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

Karl Kjer


Phylogenetic Datasets

Abstract:  My research interests are in phylogenetics and an integration of molecular biology and organismal biology. 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 1995; Kjer 1997; Kjer 1997, Kjer et al., 2006, Kjer et al., 2007a, Kjer et al., 2008). An understanding of molecular structure and function has also leading to the development of biologically sound treatment of the data (Kjer et al., 2001, 2002, Kjer, 2004, Kjer et al. 2007b, Kjer and Honneycutt, 2007, Letsch and Kjer, 2011).

My main taxon of interest is Trichoptera (see our open access review of the entire order at Zootaxa: Order Trichoptera). My long term collaborators include Drs. Ralph Holzenthal, and Roger Blahnik at the University of Minnesota, and Dr. Ollie Flint at the Smithsonian Institution. I was involved with an NSF-funded project on Hydropsychidae, with PI, John Morse from Clemson University.  These collaborations with experts on the organisms are invaluable, as they provide cross-training across molecular and morphological disciplines.  My collaborators and I have completed a study on the higher level phylogeny of the entire order Trichoptera at the family level and above (Kjer et al., 2001, 2002; Holzenthal et al., 2007).  We are currently collecting caddisflies on an NSF funded project to continue this work at the generic level.

We have been a major contributor to the Trichoptera Barcode of Life initiative.  My former student, Xin Zhou, finished his Ph.D. work in 2006 on the association of larval and adult Trichoptera, using molecular methods. After leaving my lab, Xin led the Trichoptera Barcode Initiative in Guelph.  This initiative has been very successful in generating huge amounts of COI data, which are not only useful for the barcode initiative, but are also phylogenetically useful.  Thanks to my generous collaborators, we have thousands of specimens in my freezer, all of which have had the "barcode fragment" sequenced.  Adding a second or third gene to these data should go a long ways toward bridging the gap from our earlier work on the backbone of the Trichoptera tree, to filling out the entire tree to the species level.  I would like to see this work on the Trichoptera Tree of Life Web pages.

1kiteXin Zhou is now a vice president at the Beijing Genomics Institute, leading a large transcriptome initiative called "1KITE" (for 1 K Insect Transcriptome Evolution).  This initiative is committed to sequencing 1000 insect transcriptomes, and is developing international collaborations between The U.S., China, and Germany.  I am involved with several projects from the 1KITE initiative, including the phylogeny of Insecta, Polyneoptera, Odonata, and Trichoptera.  My current graduate student, Paul Frandsen, will be evaluating genes generated from the Trichoptera transcriptomes, and applying next-generation sequencing techniques using targeted multi-plex PCR to continue our phylogenetic work.

The pattern I have developed in my collaborations has been to include organismal expertise with my own, and to include morphological characters with molecular data whenever possible. Field work and natural history questions are essential to a meaningful systematics program. I utilize Bayesian, and maximum likelihood tree reconstruction methods, and stress the importance of understanding the assumptions, strengths and weaknesses of a variety of analytical philosophies. Lab techniques in themselves, 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 phylogeny of the Trichoptera
  • Insect Systematics
  • Insect transcriptomics
  • Alignment of rRNA in phylogenetic studies
  • Development of biologically sound data treatment in molecular systematics

Former PhD Students:

Zuzana Zwigonova: 2002. Zuzana Swigonova's website

John LaPolla: 2005 John LaPolla's website

Xin Zhou: 2006 Xin Zhou's website

Jessica Ware: 2007 Jessica Ware's website


  • 2014 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.  submitted, Science. Authors listed = major contributors,  *=corresponding author. 

  • 2014 Peters, R.S, Meusemann, K., Petersen, M., Mayer, C., Wilbrandt, J., Ziesmann, T., Donath, A., Kjer, K.M., Aspöck, U.,Aspöck, H., Aberer, A., Stamatakis, A., Friedrich, F, Hünefeld, F., Niehuis, O., Beutel, R.G., and Misof, B.  The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data.   BMC Evolutionary Biology 14 (1), 52.  Open Access:  pdf

  • 2012 Harvey, L.E., Geraci, C.J., Robinson, J.L., Morse, J.C., Kjer K.M.,  Zhou, X.  Diversity of mitochondrial and larval morphology characters in the genus Diplectrona (Trichoptera: Hydropsychidae) in the eastern United States.  Terrestrial Arthropod Reviews 5(3):1-21.
  • 2012  Trautwein, M.D., Wiegmann, B.M.,  Beutel, R.,  Kjer, K.M, and Yeates, D.K. Advances in insect phylogeny at the dawn of the postgenomic era.  Annu. Rev. Entomol. 57:

  • 2011  Letsch, H., and Kjer, K.M.  Potential pitfalls of modelling ribosomal RNA data in   phylogenetic tree reconstruction: Evidence from case studies in the Metazoa.  BMC Evolutionary Biology, 11:146 Open Access: Letsch and Kjer, 2011

  • 2009  Lopez-Vaamonde, C., Wikström N., Kjer  K.M., Weiblen G.D., Rasplus, J.Y., Machado C., and Cook J.M. Molecular dating and biogeography of fig-pollinating wasps. Molecular Phylogenetics and Evolution. 52:715-26.  

  • 2009  Johanson, K-A., Kjer, K.M., and Malm, T.  Testing the monophyly of the New Zealand and Australian endemic family Conoesucidae Ross based on combined molecular and morphological data (Insecta: Trichoptera: Sericostomatoidea). Zoologica Scripta 38: 563 - 573

  • 2009  Marvaldi, A,E., Duckett, C.N. Kjer, K.M., and Gillespie, J.J. Structural alignment of 18S and 28S rDNA sequences provides insights into phylogeny of Phytophaga (Coleoptera: Curculionoidea and Chrysomeloidea). Zoologica Scripta  38: 63-77. 

  • 2008  Kjer, K. M., Roshan, U.  and Gillepie, J.G. Structural and Evolutionary Considerations For    Multiple Sequence alignment of RNA, and the challenges for Algorithms that ignore them.  in "Perspectives on Biological Sequence Alignment: Where, How, and Why It Matters".  University     of California Press.

  • 2008  Baskinger G.M., Ware J.L., Kornell D.D. May, M.L, and Kjer, K.M. A phylogeny of     Celithemis inferred from mitochondrial and nuclear DNA sequence data and morphology        (Anisoptera:  Libellulidae). Odonatologica 37: 101-109

  • 2007  Whitfield, J. B and Kjer, K. M. Ancient rapid radiations of insects: Challenges for         phylogenetic analysis. Annu. Rev. Entomol. 53:1-23

  • 2007  Holzenthal R.W., Blahnik, R.J., Prather, A.L., and Kjer K.M. Order Trichoptera Kirby 1813 (Insecta), Caddisflies. In:  Zhang, Z.-Q., and Shear, W.A. (Eds).  2007 Linneaus Tercentenary: Progress in Invertebrate Taxonomy  Zootaxa. 58 pp. 1668:639-698  Open Access: Holzenthal et al., 2007

  • 2007  Ware, J. L., M. L. May, K.M. Kjer. Phylogeny of the higher Libelluloidea (Anisoptera: Odonata): an exploration of the most speciose superfamily of dragonflies. Molecular Phylogenetics and Evolution 45(1): 289-310

  • 2007  Ware, J. L., Ho, S., Kjer, K. Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models. Molecular Phylogenetics and Evolution. 45: 289-310.

  • 2007  Kjer, K. M.,  Swigonova, Z., LaPolla, J.S., and R.E. Broughton. Why Weight?  Mol. Phylogenet. Evol. 43:999-1004 

  • 2007  Zhou, X., Kjer, K.M., and J.C. Morse.  Associating Larvae and Adults of Chinese Hydropsychidae Caddisflies (Insecta: Trichoptera) Using DN Sequences.  J. N. Amer. Benthological Soc. 26:719-742.  Open access:  Zhou et al., 2007

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

  • 2007  Zhou, X.,*  Kjer, K.M., and J.C. Morse.  An introduction to species delimitation, larval-adult association of Chinese Hydropsychidae using independent DNA sequences and adult morphology. Proceedings of the XIIth International Symposium on Trichoptera.  Bueno-Soria, R. Barba-Alvearz and B. Armitage (Eds). pp. 355-368.  The Caddis Press

  • 2007  Holzenthal R.W., Blahnik, R.J., Kjer K.M and Prather, A.L.  An update on the phylogeny of Caddisflies (Trichoptera).  Proceedings of the XIIth International Symposium on Trichoptera. Bueno-Soria, R. Barba-Alvearz and B. Armitage (Eds). pp. 143-153.  The Caddis Press.

  • 2007  Kjer, K. M., J. J. Gillespie, & K. A. Ober.  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.  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. Structural homology in ribosomal RNA, and a deliberation on POY. Arthropod Systematics and Phylogeny64:71-76

  •  2006  Kjer, K.M., Carle, F.L, Litman, J.*, and Ware, J*. A molecular phylogeny of  Hexapoda Arthropod Systematics and Phylogeny 64:35-44

  • 2004 Kjer, K.M. Aligned 18S and Insect phylogeny. Systematic Biology 53:506-514 (*With cover illustration)

  •  2004 Bischoff J.F.,* Sullivan R.F., Kjer K.M., and White J.F., Jr. Phylogenetic placement of the anamorphic tribe Ustilaginoideae (Hypocreales, Ascomycota). Mycologia 96(5): 1086-1092

  •  2004  Swigonova, Z.,* and Kjer, K.M.  Phylogeny and Host plant shifts in Trirhabda (Coleoptera: Chrysomelidae). Mol. Phylogenet. Evol. 32:358-374

  • 2004  Kjer, K.M.  Collection and preparation of Trichoptera for DNA sequencing.  Nectopsyche 2: 11

  •  2003  Geraci, C.J., Kjer, K.M., Morse, J.C. and R. J.Blahnik.    Phylogenetic relationships of  Hydropsychidae subfamilies based on morphology and DNA sequence data.  Pp. 131-136 in K. Tanida and A Rossiter (editors), Proceedings of the 11th International Symposium on Trichoptera, Osaka & Shiga.  Tokai University Press, Hadano-shi, Kanagawa 257-0003, Japan.  474 pp.

  •  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  87:1-18.

  •  2002  Kjer, K.M., Blahnik, R.J, and Holzenthal, R.W. Phylogeny of Caddisflies(Insecta, Trichoptera), Zoologica Scripta  31(1) :83-91.

  •  2001  Kjer, K.M., Blahnik, R.J, and Holzenthal, R.W. Phylogeny of Trichoptera (Caddisflies):  Characterization of Signal and Noise Within Multiple Datasets. Syst. Biol. 50:781-816. (*With cover illustration)

  •  2001  Swigonova Z.,* and Kjer, K.M.  Will Molecular Phylogenetics Elucidate Host-plant Shifts in Trirhabda  (Chrysomelidae, Galerucinae)?  Chrysomela 40/41:3, 8. 

  •  2001  Gillespie, J.J.*  Duckett, C.N., and Kjer, K.M.  Identification of a gene region that gives good phylogenetic signal for determining high level divergences within alticine and galerucine chrysomelids.  Chrysomela 40/41:10-12

  •  2000  Flores-Villela, O., Kjer, K.M., Benabib, M., and Sites, J.W. Jr.  Multiple datasets, congruence, and hypothesis testing for the phylogeny of the basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae).  Syst. Biol. 49:713-739

  •  2000  Emerson, S.B., Richards, C., Drewes, R.C., and Kjer, K.M.  On the relationships among  ranoid frogs:  a review of the evidence.   Herpetologica  56:209-230

  •  1997  Benabib,  M., Kjer, K.M., Sites J.W. Jr.  Mitochondrial DNA sequence-based phylogeny and the evolution of viviparity in the Sceloporus scalaris group.  Evolution 51:1262-1275

  •  1997  Creer, D.A.,* Kjer, K.M., Simmons, D.L., and Sites, J.W. Jr.  Phylogenetic relationships of the Sceloporus scalaris species group.   J. Herp. 31:353-364

  •  1997  Kjer, K.M.  Conserved primary and secondary structural motifs of amphibian 12S rRNA, domain III.  J. Herpetology 31:599-604 ISSN 0022-1511

  •  1996  Kambhampati, S. , Kjer, K.M., and Thorne B.L.  Phylogenetic relationships among termite families based on DNA sequence of mitochondrial 16S ribosomal RNA gene.  Insect  Molecular Biology 5: 229-238

  •  1995  Kjer, K.M. 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: 314-330.

  •  1994  Kjer, K.M.,* G.D. Baldridge, and Fallon A.M.  Mosquito large subunit  ribosomal RNA:  simultaneous alignment of primary and secondary structure.  Biochim. Biophys. Acta, 1217:  147-155.

  •  1991  Kjer,  K.M.* and Fallon, A.M.  Efficient transfection of mosquito cells is influenced by temperature at which the DNA-calcium phosphate coprecipitates are prepared.  Archs Insect Biochem Physiol, 16:  189-200.

  •  1989  Ragsdale, D.W.  and Kjer, K.M.*    Diagnosis of tracheal mite (Acarapis woodi Rennie) parasitism of honeybees using a monoclonal based enzyme linked immunosorbent assay.  Am. Bee J., 129:550-553. 

  • 1989  Kjer,  K.M.,* D.W. Ragsdale, and Furgala B.  A retrospective and prospective overview of the honey bee tracheal mite, Acarapis woodi R. Part I.  Am. Bee J., 129(1):  25-28

  • 1989  Kjer,  K.M., D.W. Ragsdale, and Furgala B.  A retrospective and prospective overview of the honey bee tracheal mite, Acarapis woodi R. Part II.  Am. Bee J., 129(2):  112-115.


    * Student work


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