We did the same analysis to see if we could still get a signal about the effects of disturbance on biodiversity, but now with the ‘reduced’ data.  We did this again at the family level.  We did this because we wanted to know if you could take a short-cut. Stated another way, if you don’t have the time or ability to figure out all the species in your research project, can you still see if there is an effect of forestry on biodiversity?

A wolf spider (Lycosidae)

A wolf spider – do you need to know its name?

Our results showed that in most cases, you do not need to know the species identity to see the effects of forestry practices on the biodiversity of spiders, beetles and moths & butterflies – you do not get as clear answers when things were grouped into Families, but the datasets with species grouped into genera were almost as good as when you group things into species.  This was surprising, because an assumption in biodiversity science is that species-level identifications are necessary and should be the ‘gold standard’ for this kind of research.  We showed that in many cases, you can get your answer by identifying arthropods to the generic level:  this can save you a lot of time (and money).   Some researchers (including taxonomists) may not be thrilled with this result as it might suggest that species are not important, and specialized taxonomic knowledge is not essential to complete biodiversity research.  This is certainly not the case, which leads me to the caveats:

1) Our results do not mean species are not important!  Instead, we are saying that if there are logistical and financial constraints, you might be able to answer your research question without having to identify all the species.   If you have a project about large-scale disturbance and are looking to see whether there are any broad affects on biodiversity, our approach might work.   However, you might miss some subtle effects, so this approach must be taken with caution.  Although our suggestion is a short-cut, it would still be important to save all the samples, and at a later time (as money and expertise permits) the species could be determined.

2) Our study is specifically geared towards research about insects and spiders in relation to large-scale forestry disturbances.  We are not saying that this will work in all situations and with all different kinds of organisms! The context is important.  Related to this, if an overarching research question is about species in an ecosystem, species-level identifications are essential.  Everything depends on the research question and the research context.

3) This general approach that we have discussed is highly dependent on what kind of organisms you are studying.  If you are working with a group of organisms that do not have too many different species within a genus, our approach may work.  If, however, there are many species within a single genus, our suggestion will not work as well.  Therefore, a researcher should look at the general relationship between the number of species per genus for their study organisms and use this ratio as a guide when thinking about taking the short-cut that we discussed in the research.

In sum, we are quite excited about this research – we think it will provide more opportunities for biodiversity projects to get done, and will help answer certain research questions when there are substantial constraints on time and money.  This is one way to be pragmatic about biodiversity research.

Please share your thoughts!

Reference:

Timms, L., Bowden, J., Summerville, K., & Buddle, C. (2012). Does species-level resolution matter? Taxonomic sufficiency in terrestrial arthropod biodiversity studies Insect Conservation and Diversity DOI: 10.1111/icad.12004

40,000 beetles and a PhD

Last Friday, my Ph.D. student, Alida Mercado Cárdenas successfully defended her Ph.D.  Congratulations, Alida!  This is a really big event, and the entire laboratory is so proud of Alida.

Alida’s thesis is titled “Ecology of beetle assemblages in a Panamanian tropical forest with taxonomic notes on Curculionidae and Histeridae“.  Yes, it is about beetles in the neotropics.  Here are some numbers from her thesis:

40,000 beetles, 73 Families, 355 species or Curculionidae, 112 species of Histeridae.   In case you weren’t already convinced, the tropics represent the heart of biodiversity science. …so many beetles, so little time.  Alida, quite literally, looked at almost 40,000 beetles.  This is stunning, and astounding.   Here’s a photo of her with a small sample of these beetles, and she’s still smiling!!

Alida with a few of her beetles.

Alida’s thesis is ambitious, fascinating and contains some important conclusions:  a) from the beetle’s perspective it matters whether a rainforest is next to shade-grown coffee compared to a pasture, b) beetle assemblages are unbelievably variable in the neotropics – in fact, she often discovered as much variation between her traps within 100’s of meters of each other as between different locations, c) seasonality (i.e., rainy/dry seasons) influences beetle communities, and d) there are a lot of species still to be described – for example, of the 355 weevil species that Alida identified, less than half of these have a name.  To help with this significant taxonomic impediment, Alida collaborated with a beetle taxonomist (Alexey K. Tishechkin)  and described three new species of Histeridae.  This is a wonderful part of her thesis, and showed that it is possible to combine different disciplines – in this case, ecology and taxonomy.

We often hear that ecology and taxonomy are disciplines that fit well together, and I’m reminded of Nicholas Gotelli’s excellent 2004 paper, titled “A taxonomic wish-list for community ecology” (published in the Transactions of the Royal Society of London B).  Here’s a quote from that paper (downloadable from here):

…The best research comes from collaborations between taxonomic specialists and community ecologists who can bring both fresh ideas and fresh analyses to the table, and take advan-tage of the wealth of information that resides in museum and herbarium collections…

It’s one thing to collaborate, but something entirely different to be able to do both.  I would argue that relatively few scientists work effectively (and publish) in both fields – I have tried to do this a little bit, and worked for a couple of years on the taxonomy of pseudoscorpions.  I have, however, never really been able to fully immerse myself in taxonomic research, and I have yet to describe a species.   Alida has clearly succeeded where I have failed.  That’s inspirational, as is Panama:

Panama

The”official” defense that happened last week represents the end point of a long, productive, and lovely time with Alida being associated with the arthropod ecology laboratory.  I began at McGill in September 2002, and Alida came to do her MSc just a year after I started.  Her Master’s was about Carabidae (ground beetle) assemblages at and near the Morgan Arboretum, and she published two fine papers from this work – one about introduced Carabidae  and another about successional patterns .  After her MSc, Alida successfully entered McGill’s NEO program, and begin her PhD on beetles of the neotropics, with Dr. Hector Barrios as a co-supervisor.  The rest is a successful story of beetles, beetles and more beetles.

Alida is kind, caring, intelligent, motivated, and a very talented academic.  I am pleased (and proud) that she is officially finished at McGill, but I will also miss her. Congratulations, Alida, and good luck with your next adventure!

And to finish, here’s a photo of a weevil (an unnamed one):

An unknown weevil, from Panama (photo by C. Buddle)