Archive for the ‘biodiversity informatics’ Category

Website News

Thursday, March 14th, 2013

For those of you that visit the web site and blog on a regular basis may have noticed over the past several months not a lot of activity. At last I am getting control of editing the content of the web site and plan on updating many of the pages. So be looking for changes over the next days, weeks and months.

The first changes have already taken place. The Haiku button has been deleted and replaced with a Search button for the museum specimen database. What this means is that there is not going to be a Haiku contest this year. Sorry to all the poetry lovers out there but I am a music lover not a poetry lover and with the loss of personal at the museum here there is no way I feel like I can take on the job of judging the entries.

The database continues to grow in record numbers. Currently there are over 60,650 records and growing. While just a drop in the bucket of all the specimens in the collection it is a start and a number that is added to usually daily. I am also taking images of the holotype labels and hope to begin uploading them soon.

Database Update

Wednesday, January 16th, 2013

The collections holding of determined Myrmecophilidae have been digitized and are available by searching our Specimen Database Portal. A link to the database is located on the Museum’s homepage. Enter the taxon name in the search engine to view a distribution map and label information for the various specimens of each species.

Lessons from Georeferencing Bumble Bees

Thursday, December 15th, 2011

Off and on in the last year I have been documenting the distribution of the bumble bees (Hymenoptera: Apidae: Bombus) of North Carolina, which is a great state for looking at niche specialization in these insects. First, we have a well-curated and bee-rich collection here, due mostly to the efforts of Ted Mitchell, who wrote a two volume series to the bees of the Eastern US based on more than 30 years curating bees in the NCSU collection. Second, bumble bees are primarily a cool temperate lineage, and the climate of the southeastern U.S. is too warm for many of the species. From west to east, North Carolina offers habitats that span cool boreal habitats, the rolling hills of the near-sea level Piedmont, and the warm grassy coastal plain, plenty of geographic variability for revealing niche preferences.

I set about the task of studying these preferences by compiling georeferenced localities for the species of North Carolina from the NCSU insect database (most records) and other available museum databases (through GBIF) and mapping the points. I discovered that most Bombus species exhibit strong trends towards one or two of the three habitat regions of North Carolina, but there were outliers. Should we trust such outliers and move on, or check them in the collection? I decided to check them.

The first lesson I learned in this process is that geographic outliers did an excellent job of targeting misIDs – the majority of such outliers, in fact, were misidentifications. Concerned, I looked at the identifications of the rest of the specimens of a few of these species and discovered that these outliers made up most of the misidentified material. Using geographic distribution greatly helped to iteratively check the quality of these determinations.

bumble bee distributions in North Carolina
Distributions of Bombus vagans and B. perplexus in North Carolina, based on specimens in the NCSU Insect Museum and at GBIF. Photos by jlucier (left) and Greg Page (right).

The second lesson is that bumble bees are prone to misidentification. Bumble bee specimens are heavily georeferenced, likely due to their abundance in collections, their ease of species-level identifications, and the importance of documenting their distributional patterns given recent declines. While this makes them great for studying niche restrictive factors, bumble bees inherently can be prone to determination error.  The majority of bumble bee species are part of various Müllerian mimicry rings with other bumble bee species. People like to make quick identifications based on color alone but in most cases there are a couple species that are easily confused if one is not looking at the detailed morphology. One such common mistake in the eastern US is Bombus vagans and Bombus perplexus (see Figure), two species that have vague discrimination between them and persistently perplex us. The Bombus affinis drawer, for example, which is a species in strong decline and a target for multiple georeferencing projects, was rife with misIDs. Many of these could be explained by B. affinis being an “in-betweener” phenotype with color variation similar to several other species. This species also had some Bombus auricomus mistakenly placed among it, most likely an alphabetical error of curation.

Finally, I learned that georeferencing errors are not insignificant and should be also checked through mapping. Some of the niche outliers were errors in assigning localities, which can be tricky when two areas have similar names (see “the danger of using Google Earth/Maps to georeference“). Overall, I have come to appreciate the value of geographic data checking for georeferenced species data. Low error can be a big deal when trying to understand geographic restrictions at a local scale.

the dangers of using Google Earth/Maps to georeference

Tuesday, March 8th, 2011

Bombus vagans, beautifully captured by J. C. Lucier.

My colleague ran into an interesting problem while georeferencing our bumble bees yesterday. It was a nice lesson for our lab group, so I thought I’d post the story here for everyone …

We’re in the process of affixing unique identifiers to all of our bee specimens, and we’re capturing the information from their labels: where and when they were collected and by whom. These metadata are typed into a spreadsheet that we eventually import into our database. The verbatim data are then queued to be georeferenced (i.e., figuring out the latitude and longitude for each locality), either manually or by using some informatics trickery to be described later. My colleague needs the Bombus data ASAP for an interesting and timely niche modeling study, so she’s carefully poring over several georeferencing resources, like Google Earth, gazetteers, etc. to predict lat and longs for these specimens. She ran into a Bombus vagans individual with this collecting event label:

USA: North Carolina
Judson
19.VII.1923
JC Crawford

Easy. We’ll just go to Google Maps, search for Judson, NC, grab the lat and long (35.002335, -78.80888), and be done with it. Next specimen … right? Well, Bombus vagans, also known as the wandering bumble bee, is largely a boreal species (see also the specimens in GBIF). Finding a specimen in the coastal plain habitat near Fayetteville, NC seemed unlikely—or maybe this bee was living up to its common name! A bit of detective work revealed that J. C. Crawford collected several other bees in the mountains of western North Carolina five days later (24.VII.1923) and that this collector’s typical hunting grounds in 1922 and 1923 were exclusively in the mountains near Bryson City. Hmmm… Diving deeper into the mystery my colleague found that there was a second Judson, NC in the 1920s, located just downriver from Bryson City on the Little Tennessee. It disappeared in the 1940s after being flooded by Fontana Lake (which resulted from the Fontana Dam). Ah ha!

Next step: look up some old maps of Swain County and estimate the lat and long for the old town of Judson: 35.40355, -83.561347 (with a generous error of 1000 meters). If we really wanted to be precise we’d try to find better maps from the 1920s-1940s, but this first pass will get my colleague going on her niche modeling analysis.

So, what did my lab group learn? 1) it pays to know the natural history of the species you’re georeferencing, 2) precise collection dates and collectors’ names are useful, 3) we can’t employ a single tool to predict latitude and longitude, no matter how user-friendly Google Earth is(!), 4) we’re better off georeferencing our specimens at the time of collection, rather than after-the-fact, 5) we need to document how we determined the lat / long and make sure this information is added to the database, especially when detective work was required, 6) natural history collections are vital sources of irreplaceable information. What if we wanted to sample bees in Judson, NC today? Perhaps there are some aquatic species we could sample using fish nets and SCUBA gear?

Note: a best practices guide for georeferencing is available from GBIF.

formalizing and extending the North Carolina Insect of the Week

Friday, September 17th, 2010

You may notice that today’s Insect of the Week post looks a little bit different, with its embedded Google Map of NCSU specimens, its more regimented categories and embedded images, etc. What’s going on? Well, Matt Yoder, a researcher in the Museum, has been rewriting certain aspects of the database software we use for digitizing specimens (mx) in order to enable Web-published species pages that directly incorporate NCSU specimens. This functionality isn’t new, mind you, as we’ve already used previous variations to publish species descriptions to the Web (e.g., this page for Alobevania tavaresi). What is new is the ability to plug the content into just about any other Web resource using the generated iframe. Next up: XML mark-up that enables the Encyclopedia of Life to scoop our content for their species pages (hence the more formalized sections of this post – Diagnosis, Natural History, etc.)

The North Carolina Insect of the Week series will roll on, showing up here on Fridays, as usual. Future pages will also be indexed on a new and improved Insect Museum database site. We’re very excited!