The Biodiversity Institute’s Genetic Sequencing Facility
A recent NYTimes article highlighted research identifying the existence of two elephant species in Africa. This is an important discovery not only for conservation purposes, but also because the researchers at Harvard, the University of Illinois and the University of York used new DNA sequencing technology that gives a much fuller picture of a critter's DNA.
My work at the Biodiversity Institute's Genetic Sequencing Facility directly relates to this kind of research. DNA sequencing data is ideal for studying cryptic species - different organisms that appear in many ways to be the same species, but may or may not actually breed with each other. Sequencing provides DNA characteristics that may help scientists figure out how many species are in a given population. Simply put, they may look the same on the outside, but their DNA sometimes shows otherwise.
The elephants discussed in the article aren't cryptic per se; they were utilizing different habitats. But there might not have been enough different physical characteristics to recognize them as distinct species. With this new study, scientists surveyed nearly 40,000 DNA base pairs. We (the Biodiversity Institute) and many other research centers do this type of thing on a regular basis, only on a smaller scale. Instead of sequencing hundreds or thousands of pieces, we may survey 2,000 to 4,000 base pairs.
It sounds like this is the first major paper to use new generation sequencing systems (that can run a cool $500,000) for a group of species. The other outstanding thing about the study is they used DNA from an extinct North American mastodon!
Please congratulate Dr. Matthew Gimmel on his acceptance of a 2.5 year European Social Fund postdoctoral fellowship to work on beetle systematics in the lab of Dr. Milada Bocakova, Department of Biology, Palacký University, Olomouc, Czech Republic. Since graduating from Louisiana State University (Dr. Chris Carlton's lab), Matt has worked as my lab manager, helping so much with my Peru project: processing an unbelievable amount of specimens, overseeing undergraduate assistants, helping to mentor undergraduate researchers in their manuscripts. Indeed, his enormous knowledge of beetles, coupled with his generosity, patience, and enthusiasm, has made him a wonderful mentor to all in our unit. Now, we must race to submit our first manuscript together — on Peru beetles, of course - before he departs Kansas for Europe.
The Chaboo lab hosted Sara López from the Ciudad Universitaria (UNAM) and the Departament of Zoology, National Collection of Insects, Mexico City, Mexico. Sara is conducting M.Sc. research on a revision and phylogeny of the genus, Ogdoecosta (Cassidinae: Mesomphaliini). Several cassidine genera have most of their species distributed in Mexico, and Ogdoecosta is one of them. Sara’s phylogenetic matrix will open new research into the biology of this little known group. We had a super time discussing morphology, characters, biology, and combing historical literature for clues of new characters, to understand how important researchers like Spaeth and Boheman defined the genus and species. Good luck to Sara in completing this important new work in Cassidinae and in becoming a badly-needed expert of the Mexican chrysomelid fauna.
Caroline Chaboo, Riley Wertenberger (KU undergraduate), and Josh Cunningham (Haskell U. undergraduate) led an outdoor insect discovery class for the Stepping Stones, Inc. school, Lawrence KS, on June 7, 2012. Fourteen 7-10 year old school kids and their two teachers were armed with insect nets and large vials and shown how to net and sweep sample insects in the Rockefeller Prairie, KU Field Station. The kids were excited to catch, study, and release a wide variety of live insects and learn a little about the prairie ecosystem.
KU Entomology has enjoyed a long tradition of weekly lunch talks given by resident entomologists and visiting colleagues. This spring, I am handling the speaker schedule, which has been a piece of cake since we are enjoying a flow of short and long-term international and domestic visitors. Dr. Barbara Hayford, a KU alumnus who is now at Wayne State University in Nebraska, spoke recently on her work, "Use of ecological niche modeling to extend knowledge on biodiversity of midges (Diptera: Chironomidae) of Mongolia. I was a M.A. student here when Barbara got her first phone call inviting her to join the Mongolia research team. It was great to hear how this program evolved 12 years later.
Another colleague, Dr. Mary Liz Jameson at Wichita State University, presented her latest research, "Scarabaeoid beetles of the West Indies". Her graduate student, Christian Beza-Beza, spoke on the Phylogeography of the Ogyges laevisimus species group and its implications for cloud forests in Guatemala (Passalidae), while her other graduate student, Mathew Moore, spoke about the biology and phylogeny of Cyclocephalini beetles (Scarabaeidae: Dynastinae). Mary Liz also overlapped with my student days at KU, so it was super to have our students meet and work on cool beetles from my Peru inventory. Their visit was timely — some identified specimens are now on display in the Peru exhibit in the Spencer Art Museum.
What an exciting day to participate in the installation of specimens and other objects in the upcoming exhibition, "39 Trails: Research in the Peruvian Amazon", curated by Dr. Stephen Goddard of the KU Spencer Art Museum. The 2011 field course in Madre de Dios, Peru, has been so rewarding in research, publications, and specimens. And now an insect-themed exhibition....in an ART museum!
Dr. Goddard and the exhibition designer, Richard Klocke, are putting finishing touches in the small display cases, closing up completed cases, and preparing the final labels and clean up. Apart from materials of individual researchers, we placed three drawers of insect specimens on display.
Richards' exclamations over these specimens were a reward in itself: for the sheer beauty of bugs and also for our hard work on diversity research in Peru.
The Aug. 6 edition of the Proceedings of the National Academy of Sciences included a large-scale analysis of bony fishes using DNA sequencing. One of the major conclusions is that tarpons, eels and their relatives (Elopomorpha) is the sister group (branched first) of all living teleosts.
Gloria Arratia, research associate in ichthyology, first published this idea in 1997 (see reference 11 in the PNAS paper). Her conclusion was based on morphology. In short, molecular analysis confirms a careful morphological analysis conducted about 15 years ago. More interesting is the fact that Gloria’s results were not widely accepted because the dominant figures in the field had championed the idea that the Osteoglossomorpha (mooneyes and bonytongues) were below the tarpons and eels on the tree. This inhibited some other ichthyologists from accepting Gloria's findings, in spite of the fact that she had the evidence and presented it clearly.
Ornithology graduate student Michael Andersen and Curator Rob Moyle are presently in Fiji, carrying out their third sampling trip across the Fiji Archipelago. They are focusing their time on Taveuni Island, which has not been sampled by ornithologists since the 1920s! They will be returning home late in December.
Pete Hosner, EEB doctoral candidate and Ornithology student mentored by Rob Moyle, received notification that his NSF Doctoral Dissertation Improvement Grant proposal has been recommended for funding. The grant, entitled TESTING THE PLEISTOCENE AGGREGATE ISLAND COMPLEX (PAIC) MODEL OF DIVERSIFICATION IN CO-DISTRIBUTED AVIAN LINEAGES, has been recommended for funding for $14,866 over 24 months. The project will use multilocus DNA sequence data to discover whether there is a link between climate and sea level changes and diversification in eight "polytypic" bird species endemic to the Philippines.
In December 2010, KU Biodiversity Institute graduate student Mike Andersen, and curator of birds, Rob Moyle, completed a three-week expedition to Fiji. This effort marked Ornithology’s third expedition to Fiji, work that began in November 2009.
They collected specimens of 23 species from two locations: the isolated Nakauvadra Range in the extreme northeastern part of Fiji’s largest island, Viti Levu; and the southern island of Kadavu. The Kadavu specimens were the world’s first from this island with associated genetic tissue samples, and the collection included three endemic bird species: Whistling Dove (Ptilinopus layardi), Kadavu Honeyeater (Xanthotis provocator), and Kadavu Fantail (Rhipidura personata), plus numerous morphologically unique island forms such as Golden Whistler (Pachycephala pectoralis) and Collared Kingfisher (Todiramphus chloris).
The Nakauvadra Range is the third locality on Viti Levu where Biodiversity Institute researchers have worked, making it possible to analyze genetic differentiation among avian populations across this oceanic island. Andersen and Moyle are developing the Fiji project in close collaboration with students and researchers in the Institute of Applied Science at the University of the South Pacific. The collections-based research effort forms the foundation for Andersen’s dissertation research on the origins and diversification of the Fijian avifauna, as well as future dissertation projects by Fijian students at the University of the South Pacific.
Kadavu Honeyeater (Xanthotis provocator) is endemic to Kadavu Island, Fiji, and is the only member of its genus found in Fiji.
Male Whistling Dove (Ptilinopus layardi) is one of four endemic bird species on Kadavu Island, Fiji.