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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!

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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

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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

Calbug fields and photos

Recent comments and questions in the discussion boards have drawn our attention to aspects of transcribing that were not clear. So, we changed a couple of things.

First, we removed the Host, Latitude and Longitude fields, because many of our labels do not contain this information.  Instead, we added an “Other Information” field where you can enter any information that is not included in the other fields. As explained in the help text, this includes things like the collecting method (e.g. malaise trap), collecting times, name of host plant, etc.  Previously, it was unclear whether you should enter locality information exactly as on the label or if you should interpret information, like abbreviations. Because many people are transcribing this highly-variable information, we would like you to enter the locality exactly as it says on the label. Otherwise, we will end up with multiple interpretations of the same locality. One exception is if there is an obvious misspelling that is not an abbreviation—it would be helpful if you use the correct spelling. Please keep looking up the country, state and county information if they are missing from the label. But, keep a lookout for locations with multiple potential counties, and do not enter a county if this is the case.

In the future we may call on you again to help us geographically reference (“georeference”) these localities. That is, determine the latitude and longitude of the localities and estimate the uncertainty around those points. It makes more sense to us to wait until we have completed the data entry so that we can group the records by locality and georeference each locality just once.

You may also have noticed that the photo quality for some of Calbug’s recent photographs is not very good. That’s because when Calbug started, we used different methods for photographing and a different type of camera. Don’t worry, the bad photos will be increasingly rare in the future.  To get an inside look at how we are taking photos now, check out this instructional video that we made last year for students and staff imaging our insect specimens.

-Joan Ball

What happened to the transcription progress?

One of the questions we have been grappling with at Notes from Nature is how to add more specimen images to the application while still showing a clear path of overall transcription progress.  On the one hand, we have many more specimen images lined up from both CalBug and SERNEC, and need to keep expanding the pool of interesting and scientifically important collections being transcribed.  On the other hand, we don’t want Notes from Nature citizen science transcribers to become frustrated by a seemingly bottomless pool and confused by constantly increasing and decreasing progress bars.  In attempting to address this challenge, we’re going to do some small tests.  We’ve added some new specimen in recent days, and would like to hear what you think about these additions.  Among the new additions, we have about 74,000 new bugs, including many bombardier beetles, dragonflies, and damselflies, as well as about 13,500 new plant specimen.  Do you like that we’ve added these new specimen images?  Were you worried by the drop in transcription percentages?  Should we work to complete “missions” with smaller subsets before adding more content?  Whatever the case, check out the new specimen on Notes from Nature!”

Tending Our Notes from Nature Garden

Sometimes in the shuffle of getting things done, we forget to explain the simplest things.   For example, where do all these images come from?  Are there more to do when these are done?   What the heck is a CalBug or a SERNEC?

So lets answer some of these questions as best we can.  As we mentioned in the “About” section of Notes from Nature, CalBug and SERNEC are both regional consortia of natural history collections — CalBug focused on western North American (predominately) insects and SERNEC on southeastern United States plant specimens.

Lets turn to the SERNEC records first.  Right now the following herbaria  (or single plant collection) are featured on the site:  The R. K. Godfrey Herbarium at Florida State University, with 8,368 specimen images available and the Mountain Lake Biological Station Herbarium at the University of Virginia with 6,990 specimen images.  Soon we plan to load a third collection of 13,511 images from the herbarium at the University of South Alabama.   This represents a small proportion of the millions of specimens found in southeastern United States herbaria, so there is still a LOT of work to do here.

CalBug has about 230,000 images already taken,of which ~33,000 have been already made available via Notes from Nature, with another 28,000 to be added shortly.  These mostly come from the Essig Entomology Museum at U.C. Berkeley but also from U.C. Riverside and the California Academy of Sciences.  CalBug will also be adding more images in the future.   The ones there now represent a select group of insect taxa including: bombardier beetles  (genus = ‘Brachinus’ or genus = ‘Metrius’), cuckoo wasps (family = ‘Chrysididae’), odonates or dragon flies,  (order = ‘Odonata’), skippers (family = ‘Hesperiidae’), and tiger beetles (genus = ‘Cicindela’ or genus = ‘Omus’ or genus =’Amblycheila’).

Video from CalBug

Like the CalBug portion of Notes from Nature?  Take a few minutes and view this video that they produced about the need for entomological museum collections and some of the challenges that they face.  It’s all part of the strategy for understanding global change.  See video here:  Global Change and CalBug

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