Rutgers School of Environmental and Biological Sciences [Dept. of Entomology]

Karl Kjer

email: kjer@aesop.rutgers.edu

Phylogenetic Datasets

Abstract:   My research interests are in phylogenetics and an integration of molecular biology and systematic methodologies. Studying the structure and function of ribosomal RNA (rRNA), I have been working on the way these molecules are used in phylogenetic studies. Alignment of rRNA is particularly problematic, and I have developed suggestions that incorporate structural information in alignment protocols (Kjer et al., 1994; Kjer 1997; Kjer 1997). An understanding of molecular structure and function has also leading to the development of biologically sound weighting schemes for molecular data (Kjer et al., 2001, 2002, Kjer, 2004).

My taxa of interest include Trichoptera, Chrysomelidae, and Odonata. We have recently completed a study on the higher level phylogeny of the entire order Trichoptera at the family level and above (Kjer et al., 2001, 2002). We are actively collecting caddisflies in order to continue this work at the generic level. Trichoptera, or caddisflies, are an order of holometabolous insects with aquatic immature stages. Trichoptera are integral components of almost all freshwater communities worldwide. The order is diverse in terms of numbers of species and the microhabitats and trophic niches the species occupy. Habitat specificity and general intolerance to pollution makes the larvae excellent biological indicators of water quality. Elizabeth Cosgrove, a graduate student of mine (Co-advised by Dr. Frank Carle), has conducted the first survey of New Jersey's caddisfly fauna, in an effort to provide a baseline for water-quality surveys. Caddisflies are also of interest to those who study animal behavior because of the net-spinning and case-making behavior of the larvae. Accurate taxonomy and phylogeny are at the core of these research foci. Collaborators in the Trichoptera project include Drs. Ralph Holzenthal, and Roger Blahnik at the University of Minnesota, and Dr. Ollie Flint at the Smithsonian Institution. I am also involved with an NSF-funded project on Hydropsychidae, with PI, John Morse from Clemson University. Another area of interest is in the Chrysomelidae, or leaf beetles and their co-evolution with plants, and plant toxins that they consume. I have been working with Dr. Catherine Duckett, from the University of Puerto Rico on this project. We studied the evolution of mimicry in the Oedionychini. Oedionychines are a subtribe of flea beetles (Alticinae). We have expanded our work to pursue the phylogeny of Alticinae and Galurucinae. We are also interested in the evolution of cucurbitacin feeding in the Luperini. Catherine and I received an NSF "ADVANCE" grant that will provided her with salary and supply money to work in my lab and at the Smithsonian for the past three years. Dr. Adriana Marvaldi is collaborating with us on this project. Catherine and I were also collaborating with Doug Tallamy from the University of Delaware, and Joe Gillespie, Doug's former student (who recently received a Ph.D. at Texas A&M University) on this project. Joe Gillespie is now working on a postdoc at the Virginia Bioinformatics Institution. One of my students, Zuzana Swigonova, finished her Ph.D. project in 2002. She has been studying the phylogeny of Trirhabda (Chrysomelidae, Galurucinae) and its host-plant shifts, and is currently working at the Rangos Research Center at the University of Pittsburgh. Another student who has recently received her master's degree, SungJin Kim, worked to test a recent morphology-based hypothesis of galerucines and alticines with molecular data. And I have another student with an interest in Trichoptera, Xin Zhou, who is finishing his Ph.D. work on the association of larval and adult Trichoptera, using molecular methods. He will be graduating at the end of 2006, and has accepted a postdoctoral position with Dr. Paul Hebert. Xin has also been advised by Dr. John Morse, a trichopterologist with extensive ties in China through professor Lianfang Yang, at Nanjing Agricultural University. Drs. Morse, Yang, and I have been awarded an NSF grant to study the phylogeny of Hydropsychidae (Trichoptera), and work on phylogeny, description, and larval-adult association of Chinese caddisflies.

Finally, I have an interest in the Odonata. Dr. Frank Carle, Dr. Mike May, and I are developing projects that combine morphological and molecular markers in the relationships among this group of aquatic insects. We are pursuing an NSF-funded project to develop a phylogeny at the family level for the entire order. This project will offer insights about the evolution of flight on earth, as well as specific insights about the development of wing mechanics in Odonata. We have two graduate students associated with this project, Jessica Ware, and Jesse Litman. Jessica Ware is working on the phylogeny of Libellulidae, including Corduliinae, and Macromiinae. She is using both molecular and morphological data, and also has an interest in wing venation. Jessica Litman just finished her masters degree on the "Palaeoptera", and will be working on her Ph.D. with Bryan Danforth at Cornell.

Laboratory facilities include several ABI capillary sequencers, with all the equipment to support it. Mike May and I are also curators of Rutgers' insect museum; a museum of approximately 250,000 specimens that is available for phylogenetic research.

The pattern I have developed in my collaborations has been to include taxonomic expertise with my own, and to include morphological characters with molecular whenever possible. Field work and natural history questions are essential to a meaningful systematics program. I utilize parsimony, and maximum likelihood tree reconstruction methods, and stress the importance of understanding the assumptions, strengths and weaknesses of a variety of analysis philosophies. Lab techniques, while important, are not the central focus of my research program, as I feel that it is much more important to have a critical understanding of how evolutionary relationships are inferred and why they are important.

Research Projects:

  • The higher level phylogeny of the Trichoptera
  • Phylogenetic relationships within the Chrysomelidae
  • Phylogenetic relationships within the Odonata
  • Alignment of rRNA in phylogenetic studies
  • Development of biologically sound weighting schemes in molecular systematics

Recent Publications:

  • In press Kjer, K. M., Swigonova, Z., LaPolla, J.S., and R.E. Broughton. 2007. Why Weight? Mol. Phylogenet. Evol. (in press).
  • In press Zhou, X., Kjer, K.M., and J.C. Morse. 2007. Associating Larvae and Adults of Chinese Hydropsychidae Caddisflies (Insecta: Trichoptera) Using DNA Sequences. J. N. Amer. Benthological Soc. (In press).
  • In press  Geraci, C. J., Kjer, K. M., and Morse, J.C. Phylogenetic relationships of Hydropsychidae subfamilies based on morphology and DNA sequence data. Proceedings of the 11th International Symposium on Trichoptera, Osaka & Shiga, Japan. Ed. Tanida

  • 2007  Kjer, K. M., & R.L Honeycutt. 2007 Site Specific Rates of Mitochondrial Genomes and the Phylogeny of Eutheria. BMC-Evolutionary Biology, 7:8.

  • 2007  Kjer, K. M., J. J. Gillespie, & K. A. Ober. 2007. Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignments. Systematic Biology 56:133-146

  • 2006 LaPolla, J.S., Schultz, T.R., Kjer, K.M., & J.F. Bischoff. 2006. Phylogeneric position of the ant genus Acropaga Roger (Hymenoptera: Formicidae) and the evolution of trophophoresy. Insect Syst. Evol. 37:197-212.
  • 2006 Kjer, K. M., J. J. Gillespie, & K. A. Ober. 2006. Structural homology in ribosomal RNA, and a deliberation on POY. Arthropod Systematics and Phylogeny. 64:71- 76
  • 2006 Kjer, K.M., Carle, F.L, Litman, J., and Ware, J. 2006. A molecular phylogeny of Hexapoda. Arthropod Systematics and Phylogeny. 64:35-44
  • 2004  Duckett, C. N., Gillespie, J. J., and K. M. Kjer. 2004 Relationships among the subfamilies of Chrysomelidae inferred from small subunit ribosomal DNA, with special emphasis on the relationship between the flea beetles and the Galerucinae. Invited book chapter to " New Contributions to the Biology of Chrysomelidae." Pierre H. Jolivet, Jorge A. Santiago-Blay and Michael Schmitt (eds.). SPB Academic Publishers, The Hague, Netherlands. pp. 3-18.
  • 2004 Kjer, K.M. 2004. Aligned 18S and Insect phylogeny. Systematic Biology 53:506-514
  • 2004 Gillespie, J. J., Kjer, K. M. and D. Tallamy. 2004 The evolution of cucurbitacin pharmacophagy in rootworms: insight from Luperini paraphyly. Invited book chapter to "New Contributions to the Biology of Chrysomelidae." Pierre H. Jolivet, Jorge A. Santiago-Blay and Michael Schmitt (eds.). SPB Academic Publishers, The Hague, Netherlands. 15 pp.
  • 2003  Duckett, C. N., and Kjer, K. M. Cladistic analysis of the Oedionychines of southern Brazil (Galerucinae: Alticini) based on two molecular markers. Proc. of the 5th Int'l. Symposium on the Chrysomelidae. 117-132. Pensoft, Sofia.
  • 2003  Gillespie, J. J., Kjer, K. M., Duckett, C. N. and Tallamy, D. W. Convergent evolution of cucurbitacin-feeding and pharmacophagy in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini). Mol. Phylogenet. Evol. 29: 161 - 175.
  • 2003  Xia, X., Xie, Z., and Kjer, K. M. 18S ribosomal RNA and tetrapod phylogeny. Syst. Biol. 52:283-295 (Science "Editor's choice" selection, Jul. 18, 2003)
  • 2003  Brosnan, S., Shin, W., Kjer, K. M., and Triemer, R. E.  Phylogeny of the Photosynthetic Euglenophytes Inferred from the Nuclear SSU and Partial LSU rDNA. Int. J. Syst. Evol. Microbiol. 53: 1175-1186
  • 2003  Kim, S., Kjer, K. M., and Duckett, C. N. Comparison between molecular and morphological-based phylogenies of galerucine/alticine leaf beetles. (Coleoptera: Chrysomelidae). Insect Syst. Evol. 34:53-64
  • 2002 Carle, F. L. and Kjer, K. M.  Phylogeny of Libellula Linnaeus (Odonata: Insecta). Zootaxa, Aug. 87:1-18.
  • 2002 Kjer, K. M., Blahnik, R. J, and Holzenthal, R. Phylogeny of caddisflies (Insecta: Trichoptera), Zoologica Scripta, 31(1): 83-91.
  • 2001 Kjer, K.M., Blahnik, R.J, and Holzenthal, R. Phylogeny of Trichoptera (Caddisflies): Characterization of Signal and Noise Within Multiple Datasets. Systematic Biology, 50:781-816
  • 2000 Swigonova Z., and Kjer, K.M. Will Molecular Phylogenetics Elucidate Host-plant Shifts in Trirhabda (Chrysomelidae, Galerucinae)? Chysomela newsletter
  • 2000 Gillespie, J.G., Duckett, D.V., and Kjer, K. M. Identification of a gene region that gives good phylogenetic signal for determining high level divergences within alticine and galerucine chrysomelids. Chysomela newsletter
  • 2000  Flores-Villela, O., Kjer, K. M., Benabib, M., and Sites, J. W. Jr. 2000.  Multiple datasets, congruence, and hypothesis testing for the phylogeny of the basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae).  Systematic Biology. 49 (4):713-739
  • 2000  Emmerson, S.B., Richards, C., Drewes, R.C., and Kjer, K.M.  2000.  On the relationships among ranoid frogs:  a review of the evidence. Herpetologica  56:209-230
  • 1997 Kjer K M: An alignment template for amphibian 12S rRNA, domain III: Conserved primary and secondary structural motifs. J. Herpetology, 31:599-604
  • 1997 Benabib M, Kjer KM, Sites JW: Mitochondrial DNA sequence-based phylogeny and the evolution of viviparity in the Sceloporus scalaris group (Reptilia, Squamata). Evolution, 51:1262-1275
  • 1997 Creer DA, Kjer KM, Simmons DL, and Sites JW: Phylogenetic relationships of the Sceloporus scalaris species group. J. Herpetology, 56:209-230
  • 1996 Khambhampati S, Kjer KM, and Thorne BL: Phylogenetic relationships among termite families based on DNA sequence of mitochondrial 16S ribosomal RNA gene. Insect Molecular Biology 5 (4) 229-238
  • 1995 Kjer KM: Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol. Phylogenet. and Evol.4 (3) 314-330
  • 1994 Kjer KM, Baldridge GD, Fallon AM: Mosquito large subunit ribosomal RNA: Simultaneous alignment of primary and secondary structure. Biochim Biophys Acta 1217 (2) 147-155

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