Source: RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY submitted to
INTEGRATING THE MORPHOLOGICAL AND MOLECULAR TAXONOMY OF TRICHOPTERA TOWARDS THE DEVELOPMENT OF A UNIFIED SPECIES DELIMITATION PROTOCOL
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0227674
Grant No.
(N/A)
Project No.
NJ17122
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Dec 1, 2011
Project End Date
Jun 30, 2015
Grant Year
(N/A)
Project Director
Kjer, KA.
Recipient Organization
RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY
3 RUTGERS PLZA
NEW BRUNSWICK,NJ 08901-8559
Performing Department
Ecology, Evolution & Natural Resources
Non Technical Summary
There are approximately a million species of insects known to science, with millions more yet to be described. With so many species, even highly trained experts have a difficult time identifying them. Within Trichoptera (caddisflies), it is extremely difficult or impossible to identity females or larvae, since the most commonly used features used to identify species are found on the complex male genitalia. The process of species identification, and description is a meticulous and time-tested science of distinguishing morphological differences that naturally occur within species, from those differences that distinguish species. As in so many other fields, molecular biology is revolutionizing the science of species identification. By sequencing a short fragment of DNA (part of the mitochondrial COI gene called the "barcode" fragment), we can identify both sexes, and all life stages of caddisflies. However, there are potential problems with the quick and easy molecular approach that scientists have always understood, but seem willing to ignore for expediency. We are proposing to solve some of these problems by sequencing a second independent gene, and working with morphological data. Merging morphological data with improved molecular protocols will help us rapidly identify hidden biodiversity. Water quality and climate change are among the most important issues we face in this century. Caddisfly larvae live in water, and different species have different tolerances to water pollution. They have narrow ranges of temperature and water chemistry requirements. Therefore, understanding which species live in a particular stream can be a powerful tool in assessing water pollution. Changes in species composition over time can be used to track global climate change. Molecular taxonomy is in its infancy, and the protocols we propose to improve the techniques in these early stages will have an impact on how we identify and describe species in the future, and may have an impact on how we broadly define our concept of species.
Animal Health Component
0%
Research Effort Categories
Basic
33%
Applied
33%
Developmental
34%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2113110113050%
1120399107050%
Knowledge Area
211 - Insects, Mites, and Other Arthropods Affecting Plants; 112 - Watershed Protection and Management;

Subject Of Investigation
3110 - Insects; 0399 - Watersheds and river basins, general;

Field Of Science
1130 - Entomology and acarology; 1070 - Ecology;
Goals / Objectives
Studying abundant aquatic insects that are differentially sensitive to pollution allows for the linkage of taxonomy with practical solutions to water quality monitoring. Tracking the expected geographic shifts in species ranges with global climate change requires an efficient system of species identification. Molecular taxonomy is still in its infancy, and we will develop solutions to the limitations of molecular species definitions that will be broadly applicable to other taxa. Ongoing collaborative research in Eastern Russia, and Nigeria will serve as model systems for using caddisfly taxonomy for freshwater biomonitoring, and we expect that this research will significantly advance research capacity in freshwater ecosystems in Russia, Nigeria,and elsewhere. Although applicable to many taxa and many ecosystems, our objectives will focus on the Trichoptera of Eastern North America, Eastern Russia, and Nigeria. We will: 1. Enhance the means for identifying distinct genetic clusters based on congruence of multiple genes. The molecular cluster protocols we develop will be broadly applicable. 2. Accelerate species discovery and description, along with the process of associating yet unidentifiable larvae with identified adults. Both these endeavors will be accomplished by generating species hypotheses through congruence of genetic clusters and morphospecies, together with supporting evidence from geographic sympatry and allopatry. 3. Build upon our collaborative efforts between the U.S. and Russia and Nigeria through reciprocal travel, collecting and cross-training between molecular and morphological methods. We propose to transform the way molecular data are used to delimit taxonomic units with Trichoptera serving as a model organism in this effort. By standardizing our vocabulary in terms of cluster identification (haplotype clusters, genetic clusters, probable species, and species), we will clarify what molecular taxonomy actually defines, while advocating for a continued strong role for descriptive taxonomy. Demonstrating that our methods work in Trichoptera will encourage the same kind of conservative multi-gene plus morphology approach in other groups. We will accelerate the rate of species descriptions by unambiguously defining genetic clusters that are associated with morphospecies. Although this method may not work for every taxon (plants, for example, would require more than two genes), we predict that it will work for many insect groups. For public outreach, we anticipate growing the Trichoptera Tree of Life site from its current 50 pages, to over 500 pages, representing most genera, complete with text, and images. This proposal will increase the representation of Russian and African taxa on this website. Finally, there are strong human resource impacts. We will be building upon our already strong ties in both Russia and Nigeria. We will be training graduate students, and postdocs in integrated taxonomy and functional biodiversity. Our laboratories have a strong history of student training, and we have been particularly strong in the advancement of women, and under-represented groups.
Project Methods
A 658 nucleotide fragment of mitochondrial COI DNA (the "barcode" fragment) will provide one piece of evidence that a group of organisms is a distinct, independently evolving lineage. To condense our genetic objective in the simplest terms, we want to provide additional data to the barcode data. These additional data will allow us to estimate phylogeny, and move toward species delimitation and description: (1) - Geography is integral to most speciation events. We will examine geographical distribution data associated with barcode haplotype clusters, determining whether or not clusters can be simply explained by geographical distance, or whether there is some sympatry and seasonal synchrony among non-overlapping clusters. These data are easily stored and recovered from the Barcode of Life Datasystem (BOLD: http://www.boldsystems.org/views/login.php). (2) - Because species are independently evolving lineages, a consideration of the phylogeny of clusters also is crucial for delimiting species. Unlinked genes sort independently, and nuclear markers will either indicate clusters that are congruent with COI barcode data, or not. We will sequence another independent molecular marker, namely 1000 nts of large subunit (28S) nuclear ribosomal RNA (rRNA), including the D1, D2, and D3 regions, in search of lineages that are reciprocally monophyletic. (3) - Unidentified specimens will be sorted according to morphological similarity, providing hypothetical morphospecies. Morphospecies will be used as a 3rd measure of distinctiveness, independent of the 2 molecular markers. When multiple independent molecular clusters converge on the same group of morphologically distinct organisms, that unit is very probably reproductively isolated. Whether or not the "unit" can be described as a "species" is a decision our taxonomists will make. Distinct morphospecies, whose distributions are overlapping with potential sister lineages, can be assumed to be species under the phylogenetic species concept (reviewed by Avise and Wollenberg, 1997). These lineages can be circumscribed at an accelerated rate, because the additional information clarifies whether observed morphological variation is more likely simply intraspecies variation (often clinal) or interspecies variation worthy of description. We propose the following vocabulary, in increasingly stringent categories. Monophyletic groups generated from a phylogenetic analysis of single genes will be called "haplotype clusters." These will include clusters generated from barcode (COI) data as well as from 28S rRNA data. When both genes, analyzed independently, converge on reciprocally monophyletic, identical groups, these groups will be called "genetic clusters." When the boundaries of genetic clusters are shared with predetermined morphospecies, then these groups will be called "probable species." Our taxonomic collaborators will then incorporate this information into formal species descriptions in taxonomic revisions.

Progress 12/01/11 to 06/30/15

Outputs
Target Audience:Scientists, evolutionary biologists, and the general public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Kjer trained 11 undergraduate students in his lab, including many from the Aresty research program, and project SUPER (women in science). Kjer hosted the 15th international symposium on Trichoptera, and solicited and distributed funds for 10 international scientists from developing countries to attend. How have the results been disseminated to communities of interest?Publications in peer reviewed journals, and talks and posters at international meetings. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We published a phylogeny of Odonata. Kjer is a co-founder of the 1KITE initiative, which recently published a phylogeny of Insecta in the journal Science (with cover illustration).

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Kjer, K.M., Ware, J.L., Rust, J., Wappler, T., Zhou, X., the 1KITE consortium, and Misof, B. Response to the comment on "Phylogenomics resolves the timing and pattern of insect evolution". Science.
  • Type: Journal Articles Status: Submitted Year Published: 2016 Citation: Shanlin, L., Wang, X., Xie, L., Tan, M., Li, Z., Su, X., Zhang, H., Misof, B., Kjer, K.M. Tang, M., Niehuis, O., Jiang, H., and Zhou, X. Mitochondrial capture enriches mito-DNA 100 folds enabling PCR-free mitogenomics biodiversity analysis. Molecular Ecology Resources.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Carle, F.L., May, M.L., and Kjer, K.M. A Molecular Phylogeny of Anisoptera (Odonata). Arthropod systematics and phylogenetics.


Progress 10/01/13 to 09/30/14

Outputs
Target Audience: Evolutionary biologists and undergraduate students in environmental science. Changes/Problems: Both my Russian and Nigerian colleagues have encountered significant challenges in meeting their commitments. I intend to continue working with what they provide me. I have finished working with the material they have sent, but will supplement what they have been unable to provide with other specimens from throughout the world, through my other collaborators. What opportunities for training and professional development has the project provided? I taught approximately 45 students in 3 years on aquatic insect barcoding in my Byrne Seminar. I trained 4 students in molecular taxonomy through the Aresty program, and another summer intern through Rutgers "project super". How have the results been disseminated to communities of interest? Three peer reviewed publications were published in 2014. I attended the Systematic Biology Society meetings in June, in Raleigh N.C., and presented a poster. There was also a 1KITE organizational meeting in Raleigh N.C. 1KITE is an international collaborative organization dedicated to insect phylogeny. What do you plan to do during the next reporting period to accomplish the goals? I have 700 Trichoptera samples from around the world that I intend to barcode with the help of undergraduate students. This not only enhances the BOLD database, it also trains students in lab techniques and molecular taxonomy.

Impacts
What was accomplished under these goals? A "barcode" in this context is a short fragment (658 nucleotides) of mitochondrial DNA, used to aid in the identification of unknown insect species. Approximately 200 Trichoptera from Russia were added to the Barcode of Life Database (BOLD). Another 200 Trichoptera from Central Africa are in progress. The Chimarra paper established the utility of barcode data to taxonomy and phylogenetics. We made major progress on the phylogeny of Insecta.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Misof, B., Liu, S., Meusemann, K., Peters, R.S., Donath, A., Mayer,C.,Frandsen, P.B., Ware, J., Flouri, T., Beutel, R.G., Niehuis, O., Petersen, M., Izquierdo-Carrasco, F., Wappler, T., Rust, J., the 1KITE consortium (83 other authors), Wang, J., Kjer, K.M., Zhou, X. Phylogenomics resolves the timing and pattern of insect evolution. Science 346 no. 6210 pp. 763-767
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Kjer, K.M., Zhou, X., Frandsen, P.B., Thomas, J.A., and Blahnik, R.J. 2014. Moving toward species-level phylogeny using ribosomal DNA and COI barcodes: an example from the diverse caddisfly genus Chimarra (Insecta: Trichoptera: Philopotamidae). Arthropod Systematics & Phylogeny 72 (3): 345-354
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Peters, R.S, Meusemann, K., Petersen, M., Mayer, C., Wilbrandt, J., Ziesmann, T., Donath, A., Kjer, K.M., Asp�ck, U.,Asp�ck, H., Aberer, A., Stamatakis, A., Friedrich, F, H�nefeld, F., Niehuis, O., Beutel, R.G., and Misof, B. 2014. The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evolutionary Biology 14 (1), 52.


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: We have submitted 3 papers to the International Trichoptera symposium proceedings. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? I have trained Dr. Tanya Vshivkova in DNA techniques. SIx Rutgers undergraduate students are being trained in my lab on Trichoptera collection, vouchering, and sequencing. I taught a class on DNA barcoding for 20 undergraduate students for the Byrne seminar. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Three papers have been submitted. I expect that these papers will be published. I intend to continue with my undergraduate teaching. I continue to receive specimens from international collaborators, and these will be sequenced.

Impacts
What was accomplished under these goals? We have expanded the Trichoptera barcode of life database (BOLD) from Russia by 20-fold. These data have been submitted to the BOLD website.

Publications


    Progress 01/01/12 to 12/31/12

    Outputs
    OUTPUTS: My graduate student, Paul Frandsen, and I attended the International Trichoptera Symposium, in Vladivostok, Russia, in July, 2012. We presented talks, met with collaborators, and collected specimens after the conference during a 2 week collecting trip in the Russian Far East. Kjer developed a course for the Rutgers Byrne Seminar Series, in which Freshman are introduced to the research done at Rutgers. Students collected, photographed insect larvae, then sequenced them and submitted the sequences to the Barcode of Life Database (BOLD). PARTICIPANTS: Karl Kjer supervised the project. Paul Frandsen, graduate student, collected data. Dhara Patel, undergraduate student, learned PCR TARGET AUDIENCES: Freshwater biomonitoring scientists are interested in the molecular taxonomy of Trichoptera. Students at Rutgers learn about aquatic biodiversity and biomonitoring with molecular data. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

    Impacts
    We learned that the Barcode of Life database was able to identify 22 out of 23 randomly sampled insect larvae to genus, and all North American Trichoptera could be identified to species.

    Publications

    • Trautwein, M.D., Wiegman, B.M., Beutel, R., Kjer, K.M. and Yeates, D.K. 2012. Advances in Insect Phylogeny at the Dawn of the Postgenomic Era. Annu. Rev. Entomol. 57:449-68.
    • Harvey, L.E., Geraci, C.J., Robinson, J.L., Morse, J.C., Kjer K.M., Zhou, X. 2012. Diversity of mitochondrial and larval morphology characters in the genus Diplectrona (Trichoptera:Hydropsychidae) in the eastern United States. Terrestrial Arthropod Reviews 5:1-21.