Archive for the ‘curation’ Category

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.

Database Update

Tuesday, January 15th, 2013

I just finished capturing the label data for the specimens of the Scaly Crickets, Mogoplistidae. Members of this family are small, wingless or very short-winged crickets. They occur on bushes or beneath debris in sandy localities near water. Many of our specimens were collected at or near the coast and by the noted Orthopterist, B.B. Fulton.

2011 resolutions – how did we do?

Tuesday, January 10th, 2012

Happy (quite belated) new year! December 31 came and went, as did the NSF DEB pre-proposal deadline (January 9!). We’ve been slammed with personnel changes, courses, meetings, manuscripts, and proposals these last few months, but we definitely want to make time to revisit our resolutions from last year, acknowledge our accomplishments in 2011, and then make a few resolutions for 2012. First, how did we do with respect to our 2011 goals?

  1. Finish profiling the collection – We’d profiled our pinned specimens in 2010 and aspired in 2011 to establish protocols for profiling our ethanol-preserved and slide-mounted collections – and then, of course, to actually profile these collections. So, how did we do? Our newest team member, Heather Campbell-Melvin, did a stellar job of evaluating our wet collection, a summary of which was presented at ECN last November. Watch this blog for a thorough account of our metrics. As for the slides … we haven’t touched them yet, primarily due to resource constraints. It’s the collection of least concern for us, based on our anecdotal profiling, so I am comfortable putting it off until 2012. Overall I’m going to declare this resolution a success.
  2. Monitor humidity and pest traps twice a month and publish results to the Web – After a quick rethinking of our workflow we chose to monitor the pests only once a month. Other than that change we did indeed manage to establish a rhythm and maintain it throughout the year. Our results are available on the calendar. This resolution was a success, and we’ll carry it into to 2012.
  3. Thoroughly inventory, label, and track Museum equipment and supplies – We have quite a supply of insect collecting gear, bought from a variety of sources. Some of this gear needs to be available for other parties within the department, including gung-ho students and instructors for Entomology classes. The rest of the gear is dedicated to Insect Museum missions. In 2011 we wanted to get organized about this equipment (a spreadsheet inventory) and track our loans of this gear. We did manage accomplish these goals, and I’d call this a success.
  4. Database Aphididae – Substantial progress was made towards this goal, mainly because we had world aphid experts visit us for an epic slide-scanning event (Bob Foottit and Eric Maw, from the CNC). More on this later, but our aphid slides have been scanned and are in the process of being processed. Huge success here, though we couldn’t have done it without help from our Canadian friends!
  5. Portage data to the Global Biodiversity Information Facility – As I said last year, we’ve been close for a long time to getting this done. We’re basically ready, in that our database has been configured to export data in the right format, but we’re not sharing yet. Too many distractions late in 2011. So, I have to declare this resolution a failure, though it probably (hopefully) won’t be a failure for very long.
  6. Offer another 52 North Carolina Insects of the Week – Astounding success! These posts are my favorite, as they force me to look at specimens and dive into the literature to learn about insects I don’t usually get exposed to. Our 104th will be this Friday, which marks exactly two years’ worth of North Carolina insects. I expect the posts to continue after that but to be much more erratic, as we shift gears and blog about other topics (more soon).

Up next: accolades, big changes, and resolutions for 2012.

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.

fall 2011 update, part 3 – (near) future directions

Thursday, September 1st, 2011

We have a rather full schedule for the next few months, with respect to some of our scheduled goals. One of our New Year’s resolutions was to finish profiling the collection. I doubt we’ll be able to finish the slides (or even start), but we’re making progress towards determining our wet collection metrics. We’ll write them up and describe our results soon. We’ll follow this process with tests of methods we think will be useful for digitizing wet collections (imaging and digitizing collecting event data). Hopefully we’ll remember to blog these tests as well, as another way to get feedback about workflows.

I mentioned we’re up to 1,540 GigaPans and will soon push that number upwards again. We’ve already demonstrated the utility of these drawer images and hypothesized a number of potential applications for these resources … but can their utility be quantified more robustly? How do entomologists interact with collections? Can we refine the digitization process to make it more effective for these users? We’re working with Babi Hammond, a library scientist at UNC-Chapel Hill and recent CollectionsWeb intern, to address exactly these kinds of questions. Step one was recently initiated – a survey for entomologists. We’ll present early results at the next ECN meeting in Reno, NV.

Finally, we’re toying with the idea of developing a dynamic manual of insect collections management, one that represents the protocols used by the NCSU Insect Museum but which is also available for anyone to peruse and even comment on. What’s the best way to house and monitor one’s collection of wet-preserved material? What kind of racks should we use? What are the alternatives to naphthalene? How should we establish a pest monitoring protocol? We’ve had to research each one of those questions and more, so why not make our syntheses of these issues available for others? The manual actually already exists as a wiki, but we want to spend a few months making sure it represents the total of our philosophy. Anyone know of similar resources? Do other collections avail their protocols in obvious ways? It’d help to measure our methods against theirs/yours!

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.