Blogs

Monday, October 10, 2011

Specify Software Sustains 20% Growth

Specify logo

Specify is now the database management of choice for over 375 biological collections worldwide. The Project is sustaining a 20% annual growth in the number of supported biological collections. In addition to offering research community software helpdesk support, the Project has produced 11 software updates in 2011, many of them extending and enhancing features researchers have requested for more effective management and analysis of specimen information.  Recent research funding awards by the U.S. National Science Foundation's 'ADBC' initiative for accelerating the computerization of information associated with biodiversity specimens have stimulated additional research repository adoption of Specify for their project data management.

The Specify Project has a number of new capabilities and releases planned for 2011 and 2012 including: (1) a Specify web client for remote access (editing, querying, reporting, etc.) over the internet to remote Specify databases (being developed in collaboration with the Swedish Natural History Museum), (2) release of the new Scatter-Gather-Reconcile or "SGR" capabilities which allow researchers to look for specimens which are related or duplicative to their own (in collaboration with the University Autonoma de Barcelona), and (3) innovative data entry software for acquiring specimen images for digital archives and specimen label data computerization.

The ultimate goal of mobilizing the locality, species identity, and collection date information associated with biological specimens into databases and onto the web is to provide easy open access to the information for biodiversity documentation and analysis, and for forecasting the impacts of climate change on species ranges.

Wednesday, December 22, 2010

A Symposium and an Ancient Seaway

This past month I co-chaired a technical session at the national Geological Society of America conference in Denver. The session was entitled "Paleontology, Paleobiogeography, and Stratigraphy of the Late Cretaceous North America Seas: A Tribute to Bill Cobban." Dr. Cobban is a scientist at the US Geological Survey who has over 60 years of experience working on the statigraphy and paleontology of the Late Cretaceous Western Interior Seaway. The Western Interior Seaway (WIS) ran through the middle of the U.S. during the Cretaceous (about 65-100 million years ago) and was home to some amazing seafaring creatures, including the mosasaur that hangs over the doorway to the KU Natural History Museum.

I gave a talk entitled "Using GIS to investigate bias in the fossil record: a case study of the Late Cretaceous Western Interior Seaway of North America." In that talk I presented some tests that I performed to assess how good the fossil record in the WIS is. I was curious if the fossil record is biased in any way that would prevent us from mapping out the ranges of prehistoric species. The factors that I'm particularly interested in are competition, environmental change, and whether biological interactions between species are more or less important than environmental changes in determining which species go extinct and which do not.

I relate my research to the current biodiversity crisis: when you are trying to understand how invasive species, habitat fragmentation, and climate change are going to affect species in the future, there is a WEALTH of information (~544 million years in fact) in the fossil record that provides exactly that. The fossil record tells stories of how critters responded to species invasions and habitat loss and it teaches us about the effects of climate change and sea level fluctuations. These are the very factors that conservationists consider when attempting to save habitats and species.

One of the symposium's invited talks was by Neil Landman, a renowned cephalopod paleontologist from the American Museum of Natural History. He spoke eloquently on the life history of scaphite ammonites. Scaphites are shelled cephalopods (similar looking to modern Nautilus, also related to squid and octopi), but instead of having a properly coiled shell (like the Nautilus, their shell straightens out a bit at the end. Neil is probably one of the world's expert on scaphites. His talk described his latest interpretation of how these animals caught prey, what kind of prey, how they swam, at what orientation they held their body in the water column, how they reproduced, etc. Late Cretaceous cephalopds got SUPER weird, so this sort of talk is *really* exciting for folks like me who are into cephalopods and life in general in the WIS.

Overall, we had a very nice day talking about the current status of Late Cretaceous WIS research from a variety of geologically related fields: geochronology (age-dating the rocks), biology (mostly cephalopods, but also foraminifera, mosasaurs, sharks, etc.), biogeography, mapping, stratigraphy, and biostratigraphy. We are still working to better understand a number of the animal groups and how they might be used to date rocks. The great news is that it looks like the fossil and rock records are good enough to test many of our questions!

Tuesday, November 30, 2010

Winter Orchids

winter orchid

When the cold winds of November tug the last leaves from the maples, basswoods, and elms, orchids probably are the farthest thing from most Kansans’ minds.  However, fall, winter, and early spring are the best seasons to search for one of the state’s more secretive plants – the puttyroot orchid or Adam-and-Eve [Aplectrum hyemale (Muhl. ex Willd.) Nutt.].  The plant’s specific epithet “hyemale”, referring to winter, alludes to the plant’s habit of producing a winter leaf.  The name puttyroot is a reference to sticky substance released from the crushed tubers, which usually occur in pairs (hence the name Adam-and-Eve).

Puttyroot has evolved a fascinating strategy to survive in the low-light environments of rich, deciduous forests.  As forest canopies develop in the spring, light limits the ability of understory plants to photosynthesize.  Consequently, many herbaceous species flower and fruit in the spring, before the canopy fills in, or in the fall, when the canopy begins to thin.  Puttyroot takes this strategy to an extreme.  Each plant produces a single, elliptic, dark green, pleated, 3-6 inch-long leaf in the fall.  The ground-hugging leaf remains green and photosythetic from fall through winter and into spring, producing sugars needed by the plant to grow.  From late May into mid June, some plants will produce a single, 10-20 inch-tall flowering, each bearing a dozen whitish purple or brownish white flowers near the tip.  Ribbed, pendent fruits – each about 1 inch long – mature through the summer and persist into the fall, leaving another clue to the plant’s presence.  

Populations of puttyroot are documented in 10 eastern Kansas counties (Anderson, Coffey, Crawford, Douglas, Franklin, Johnson, Leavenworth, Linn, Miami, and Wyandotte).  Most occur in moist, maple-basswood forests or cottonwood-dominated floodplain forests along rivers and streams.  Populations generally comprise a few, closely-spaced individuals, but large populations can contain several hundred plants.

The next time you head out to your favorite forest trail for a fall or winter walk, keep an eye to the ground.  If you are lucky, you may spy the distinctive leaves of this forest gem.  If you do find this rare Kansas orchid, plan a return visit to marvel at its amazing flowers and fruits in the dim light of the forest floor.

Wednesday, September 7, 2011

Waste Not, Want Not

fish

Like any good ichthyologist, I keep saltwater fish.  When I lost a Banggai cardinalfish recently, how did I deal with this tragedy? Not by flushing it or starting a pet cemetery, but by turning that loss into a gain for the Biodiversity Institute's Ichthyology collection. 

It is true that aquarium fish make less than ideal specimens.  It is impossible to get accurate, reliable information on the natural habitat, behavior, distribution, and population structure of such a specimen.  However, for large-scale genetic studies, a specimen without such data can still provide valuable insight into the evolutionary relationships among fish species.  Likewise, we can gain important morphological information to further inform our ideas on the evolution of structures like jaws and tails.

So how does a fish reach scientific immortality after passing on to the great aquarium in the sky?  First, and not surprisingly, it's important to get the fish into the freezer as soon as possible to keep it from decomposing (genetic material starts to break down quickly as the fish decomposes).  When we are ready to process the fish, we first take photos of it, since preservation often causes bright colors and patterns to fade. Then a small piece of muscle is taken from one side and added to our tissue collection--this leaves the other side of the fish intact for morphological studies.  We then inject the fish with formalin and store it in alcohol, or clear and stain it.

While at first blush this may seem perverse, my cardinalfish now lives on as frozen tissue and fluid specimens, where it will provide valuable genetic and morphological information for researchers and students.  I know I would much prefer that to being flushed.

Tuesday, August 2, 2011

Recent Discovery in China Relates to KU Research

fossil

While a recent discovery may change textbooks and the way that many scientists think about bird and dinosaur evolution, it comes as no surprise us.

This week, Xing Xu, H. You, K. Du and F. Han published in the journal Nature a reanalysis of early bird evolution. The analysis knocks Archaeopteryx off its perch as a grandfather to later birds. 

KU has been the central hub for the discovery of the fossil bird beds in the Early Cretaceous of China with the description of the primitive bird, Confuciusornis, and has continued to be involved with all the new discoveries coming out of this region in part through an alumnus of the KU vertebrate paleontology program.

The alumnus, Zhonghe Zhou, presently leads Chinese studies in that region and was recently elected to the prestigious National Academy of Sciences.  Zhou and one of the paper’s authors, Xing Xu, had already precipitated a revolution in our understanding of bird evolution with the discovery of the four-winged gliding bird/dinosaur, Microraptor. With Microraptor, they showed that bird flight began with gliding. 

Zhou has a long-term collaboration with KU vertebrate paleontology researchers at the Biodiversity Institute. Preparator David Burnham, collection manager Desui Miao and I regularly visit China to work on early birds. Our research also has suggested that Archaeopteryx along with other archaic birds represents a side branch that split off much earlier than the new bird, Xiaotingia, and its sister Anchiornis, another four-winged gliding animal. 

While the recent paper in Nature calls these animals “feathered dinosaurs,” we think that they and their common ancestor with modern birds can be best considered true birds. Rather than removing Archaeopteryx from Aves because its avian features were shared with birdlike dinosaurs, we place a stronger emphasis on these features thereby pulling the dinosaur-like birds into Aves. This limits these flying, feathered animals to the Class Aves and pushes the origin of birds into the Early Jurassic or Late Triassic at about the same time as the dinosaurs themselves.

Friday, February 4, 2011

Lifemapper + VisTrails = Better Science

Lifemapper logo

We have combined Lifemapper and VisTrails software to create an intuitive and powerful new way to analyze species distributions. Lifemapper is our NSF funded species distribution mapping and modeling initiative. VisTrails is a scientific workflow management system developed by the Scientific Computing and Imaging Institute at the University of Utah.

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Workflow systems allow scientists to assemble complex computational pipelines consisting of sequential tasks which are stitched together using a single desktop software program. Typically an automated research workflow will start by inputting data from an external source, then dragging that data through one or more computational or modeling tasks, and then outputting the results in formats which can then be analyzed. LM3 LogoData output formats might include geographical maps, numeric data sets or statistically summarized results. Workflow management software is integrative by design and it is an excellent tool to connect internet data and computer processing services together across institutional and  discipline boundaries. VisTrails is particularly suited for our Lifemapper Project because of its capabilities for integration with internet-accessible data and services and because of its strength with capturing the metadata or 'provenance' information associated with research workflows.

We have developed software extensions that computationally integrate VisTrails' functions with our Lifemapper Project's web services for species distribution modeling. Technically, this integration includes interfaces to post and retrieve species occurrence sets from our installation of theVT Logo Global Biodiversity Information Facility's global database of museum specimen data points. This software integration allows biodiversity researchers to quickly compose and execute species niche modeling experiments, using VisTrails' drag-and-drop workflow creation software.  Our latest Lifemapper VisTrails software (version 1.1.0) introduces the following features:

Lifemapper Ecological Markup Language (EML) Reader Software

EML is a standard, XML-based language for describing and archiving all of the background information  or 'metadata' associated with research data sets in environmental biology.  The Lifemapper EML Reader software enables researchers who map and model species distributions to automatically store the metadata associated with a Lifemapper/VisTrails workflow (modeling experiment) in an EML archive file.  An EML file would include metadata on such things as sources and formats of input data, any pre-processing steps or data filters that might be used, parameters for the modeling algorithms, as well as information about the resulting output files. This new capability makes complex modeling experiments easier to manage, archive and reference.  Best of all, storing Lifemapper/VisTrails metadata in EML files, enables the species range modeling experiment to be easily re-executed by the same or other researchers.  Being able to fully reference, re-use, and repeat a complex computational niche modeling process directly results in more transparent and verifiable science.

Enabling VisTrails for OpenLayers Display 

OpenLayers is open source software product which enables the creation of sophisticated map displays with point and click manipulation functions such as panning and zooming.  With our latest LM / VT client release we have enabled VisTrails' output screens to provide these mapping functions.  These new capabilities in VisTrails greatly facilitate the research exploration of species distribution maps and model outputs produced by running VisTrails / Lifemapper workflows.

Simplified Algorithm Inputs 

In previous versions of our Lifemapper / VisTrails this integration, species model algorithm parameters had to be specified, even if using default values. While it is still possible to change model parameters, default settings are now automatically applied.

Simplified Inputs and Outputs 

VisTrails works with software modules that are selected from a screen listing and dragged and dropped into a workflow workspace.  Modules have data Inputs and outputs as data are brought into a workflow, streamed through various processing steps and then output for analysis.  In our latest software we have simplified input and output links for Lifemapper's species niche modeling components, which makes the creation of new workflows faster and easier.

Our Lifemapper / VisTrails client allows one to wield the power of the Lifemapper web services inside a desktop application.  Researchers can quickly connect elements together without worrying about the work behind the scenes.  No studying APIs.  No constructing HTTP requests.  Just click, connect, and go!  The Lifemapper / VisTrails client software can be downloaded from the Lifemapper Project web site at: http://lifemapper.org

For assistance with installing or using Lifemapper / Vistrails software for research, send e-mail to: lifemapper@ku.edu or call the helpdesk at 785.864.4400.

Saturday, January 28, 2012

Venezuela 2012, part 1

Greetings from San Carlos del Zulia, Venezuela. I'm a bit over a week into my first expedition of the year — this one to continue our aquatic insect survey efforts in Venezuela. We've spent he last 8 days driving around the country and splashing around in various rivers and lagoons. It is hard for me to believe, but this is my 10th trip to Venezuela since my first in 2006. And, in terms of general volume of material and 'good stuff', this might be the best. We hit the dry season perfectly — when it is well underway and rivers and low and lagoons are reduced, but before things really get dry. A number of great sites on this trip, and it will take months get through these dense samples when I return. One highlight was getting up high in the Andes and collected at some lagoons over 12,000 feet — the highest we've gotten samples to date. More soon.

Tuesday, December 30, 2008

And so it begins

It has been a long but nearly flawless 15 hours of traveling today, beginning with the 3:30 a.m. shuttle pick-up in Lawrence to clearing customs in Maracaibo, Venezuela, at 8:30 p.m. (quick fact: Venezuela has its own time zone, which is 30 minutes ahead of Eastern Standard Time). My colleagues from the Universidad del Zulia, Mauricio Garcia and Jesus Camacho, greeted me at the airport. We retired to Mauricio’s house to unwind and catch up for a couple of hours.

The immediate issue upon arrival that always splashes me in the face like a bucket of cold water is switching over exclusively to Spanish. Usually it takes me a week to get back up to a functional level. Having only been gone for 5 months, it shouldn’t take very long. On the plane there was some confusion over seat assignments, and I got some very strange looks when I was trying to sort it out. Later I realized that I had confused the words “sentarse” (to sit) and “sentirse” (to feel), and had essentially been saying something like “I think I’m supposed to feel there” and “I can feel where you were feeling.” The next few days of the trip will be devoted to some of the more mundane housekeeping and logistical issues, such as making and confirmation reservations, scouting a few local field sites before the full field crew assembles, and getting all our gear in order and packed in a semi-efficient manner. Of course, celebrating the New Year will be thrown in there as well. The main expedition does not start until next week, after my other US collaborators arrive.

Tuesday, December 30, 2008

Clean water

Curious children often observe scientists such as my collaborator, Mauricio Garcia, whenever we're collecting insects

Mauricio, Jesus and I scouted a few new field sites today in the Serrania de Perija- the mountainous border region that forms the western boarder with Colombia. Just a few hours from the relatively affluent oil city that is Maracaibo, the roads gradually narrow into small dirt paths winding around large rural haciendas (ranches) and indigenous communities. Cars give way to burrows and horses as the primary (and functional) means of transport.

Sunday, August 2, 2009

Endgame: Caracas for a course on biodiversity

The last week has been a bit hairier than normal. Joined by another Colombian water beetle student, we flew down to Puerto Ayacucho in southern Venezuela to scope out some new sites. No need for details at this point but things did not go quite as planned. The fact that an American and a Colombian were traveling together along the boarder with Colombia the day after Venezuela shut down all relations with Colombia because of perceived US military aggression (likely) played a role, if you are curious. But, enjoy the two landscape photos of this area below that make it one of my favorite places in the world. After a very (very) long, 13 hour bus ride, I'm now in Caracas to participate in a Neotropical Biodiversity course put on by IVIC (the national Venezuelan Institute of Scientific Investigation). My 30 minute talk tomorrow will be the first full-length presentation I attempt to give entirely in Spanish...we shall see how that goes. This marks the final phase of the trip...I return to Kansas on 6 August.