Visual Chronologies of Names

One of the things to realize about the site is that it is now as much a research project as it is an information portal (it didn’t start this way…maybe I’ll write up the history of the site at some point). The research project end is a bit poorly defined, but could roughly be viewed as “what types of things can I say, infer, or visualize about fiddler crabs if I collect a whole lot of data on the back end.” Yeah…not very specific.

One idea that had been floating in the back of my mind for quite awhile was how to to visualize changes in taxonomic name usage over time. If one name replace another, how do we show that visually? Not surprisingly, others have thought about this and come up with some solutions. In late December I was sitting in an airport preparing to leave the country for the holidays when I stumbled across a blog post by Rod Page, Taxonomic name timelines for BHL, about just such a question. He mentioned an earlier project called Synonyms that would produce nice looking name chronology charts by mining data from the Biodiversity Heritage Library; unfortunately, Synonyms had gone defunct and Rod had hacked together a rough replacement (as is his wont to do). The Synonyms graphs were exactly what I had been trying to come up with so immediately made note to try to do this with my own data when I got back.

It only took me a few hours in early January to extract the data I needed and get some basic-Synonymy style charts plotted. It took quite a bit longer to fiddle with their formatting to get them “just right.” Let’s look at an example.

For a simple case, let’s compare the names of the genera. For most of their history, fiddler crabs have been placed in one of two genera: for most of the 19th century they were considered to be Gelasimus; since the start of the 20th century they have mostly been placed in Uca. Most of the other genera which have included fiddlers (23 in total) make up a tiny proportion of references relative to these two. Here are their chronology plots (I’m still struggling to come up with a good name for these):



These charts represent the number of publications per year that used each genus as an accepted name (whether a publication named one species or ten, it only counted as one valid use of the name).

Caveat: the database is still largely incomplete after about 1977, so the parts of the figure from the last 40 years are not representative of the full pattern.

A few things stand out from looking at these charts  (some of which I knew already):

  1. Generally, references to fiddler crabs skyrocketed starting in the 1950’s (this is when fiddlers really started being  used as model organisms to study certain aspects of behavior and physiology).
  2. It took about 15 years for the transition to Gelasimus to Uca to really take hold; from the late 1890’s through the late 1910’s, both genera were used in roughly equal numbers.
  3. Although Gelasimus was technically abandoned by taxonomists at the start of the 20th century, the genus continued to be used at a small, but steady pace at least through the 1970’s. It’s hard to see on the graph, but there has been at least one use of the genus as valid as recently as 2006.

Something not obvious from this chart: most of the uses of Uca prior to 1897 are actually references to a different type of crab. For most of the 19th century, Uca was used for crabs in the genus we now call Ucides (the somewhat tortured history of these names has been discussed by others and is summarized in the Systematics section of the main website).

To some extent, these figures aren’t quite as exciting as I’d hoped they’d be, but they still visually illustrate the name usage in a direct and attractive way. These charts are not live on the website yet, but the capability to add them is now built-in to the code and graphs depicting name usage for binomials and specific names, as well as directly comparing synonyms will all be made available at some point in the future, once a few more kinks are worked out.

Once again, into the breach…

On occasion in the past I’ve attempted to start a blog and each attempt has ended rather abruptly with rather few posts. We’re going to try this again and see what happens.

This particular blog is attached to my fiddler crab website ( and will mostly be focused on thoughts about these little critters and their biology and evolution, the website, the science, or related issues such as biodiversity informatics and cyber taxonomy. Or maybe just other stuff as it occurs to me if I find I have nowhere else to vent.

The look of the blog is amazingly bare bones right now, but we’ll see about sprucing it up into something slightly more visually appealing as I get into the hang of this (or not).

I’ll probably tackle the first real posts in the next day or so. I’ve got a couple of topics already in mind…