Biomedical subjects

Karl M Kjer

Publications and source records attributed to Karl M Kjer.

5 recordsLinked to original sources

PubMed2004

Phylogeny and host-plant association in the leaf beetle genus Trirhabda LeConte (Coleoptera: Chrysomelidae).

The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was reconstructed from mitochondrial COI and 12S rRNA fragments, nuclear ITS2 rRNA, and morphological characters. Both parsimony and mixed-model Bayesian likelihood analyses were performed. Under both methods, the mitochondrial and nuclear partitions support the same backbone phylogeny, as do the combined data. The utility of the molecular data is contrasted with the low phylogenetic signal among morphological characters. The phylogeny was used to trace the evolution of the host-plant association in Trirhabda. The recovered phylogeny shows that although the host-plant association is phylogenetically conservative, Trirhabda experienced one shift to a distantly related host-plant family, 6 shifts between host-plant tribes, and 6 between genera within tribes. The phylogeny reveals that Trirhabda were plesiomorphically adapted to tolerate complex secondary compounds of its host plants and this adaptation is retained in Trirhabda species, as evidenced by multiple shifts from chemically simpler host plants back to the more complex host plants.

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PubMed2004

Aligned 18S and insect phylogeny.

The nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.

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PubMed2003

Convergent evolution of cucurbitacin feeding in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini).

Historically, chemical ecologists assumed that cucurbitacin feeding and sequestration in rootworm leaf beetles is a remnant of an ancient association between the Luperini (Coleoptera: Chrysomelidae; Galerucinae) and Cucurbitaceae (ancestral host hypothesis). Under this premise, rootworms that do not develop on cucurbits but undergo pharmacophagous forays for cucurbitacins are thought to do so to supplement novel host diets that lack these bitter compounds. The ancestral host hypothesis is supported from studies of pyrrolizidine alkaloid pharmacophagy in Lepidoptera but has not been subjected to phylogenetic analysis within the Luperini. New evidence that this feeding behavior is better correlated with an adult affinity for pollen than with larval host offers the possibility that Old and New World rootworm species with an affinity for cucurbitacins converged on this behavior through apomorphic taste receptor modifications (loose receptor hypothesis). Here we test the monophyly of cucurbitacin feeding within the Luperini by using nuclear and mitochondrial sequence data to infer phylogenetic relationships among 49 taxa representing tribes of the Galerucinae and subtribes of the Luperini. The resulting phylogenetic hypothesis is mostly concordant with existing tribal and subtribal delineations within the Subfamily Galerucinae sensu stricto (Galerucinae not including the flea beetles). The establishment of ancestry among the subtribes of the Luperini refutes the monophyly of cucurbitacin feeding and cucurbit specialization, with the New World Diabroticina being paraphyletic to the Old World Aulacophorina and cosmopolitan Luperina. These data unambiguously support the convergent evolution of cucurbitacin feeding in rootworms and are inconsistent with the ancestral host hypothesis.

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PubMed2003

18S ribosomal RNA and tetrapod phylogeny.

Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive evidence of different genes providing significantly different estimates of phylogeny in higher organisms" (p. 156; Huelsenbeck et al., 1996, Trends Ecol. Evol. 11:152-158). Our research indicates that the previous discrepancy of phylogenetic results between the 18S rRNA gene and other genes is caused mainly by (1) the misalignment of the sequences, (2) the inappropriate use of the frequency parameters, and (3) poor sequence quality. When the sequences are aligned with the aide of the secondary structure of the 18S rRNA molecule and when the frequency parameters are estimated either from all sites or from the variable domains where substitutions have occurred, the 18S rRNA sequences no longer support the grouping of the avian species with the mammalian species.

Algorithms↗

PubMed2003

Phylogeny of the photosynthetic euglenophytes inferred from the nuclear SSU and partial LSU rDNA.

Previous studies using the nuclear SSU rDNA have indicated that the photosynthetic euglenoids are a monophyletic group; however, some of the genera within the photosynthetic lineage are not monophyletic. To test these results further, evolutionary relationships among the photosynthetic genera were investigated by obtaining partial LSU nuclear rDNA sequences. Taxa from each of the external clades of the SSU rDNA-based phylogeny were chosen to create a combined dataset and to compare the individual LSU and SSU rDNA datasets. Conserved areas of the aligned sequences for both the LSU and SSU rDNA were used to generate parsimony, log-det, maximum-likelihood and Bayesian trees. The SSU and LSU rDNA consistently generated the same seven terminal clades; however, the relationship among those clades varied depending on the type of analysis and the dataset used. The combined dataset generated a more robust phylogeny, but the relationships among clades still varied. The addition of the LSU rDNA dataset to the euglenophyte phylogeny supports the view that the genera Euglena, Lepocinclis and Phacus are not monophyletic and substantiates the existence of several well-supported clades. A secondary structural model for the D2 region of the LSU rDNA was proposed on the basis of compensatory base changes found in the alignment.

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