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Adventures in the field: How do insect museums get these specimens anyway?

As you pour over images of our fascinating CalBug specimens, you may ask yourself how these insects ended up in the museum in the first place. Many of the labels you are transcribing date back to 60-100 years ago, but don’t let that fool you into thinking that museums are places to that just store old specimens. Scientists are still adding to museum collections every day, but how we use specimens now is often in ways that Entomologists 60 years ago could not have imagined.

As a PhD student in the Essig Museum of Entomology, I have had many opportunities to work with insect specimens within a museum. However, this summer I had the chance to go on a month-long expedition in the Appalachian Mountains of North America to collect live insects in the field. My dissertation research involves understanding the diversification and evolution of ground beetles in the genus Scaphinotus. Often referred to as “snail-eaters,” these nocturnal beetles have developed an elongate head and mouthparts, including escargot fork-like jaws and huge sensory palps that allow them to find and feed on snails and slugs. They are flightless and live in predominantly montane habitats. This makes them interesting candidates for studying how body-forms of species change over time, possibly adapting to feeding preferences.

Scaphinotus5

Insect specimens already housed in museums provide a great deal of information about morphology, distribution, seasonality and even behavior, however there is one thing they generally cannot provide- good quality DNA! So today entomologists are frequently heading to the field to collect specimens specifically to extract their DNA. This is why I went on my recent trip to the Appalachians, where I hoped to collect as many as 20 Scaphinotus species to use in my research.

A month-long field excursion requires careful planning and preparation. My trip included visits to 5 states and as many National Forests, where I camped and hiked long-forgotten trails in search of these elusive little beetles. Of course no amount of planning can prevent one from running into a month-long bout of stormy weather! And so it was, my first big trip into the field was vexed by torrential rains, flooding, lightning, thunder, and even a tornado! But in spite of all that heavy weather, rain and mud, I did manage to find a few Scaphinotus (the beetles were possibly as unhappy about the weather as I was!).

Flooded

I came away from the trip with a far greater understanding and appreciation of what it is like to be in the field collecting specimens first hand. I also chalked up nine additional species whose DNA will contribute to my dissertation research, and will be made available to other scientists worldwide via CalBug and the Essig Museum of Entomology at UC Berkeley.

-Meghan Culpepper

Behind the scenes at the CalBug Project.

http://www.calacademy.org/sciencetoday/calbug/5513353/

Wonder where all those specimen images come from? Who are the people working in the museums? What does it look like? Take a behind the scenes look at the Essig Museum and the CalBug project in a new video produced by the California Academy of Sciences.

Seeking participants for December hackathon!

iDigBio and Zooniverse’s Notes from Nature Project are pleased to invite you to participate in a hackathon to further enable public participation in online transcription of biodiversity specimen labels.  The event will occur from December 16-20, 2013, at iDigBio in Gainesville, FL, though you may choose to participate in a subset of the days based upon the schedule.   We are especially looking for participation from the most enthusiastic and committed citizen science transcribers!  This is a great opportunity to have a direct influence on expanding this tool in the directions you would like to see it go.

The hackathon will produce new functionality and interoperability for Zooniverse’s Notes from Nature  and similar transcription tools.  There are four areas of development that will be progressively addressed throughout the week.

  1. Linking images registered to the iDigBio Cloud with transcription tools in order to alleviate storage issues.  (Monday)
  2. Transcription QA/QC and the reconciliation of replicate transcriptions.  (Remainder of week)
  3. Integration of OCR into the transcription workflow.  (Remainder of week)
  4. New UI features and novel incentive approaches for public engagement.  (Remainder of week)

There will be opportunities to narrow the focus in each category of activity in a teleconference tentatively scheduled for early in the week of November 25 (and also at the TDWG meeting and the iDigBio Summit, if you are attending either of those events).

If you are interested, please get in touch with Austin Mast (amast@bio.fsu.edu) by Wednesday, Nov 1.  iDigBio has budgeted some funds to support travel costs.

With best regards,

Austin and Rob Guralnick (UC-Boulder), co-organizers

A new milestone!

The Notes from Nature team is proud to report reaching the new milestone of 300,000 transcriptions completed!  This has been made possible by the generous and committed efforts of nearly 4,000 citizen scientists from around the globe.  We look forward to continuing the project and sharing more biological collections with you in the near future.  Thank you citizen scientists!

To continue growing and expanding, we are interested in your feedback.  What excites you the most from Notes from Nature so far?  How would you like to see it evolve?  Leave a comment and let us know!

On the radio!

This morning I had the opportunity to join WTJU’s Robert Packard on the Soundboard program to talk about Notes from Nature.  Click here to listen to the clip! 

250,000 Transcriptions!

Since our launch several months ago, the Notes from Nature citizen science community has transcribed 250,000 specimen labels!  This is an incredible achievement, and shows promise for where this project can go.  We’re indebted to the citizen scientists out there who love this work and have taken it upon themselves to contribute to science in this way.

Some highlights:

  • Over 3,500 citizen scientists from around the globe participating
  • Over 8,800 plant specimens completed (completion requires at least three transcriptions to ensure quality through consensus)
  • Over 16,000 insect specimens completed (same requirement as plants)
  • Over 25 bird ledger pages completed – these are WAY more time intensive, and were only added days ago (same completion requirement as others)

We’ve learned a lot during this period, and are now in the process of figuring out where to go next, and how to involve bigger crowds of citizen scientists and more interesting collections from around the world.  Our recent call for new collections has garnered interest from curators across the US and Europe, and we hope more will be in contact soon.  It’s a very exciting time.

Thank you for all your support!

What good are moths?

hummingbirdmoth

Hummingbird moth, Hemaris thysbe. Photo: Joyce Gross

National Moth Week has arrived. Across the country museums and community groups are celebrating the splendor of one of the most diverse herbivore groups on earth. To join in the fun the team at the Essig Museum imaged our collection of hawk moths (family Sphingidae) for the Notes from Nature project – they are sprinkled in with the other CalBug images. Hawk moths (or sphinx moths) range from medium to very large in size, from very cryptic to conspicuously colored, and from day-flying humming bird and bumble bee mimics to night-flying ghosts of the dark forests. Hawk moth caterpillars are known as hornworms, because of the horn-like spike on their hind-end, and include major pests of tomatoes, tobacco, and other crops. See what species live in your state by searching the Butterflies and Moths of North America website.

Moths and butterflies comprise the order Lepidoptera. The name comes from Latin meaning “scale-wings,” referring to the layers of microscopic scales that make up the color patterns on the wings and body (that powder you got on your fingers if you ever touched a butterfly’s wings). These scales can take on many shapes, sizes, and colors depending on their role in camouflage, mating, or protecting eggs. Scale color patterns are very useful in identifying different species of Lepidoptera – most Americans can recognize a monarch butterfly by its black and red pattern. But they are also the focus of very intense research in evolutionary development, biomechanics, biochemistry, and other areas of ecology and evolution. In one of the Hawaiian moths that I study (Cydia) there are special pouches on the male wings that contain pheromone-producing glands and special “sex” scales that help disperse the mate-attracting odors.

sem_cydiamoth

Scanning Electron Micrograph of typical and “sex” scales of a Cydia moth. Image: PT Oboyski

As an entomologist I am often asked, “What good are mosquitoes?” Or, “What good are cockroaches?” Or especially because they are the focus of my research, “What good are moths?“ People are most familiar with pests of human enterprise, such as clothes moths (Tinea pellionella and Tineola bisselliella), meal moths (Plodia interpunctella), and various garden pests such as cutworms. But these are a tiny fraction of moth diversity. Also, keep in mind that all animals feed on something and live somewhere. The only thing that makes some of them pests is that they feed on things we rather they didn’t in places we don’t want them to. Imagine if we placed a high value on large piles of manure, then dung beetles would be considered pests as well. But there are also species we think of as beneficial. A great example in the northwestern United States is the cinnabar moth (Tyria jacobaeae) whose caterpillars were imported to feed on tansy ragwort, a pest plant from Eurasia toxic to cattle and other animals. Caterpillars in general keep plants from taking over the world. In turn they are kept in check by their predators, including bats, birds, and parasitic flies and wasps.

cinnabarmoth

Cinnabar moth caterpillars and adults, biological control agent for tansy ragwort. Photos: Wiki Commons

Speaking of bats … Did you know that some moths have a tympanum (like our ear drum) that is tuned to the echo location signal of bats? Upon hearing the signal of an approaching bat they begin evasive maneuvers. Some tiger moths even send a signal back to bats saying, “You don’t want to eat me, I don’t taste good.” Recent research suggests that hawk moths produce similar warnings to bats, possibly because they do not taste good (many hornworms feed on toxic plants) or possibly because they have spiky legs that are difficult to swallow.

So what good are moths? Apart from being biologically fascinating, aesthetically pleasing, and behaviorally wondrous, amazing aerial acrobats, important links in food webs and controllers of pest plants, good classroom pets, figures in myths and fables and symbols of change, and important models for ecological and evolutionary research, I guess not much.

– Peter Oboyski

Viva la revolucion

Notes from Nature recently surpassed its 200,000th transcription!  Given this milestone, it seems like a good opportunity for the Notes from Nature team to do two things: 1)  We want to show a bit more where – geographically – we have filled in some data gaps; 2)  We want to talk a bit more about the Bigger Picture.  Where do these transcriptions go after they get done!?  We have talked a lot about the scientific uses of these data, and individual projects, but there is a bigger mission and one the Museum world is grappling with right now — how to simultaneously live in an analog and digital world.

Before we talk more about the Big Push to digitize records and get them mobilized for the good of society, lets do something a bit more close to home.  Below is snapshot of an intensity map which shows work done by transcribers state by state.  We focus on the United States here simply because we have had good dropdown list for USA states and could therefore easily get this map made without too much muxing.  We have gotten have gotten a lot of help from transcribers in other counties and you can see more about that in our previous post. You can explore the map in more detail:  click here to see the map .   We made this by simply tallying each record with a particular name of a state, and then linking those state names using a service provided by Google called Fusion Tables.   California (with 64,346 transcriptions) and Florida (with 21,283) make up a lion share of the transcriptions, but there is a lot of effort in the Southeast and West as well.  All things one might expect given the regional foci of CalBug and SERNEC.  Surprising, North Dakota has 1,518 transcriptions completed and Minnesota 2,109!  Go Upper Midwest!

Screen Shot 2013-07-17 at 4.08.53 PM

Merge of nfncountrystateCOUNT and US Regions State Boundaries

All this work really does feed into a larger effort that is happening here in the United States and around the world to make museum data available for broad use.  This isn’t just for scientists, but also for formal and informal science education and the broader public.  Museum specimens are obviously of great value — they even tell us more than the who, what, where, when which serves as a basis for documenting trends in changes in distribution and seasonal and yearly timing events such as emergence from hibernation.  Each specimen yields further secrets — whether it is DNA that can be extracted from the tissues, body size and relation to physiology, and so on.  They also tell stories about landscapes and peoples in the past, and about our own histories.  In this sense, natural history tie into the much larger picture of multiple cultures.

Up until recently, if you wanted to see this vast treasure trove of data, you had to get a special pass to enter the collections, and there under the watchful eyes of curators and collections managers, you could examine specimens.  Museums have always been places where visitors are most welcome, but physically moving around specimens, and figuring out which collection had what remained a challenge.  While access is critical, museum curators have to balance considerations related to the conservation of these precious objects.

In the last ten years, a revolution is unfolding and museums worldwide are digitizing their collections so that the contents can be discovered, searched, and used more effectively and by more people.  This work is very challenging.  Many folks involved in this endeavor have lamented that years of databasing and a lot of time and effort invested in building system to publish data and make them available… and still only 2-3% of the total number of records in museums (based on our best estimates) are digitally discoverable.  We have to hope there is a way to make this whole process more efficient.

So at some point, CalBug and SERNEC will take the hard work done by transcribers and make those digital records available to everyone.  You can see some of the progress that has already happened by checking out projects such as VertNet, GBIF, Map of Life and iDigBio. One of the goals of these projects is to bring together data from various sources in order to create a “one stop shop” for the discovery of biodiversity information.

In sum, the bigger story is that we are witnessing a revolution in how museums make their resources available.  Thanks for taking part and viva la revolucion!

-Rob Guralnick

National Moth Week

Did you know that July 20-28, 2013 is National Moth Week?  You can take your love of the Notes from Nature CalBug moths beyond transcriptions by participating in moth observations in the natural world.  Check out details for participation here:  http://nationalmothweek.org/

Calbug’s Dragonfly Research

If you are working on Calbug transcriptions, you’ve probably seen some dragonflies and damselflies pop up.  So, I wanted to take the opportunity to let you know how I’m using data from these specimens in my Ph.D. research.

But first, why study dragonflies?  First of all, these charismatic aquatic insects have been well-collected over time, making them good subjects for studies of change in community composition and distribution. Dragonflies also have a range of known pollution tolerance-levels and are useful indicators of general habitat degradation for freshwater habitats. They may be particularly good indicators of biological effects of climate warming. Studies in Great Britain have shown that the ranges of many species have expanded, range boundaries have shifted northward, and first-flight days are occurring earlier as a result of climate warming since 1960. Many of these changes are occurring faster or are more pronounced than in other groups. For example, one study found that dragonflies in Britain have experienced range shifts averaging 88 kilometers (km) northward, compared to 53 km for butterflies. Overall, dragonflies tend to like warmer habitats, and their high dispersal ability may allow them to respond more quickly to climate warming. At the same time, some species, usually those specialized for stream habitat or certain types of wetlands, are experiencing significant range reductions.

Eight-spotted Skimmer, perching. Photo © Ray Bruun

Eight-spotted Skimmer, perching. Photo © Ray Bruun

California is an interesting place to study changes in aquatic insect communities, because this relatively dry region has experienced drastic changes in aquatic habitat over the past 100 years. For example, irrigation for agriculture across the previously dry Central Valley has created more permanent freshwater habitats throughout the summer. The state has also experienced a dam-building frenzy over the past 100 years… 1400 dams now block the flow of every major river and most minor ones across the state. This eliminates significant portions of flowing water habitats and increases the amount of lake-type habitat. The human population of California has also dramatically increased from around 2.7 million to 37 million people over the past century. So, water demand is high and landscapes are becoming more and more dominated by urban areas and agriculture. So, how are these changes influencing plants and animals?

My research addresses this question by focusing on dragonflies and damselflies, collectively known as Odonata or “odonates.”  In one study, I’m using the locality and date information for each specimen in our collections to compile species lists for different California counties and time periods. The goal is to identify changes in odonate communities—such as species richness and the percentage of habitat specialists versus generalists—from the species lists, and identify species that are expanding or contracting in distribution. Museum collections, however, have some problems with their data, as you probably are beginning to realize after participating in the data entry! One is that collecting effort varies for different regions and time periods based on the interest of collectors. We can try to correct for this using a combination of statistics and smart data selection. For example, some researchers have used a relatively new statistical method that incorporates the length of species lists for sites or regions as a measure of effort for that area. This assumes that regions with longer lists had higher effort (an assumption that often, but not always, holds true). In regions with short lists, you would expect to find more species than were actually present in the records. In particular, some species that are harder to find or are less common may occur in more regions than what is represented in the collection. After accounting for effort, the ultimate goal is to determine whether changes in landscape variables, such as temperature, precipitation and human population influence communities across regions.

I have also resurveyed sites originally sampled by C.H. Kennedy (a collector you may come across!) in 1914. While he left comprehensive lists of species collected at specific sites throughout California and Nevada, he did not indicate the dates that he visited each site in his notes!  So, I used information from the specimens to reconstruct specific dates that Kennedy sampled each site, and then visited the sites within a week or so of the original sample date. In preliminary work comparing his surveys to my own, I have found that communities are becoming more similar across sites—we are seeing a homogenization of dragonfly communities, which may reflect the spread of urban and agricultural landscapes.

Hopefully, this gives you a taste for how we might use some of this data. We will keep you posted on the results!  And, feel free to email me, at jball@berkeley.edu , for more information on this research.

– Joan Ball

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