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.
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.
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.
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: email@example.com or call the helpdesk at 785.864.4400.
We woke up at 4 o’clock this morning and we’re on the trail shortly before 5 a.m. We were planning to reach the summit of Voltzberg to watch the sunrise. Of course, this meant we had to hike there in the dark and there is really only one way to describe pre-dawn jungle: pitch black. If you get stuck in the jungle at night, without a light source, you better just hunker down and pray for morning because you are in for one terrifying ordeal.
After about a thirty minute hike, we arrived at the base of Voltzberg. For the next twenty-five minutes, we scrambled over slick boulders, dodged a column of army ants (which zigzagged over our path no less than four times), tried our best to avoid prickly and spiny plants (which is difficult because it seems like every tree, bush, fern, and flower is armed and ready for battle), and silently hoped that no snakes would decide to fall on our heads. Once we had cleared the tree line, the real fun began. The next stage of our ascent involved scrambling up several hundred feet of algae-coated, dew-slicked granite (which rates about a 9.413/10 on the International Standardized Slipperiness Scale). However, that wasn’t all. The slope of the mountain was steep to say the least and I swear there were times when we were going almost straight up. The combination of the terrain and the exacerbating conditions made for a climb that was mildly nerve-wracking at times.
However, we did all make it to the top and almost right as the sun was breaking through the clouds. It was a truly magnificent and spectacular thing to witness with the clouds rising over the jungle and the fiery, orange sun rising next to the adjacent inselberg.
A major Midwest snowstorm during the Christmas holiday delayed the 36-hour journey for our intrepid herpetology team, but we eventually made our way from snowy Lawrence to the Kansas City airport. The very long plane trip to Manila included a layover in Minneapolis and a layover in Japan.
Over winter break, Herpetology curator Rafe Brown is leading a team of KU students to the Philippines. The group's research will help scientists better understand the biodiversity of the Philippines, an archipelago of some 7,000 islands.
I am a new graduate student in the Division of Herpetology in the EEB department. I am interested in studying the evolutionary history, biogeography and morphology of frogs from Southeast Asia.
This will be my first field expedition and I’m very excited. I will on this trip from December 30th, 2009 to January 21st, 2010 with several others from the KU EEB department. We will be going to Mt. Palali, in the Caraballo Mountains of Nueva Viscaya Province, in the Philippines. The purpose of this trip is collect specimens that will be used in current and future research involving the biodiversity of the Philippines.
Today I made the big hike up the mountain to our first campsite. The hike was ridiculous. Five hours of scrambling up the mountain rainforest. We started at about 200 meter elevation and ended at 1432 meters. The path was steep and slick with mud. After the first 30 minutes I thought I was going to throw up! I think that was because I was trying to keep up with the porters. Aloy, Perry and I ended up going at a slower pace that was exhausting, but doable. Despite thoughts of my legs giving out from under me midstep, I was having fun hiking through my first Philippine rainforest (my first hike in Asia, really). The rainforest was wonderful – full of trees, vines, bamboo, epiphytes, bird and insect calls, and the occasional giant, mossy boulder. Victory was sweet when I finally made it to camp covered in mud, sweat, Mt. Palali dew, and a little dash of blood.
We made the hike in five hours. The day before, the boys took eight hours. Of course, the boys had to carry their big packs for a good portion of the hike while I only had my daypack. If I had to carry my big pack, I think my heart would have exploded. I wonder if I can hire a porter to carry me down the mountain when it’s time to leave?
For future reference, here’s a quick list of our field team for this expedition:
University of Kansas — Rafe, Luke, Luis, Anthony, Brian, and me. Luis is collecting birds for the ornithology department and the rest of us are collecting reptiles and amphibians
National Museum of the Philippines, PNM — Arvin (herpetologist), Rolly (ornithologist), Josefa (mammalogist), Perry (entomologist — ants, specifically).
Wildlife Conservation Society of the Philippines, — Aloy (mammalogist)
Project Team — Enteng, JB, Nevong
On the last night at Barangay Maddiangat, the town officials hosted a dinner for us. I guess one of the assistants to one of the officials was really charmed by me. Peelan (sp?) couldn’t really speak English, but the officers and the Philippino members of our field trip were more than willing to pass on the message that he wanted a picture with me. Over a few bottles of tanduay and leftovers from the dinner, my conversation with the town officials took an unexpected turn near the end of the evening. It went something like this:
“Peelan here is a good man. Thirty years old.”
“Oh…ummm. That’s great?”
“Do you remember having that big green vegetable on Mt. Palali? Sayote?”
“Yes…I think so”
“Well, if you marry Peelan, you would have all the sayote that you want. He grows it on his property”
“Oh, really? Well…ummm..”
“He also drives a motorbike. You could take rides on his motorbike”
Rafe took plenty of pictures of me and the town officials and Peelan during this exchange of words. I still don’t know how serious they were about this marriage proposal. Hmm. Thankfully Peelan was carried off by his boss in a drunken stupor, so I never had to give him a final answer. Enteng was especially amused by this and said that I will be dreaming about Peelan and muttering his name in my sleep now.
Overall I thought my first field expedition was a success and very memorable. I learned a great deal about the herpetofauna of the Philippines and what’s involved in field work. It’s quite exciting and a lot of fun — a real adventure in my eyes.
I’m in Manila, flying home tomorrow on the 21st. Let me sum up my last few days at the Barangay Maddiangat. Again, cold, rainy weather resulted in poor collecting at our third and last site. We collected about 580 specimens total on our three week expedition. I think we were estimating a collection size of 600 to 800 specimens. I was really hoping to find some Draco — the flying lizard. Arvin had miraculously caught a single specimen up on Mt. Palali near the end of our stand on the mountain. We never caught any Varanus monitor lizards that were thought to be on Mt. Palali either.
This poor weather led to a large amount of downtime while staying at the Barangay Hall and resulted in me spending a lot of time with that group of Maddiangat kids. We played tag, basketball, hide-and-seek, and kick ball. I loved making them laugh. They sang me songs they learned at school and tried to teach me some words in Tagalog. I watched cartoons with them on the television set in the Barangay Hall. They were a great little group of kids and I absolutely loved having a chance to interact with them. One day they watched us prep specimens and they got a crash course on the herpetofauna of their town and Mt. Palali.
Words they taught me (that I still remember — after confirming the proper spelling in my dictionary):
Flower — Bulaklak
Lizard — Butiki
Frog — Palaka
Snake — Ahas
Rain — Ulan
Stone — Bato
On the 18th, we had driven three hours away to a nearby lime stone cave system in search for geckos. We only manage to bring home a tail from a single skink. Fantastic cave system, though. We were up to our waists in water for part of that little adventure.
On the morning of the 16th, we hiked down from the second camp to spend a few days herping around the Barangay Maddiangat (elevation 200m) at the base of Mt. Palali. Once again, unexpectedly cold weather at the second camp resulted in low amounts of specimens being collected — at least for the herpetologists. I think the ornithologists were doing really well the whole time on Mt. Palali. Hopefully the lower elevation of Maddiangat would have hotter, more humid weather that would result in better herping conditions.
After we arrived at the baranagy hall (where we’d be camping out of), the boys and I walked across the street to a sari-sari store and we pigged out on junk food. Sari-sari stores are little food stands that are brightly decorated with all different types of cookies, crackers, chips, sweet bread, and candy. Any single item averages about 5 pesos (about 10 cents USD). Camping across from one of these little gems of the Philippines has led to me making several trips a day to purchase and consume junk food that has fueled a sugar high that has spanned across these past few days.
At night we have tried herping at a few different locations, but sadly the most common herp in town is Bufo marinus — the cane toad. In short, it’s an invasive species from central America that people purposefully introduced into the Philippines (among other countries) to help with pest control. The cane toad, unfortunately, prefers a diet of local frog species over agricultural pests.
I have befriended a group of local kids that use the Barangay Hall as a playground. They call me Madam Allie. And now the other members of the field team call me Allie Palali.