Trichoptera (Caddisflies) are insects whose adults look like moths, which are their closest relatives. Because Trichoptera larvae live in water, and because different species are differentially tolerant to pollution, quantitative sampling of these larvae is commonly used to monitor water quality. However, biomonitoring requires accurate taxonomy, which is currently unavailable for Trichoptera in the Tropics. With this research, a phylogeny representing 80% of the world's Trichoptera genera will be constructed from both molecular DNA sequence data and morphological data, and an accurate taxonomy for the group will be obtained. This new phylogenetic framework and classification will allow placement of newly discovered species and focused analysis on differential sensitivity of species to water pollution.
There is currently a large, independently funded effort to collect short pieces of DNA that can be used to quickly identify species by their unique DNA sequences (called 'barcodes'). Additional data will be collected in coordination with the Trichoptera barcode initiative in order to extend the utility of these sequences to phylogenetics. Training in all aspects of modern taxonomic and phylogenetic methods will be provided to undergraduate and graduate students during this research. This work will also have an impact on human health because Trichoptera are extensively used in biomonitoring for water-quality assessment.
The goal of our grant was to develop a phylogeny for Caddisflies (Insecta: Trichoptera). Data was collected from both PCR-based and "next-generation" techniques. The grant originally promised only the first of these, which were collected before 2010 for 250 caddisfly species. These data left several important phylogenetic questions unresolved. It became clear that the future of phylogenetics was in "big data" from new technologies. With this in mind, Kjer helped organize the 1KITE initiative (www.1KITE.org). This group collected transcriptomes from 38 caddisfly families. To fill out the remainder of higher level diversity in the group, Kjer and Frandsen collected 900 genes from 280 caddisflies, using hybrid capture techniques. Hybrid capture techniques target hundreds of individual genes, and can work with degraded DNA. All these data can be carefully merged together to generate a phylogenetic framework for the entire group. Caddisfly larvae live in water. With over 14,000 species, each with its own tolerance to water pollution, caddisfly bioinventories can be used to calculate water quality. However, larvae are difficult or impossible to identify. As a solution, we provided thousands of specimens to the Trichoptera barcode of life initiative. This initiative uses sequences of a short fragment of mitochondrial DNA in order to facilitate the identification of species from larvae, or other difficult to identify samples. With the samples we have provided, any caddisfly from anyplace in the world is likely to find a close match in this database. The 1KITE initiative, organized while Kjer was supported by NSF, has generated approximately 15 trillion nucleotides from 1400 species throughout the insects. The Trichoptera subproject within this initiative has successfully sequenced over 3500 genes, which will provide a resource for Trichoptera research in the future. Using Trichoptera transcriptome sequences to design probes, we were among the first to successfully use hybrid enrichment for insects. Since 2010, Kjer has been dedicated to generating genomic data, and teaching students how to analyze it. 1KITE was founded by Kjer, his former student, Xin Zhou (supported by NSF from 2003-2006), and Berhard Misof. Kjer brought his former student, Jessica Ware (supported by NSF 2004-2008) into 1KITE. Kjer’s student, Paul Frandsen was supported on this grant, and will be finishing his thesis in 2015. Paul learned to write computer code in both Python and C++ languages, and won a competitive Google "summer of code" fellowship, with which he developed a software program designed to generate partitions within genomic datasets. Paul already has offers for postdoctoral training. The grant also trained Dr. Robin Thomson under the direction of Ralph Holzenthal. Robin is currently the collections manager at the University of Minnesota. Postocs, Jessica Thomas, and Elizabeth Scott have found additional postodoctoral positions. Elizabeth Scott has successfully won NSF support for her project on frogs. Kjer has trained dozens of undergraduates in his lab. Most notably, Dhara Patel and Julianne McGlaughlin through the Douglass "women in science" program, and others through the Aresty research program at Rutgers. Kjer developed an undergraduate research program at Rutgers that has trained 60 undergraduates to collect, photograph, amplify and sequence Trichoptera DNA, and submit barcode data to BOLD (the barcode of life database). Fourteen peer reviewed journal articles that acknowledge this grant have been published, along with 2 book chapters, and 19 presentations at national and international meetings. Kjer and Holzenthal have contributed over 50 pages to The Trichoptera Tree of Life Web pages. Kjer will be hosting the XVth International Trichoptera Symposium at Rutgers. Kjer, and Frandsen organized the The Trichoptera Research Group on FaceBook, so that international workers could communicate on an easily accessible site. The phylogeny has led to a stabilized taxonomy of Trichoptera, and progress was made in stabilizing the classification of Hydroptilidae. Monographs and species descriptions were produced by Holzenthal and Thomson. Conclusions can be made about the mode of behavioral transitions between aquatic caddisflies and their closely related terrestrial moths. The emergence of the most recent common ancestor of Trichoptera was dated to 170 million years ago. Recommendations were published for integrating disparate datasets from DNA barcode data, the standard "toolbox" genes, and transcriptomes. The largest datasets ever produced for insect phylogenetics through the 1KITE initiative are now available, and the first of these papers has been published in Science. Kjer and Frandsen were among the first to demonstrate the utility of anchored hybrid enrichment (hybrid capture) methods in insects. Recommendations were published for the construction of large phylogenies with limited resources, such as barcode data plus a single rRNA fragment, and this method could be used to fill in the tips of the tree at the species level. We now have over 45,000 individuals in the Tricoptera Barcode of Life Databsase. The majority of the diversity in this database comes from our efforts.
