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.
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.
In the five years since the fungal disease white-nose syndrome was discovered in New York, the disease has spread to more than 190 sites in 16 eastern states and two four Canadian provinces. At one Canadian site alone, 5,000 bats died.
In this week's ScienceNews, the bats -- and the scientists working to study the disease -- are the subject of the cover article.
Named for its devastating impact, the fungus, Geomyces destructans latches onto living bats in the dead of winter. The fungus takes root during the winter hibernation period for bats such as the little brown bat, which suffers a 90 percent mortality rate from the fungus. At one New York location, the number of bats hibernating there went from 200,000 to only 2,000 in just three years.
Scientists aren't just documenting the disease's spread and its potential devastation to ecosystems. They are also looking for antifungal solutions to halt the spread of the disease or help the bats resist it.
You can read more this research in the latest issue of ScienceNews (https://www.sciencenews.org/article/helping-bats-hold)
Fieldwork may be completed for this season in Peru, but now we must shift our focus to processing the thousands of specimens we have brought back with us. Since the specimen bags (whirlpaks) travelled back without preservative Ethanol,we spend a week adding EtOH to this large volume of samples. It is a smelly job: if the samples were left untreated, these precious specimens would rot. Finally, we store the collection (in a fridge) to sort each bag. It is a long road before we can have a beautiful identified pinned collection sitting in a drawer in our entomology collections.
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.
Summertime means summer fieldwork for many academic scientists, but some researchers skip the far-flung places in favor of urban habitats close to home.
There are plenty of places to look at adaptation and evolution in cities, notes a recent article in the New York Times. Reporter Carl Zimmer talked with biologists who study urban populations such as mice, ants and fish inside the city's borders. The scientists included Dr. Jason Munshi-South, who is tracking changes in urban populations of animals. Munshi-South is studying white-footed mice, which inhabited the forests that became New York City, and over generations have adapted to city life.
Munshi-South studies mice he finds by visiting parks around New York such as the 130-acre Highbridge Park. Using DNA analysis, he and his colleagues have found that the populations of mice in each park are genetically distinct from the mice found in other parks.
There are many examples of urban adaptation, the article notes: "White-footed mice, stranded on isolated urban islands, are evolving to adapt to urban stress. Fish in the Hudson have evolved to cope with poisons in the water. Native ants find refuge in the median strips on Broadway. And more familiar urban organisms, like rats, bedbugs and bacteria, also mutate and change in response to the pressures of the metropolis. In short, the process of evolution is responding to New York and other cities the way it has responded to countless environmental changes over the past few billion years."
Other scientists interviewed study populations of ants within the medians of New York City street, and the affect of PCBs on Hudson River fish.
Closer to home, Biodiversity Institute scientists have looked at populations at parks and wildlife areas surrounding Lawrence, and once even documented a giant resin bee in a Lawrence backyard. The bee turned out to be the first one (http://www2.ljworld.com/news/2009/jan/12/beekeeper-elective-course-piques-interest-insect/) authoritatively identified west of the Mississippi River.
Check out the full article about New York biologists and their urban research here (http://www.nytimes.com/2011/07/26/science/26evolve.html?_r=2&hp&)
Costa Rica has been a blast! From collecting beetles in pristine rainforest to relaxing outside Kiri Lodge on a warm tropical night, Costa Rica has exceeded my expectations for an international expedition. Firstly, all the people we came into contact with were pleasant, generous people who were always eager to help regardless of our lack language skills. I am very impressed by the Costa Rican people (especially Laura our hostess from Kiri Lodge) and their geniality has added immensely to our overall experience
Secondly, the country itself is beautiful with its misty mountains and luscious rainforests. Our week in Tapanti National Park gave us a glimpse of the diverse fauna and flora that makes this country so ideal for research. Lastly, our collaborators from the Universities of Delaware and Costa Rica were all excellent, amiable researchers. The graduate students from Delaware were always ready to help me with identifications and their jovial dispositions made the trip very entertaining. Despite our lack of communication, the students from Costa Rica helped us set-up traps and collect while their advisor, Monika, was perhaps the most helpful and likable person we encountered during our trip. My time in Costa Rica has been the most memorable trip I’ve experienced and I can say with certainty that I will return to this halcyon country.
I know it sounds cliché, but it’s hard to believe how fast the last two weeks have gone by. I have made plenty of memories: from wading across the Rio Orosi, to scrambling around rock seeps in search of Oocylcus, to humming the Jurassic Park theme with Frazier as we bounced along in the back of a pickup as it hurtled through the rainforest. I know I will never forget my time here in Costa Rica. I left the United States, a young, naïve gringo, and soon I will return a slightly older, ruggedly unshaven, moderately less naïve gringo who has had some of the coolest experiences of his life.
Eve of departure
End of an experience
Soon I will return
Rain, rain, rain. I am beginning to understand why it is called a “rainforest.” I feel like I have experienced more rain in the past several days than in the previous nineteen years of my existence combined. But hey, you need water to find water beetles, so I guess I shouldn't complain.
Yesterday morning, we went into the old growth part of the forest, where only a select few — including our sciency selves — are allowed to go. We were there to service the FIT traps that we had erected several days earlier. On the way up to the first trap we made an exciting discovery: tapir dung! While that may not seem like an incredibly sweet find to most people, I was really excited. A short while later, we encountered more mammalian awesomeness when we encountered a pair of coatis as they passed through the forest. They were quite wicked (in the New England sense of the word), especially as I had been keeping my fingers crossed in the hope that I would get to see them on this trip. All in all, it was a very successful day, as I finally got my tropical mammal fix (not counting the adorable, fluffy puppies at the lodge) on top of collecting a number of cool water beetles.
At first you won’t see many beetles…” a piece of advice given to me regarding collecting in the tropics. I thought that was a lie. I’ve seen the photos of brightly colored scarabs and blacklight sheets full of insects. This advice echoed in my head today as I entered the Costa Rican rainforest for the first time today. Sure enough, beetles did not throw themselves at me! I had to seek them out as I would in any other place. The beetles that I study for my dissertation research are known as riffle beetles, and they live in fast-flowing streams throughout the world. The first stop on the hunt for riffle beetles was a relatively small stream (or Quebrada as they are known in Spanish) draped in mosses and mist, close to the Lodge. I collected with the help of Frazier and the students from UCR. It took a few tries, but before long, we had collected a diverse batch of elmids. It looks like this is going to be a good trip after all!
I had my first in-the-field birthday today. Monica, a curator and professor at the University of Costa Rica whom has joined us this trip into Tapanti National Park, graciously baked us a b-day cake. I’m not big on celebrating birthdays, and I had in fact forgotten about today, so if it weren’t for, I’m assuming Andrew’s insistent pursuit, my birthday would have gone un-noticed/-celebrated.
Crystal couldn’t finish her dinner today, so I had both our dinners. Two fish heads were also consumed and on another note still no sign of an army ant emigration column. Unfortunate, considering I’ve seen more species, and genera, than last year’s trip in March.
Today’s agenda, for those that are keeping track was sifting, sifting, sifting.
The sole purpose of this post is to show off this giant leaf.