PMC:3091644 / 20895-27224 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091644","sourcedb":"PMC","sourceid":"3091644","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091644","text":"Phylogeny of Taenia\nUsing a variety of shared characteristics including those defining adult morphology (particularly the organization of male and female reproductive organs) and larval structure, Hoberg et al. [6] compiled 27 characters for 30 species of Taenia. Parsimony analysis found 4 equally parsimonious trees, and the consensus tree has since been used to infer patterns of intermediate and definitive host association [1]. Inferred switching between carnivore definitive hosts led Hoberg [1] to conclude that ecological shifts have been greatly responsible for the patterns of radiation in Taenia. This study highlighted the likely role of climatological and ecological perturbation in influencing host-parasite associations in the genus. The morphology-based phylogeny has not been supported by partial molecular data sets from subsets of taxa, but establishing a reliable phylogeny for the genus clearly has important consequences.\nEarly attempts to infer molecular phylogenies of Taenia have been hampered by the availability of different species, and the application of relatively crude models of molecular evolution. Nevertheless, two studies provide perspective in assessing estimates from new complete mtDNA and the morphological data. De Queiroz and Alkire [57] compiled available partial cox1 data and partial nuclear large subunit (28S) rDNA data to infer a phylogeny including 11 species of Taenia. Lavikainen et al. [58] sampled multiple isolates of 9 Taenia species for partial cox1 and partial nad1 genes; this built on data collected by Gasser et al. [59]. In each of these studies, all the species for which complete mtDNAs are now available were included, thus allowing direct comparison of phylogenetic estimates of 7 species of Taenia.\nAlignment of all protein-coding genes of Taenia mtDNAs and outgroups provided 3,324 unambiguously aligned amino acids available for phylogenetic analysis, of which 1679 were variable and 1,009 parsimony-informative. Alignment of all nucleotides provided 11,393 unambiguously aligned sites, of which 9,378 were variable and 5,901 parsimony-informative. To avoid potential problems of saturation, only coding positions that were shown to be unsaturated were included in the nucleotide analysis; leaving 7,655 unambiguously aligned sites of which 3,680 were variable and 2,365 parsimony-informative. Bayesian analysis yielded phylogenies with maximal nodal support throughout the amino acid (Figure 1a), and nucleotide (Figure 1b) estimates. The interrelationships of Taenia based on complete mtDNAs were different between estimates from amino acids and nucleotides, and previously estimated phylogenies based on either morphology (Figure 1c) or molecular data (Figure 1d and 1e). Consistent among all phylogenetic estimates is the sister group status between T. asiatica and T. saginata, as expected, since these species are known to be very closely related [44]; recent evidence has demonstrated on-going hybridization between these species [60]. Molecular estimates from complete mtDNAs, partial mt and nuclear gene fragments consistently reveal T. multiceps as most closely related to T. saginata + T. asiatica. The placement of T. multiceps in this clade suggests a common intermediate host of members of the Suidae (pig family). Additional taxon sampling is required to further test the inferences of intermediate and definitive host switching in the genus made by Hoberg [1]. Beyond this clade, no two molecular estimates are identical with respect to the remaining species. The interrelationships of T. hydatigena, T. crassiceps and T. pisiformis in the mtDNA analysis are different from one another, but together they clearly form a clade (united by each using members of the Canidae as definitive hosts), in contrast to previous estimates. It is noteworthy that the nodal support in previous studies, using only small fragments of DNA, was generally very poor throughout the estimated phylogenies (not shown), in contrast to the very robust support offered by complete mtDNA amino acid analysis. Although additional evidence is required to resolve the interrelationships of the T. crassiceps, T. hydatigena and T. pisiformis clade, the analysis of amino acids suggests additional mtDNAs of Taenia species can be incorporated readily to provide a wider estimate of taeniid phylogeny.\nFigure 1 Phylogenetic estimates of the interrelationships of 7 Taenia species for which complete mtDNAs are available, based on: a. Bayesian analysis of all alignable amino acids of protein coding genes from complete mtDNAs, b. Bayesian analysis of all alignable, unsaturated nucleotides from complete mtDNAs (8 partitions; see text), c. cladistic analysis of morphology [6], d. maximum likelihood and parsimony analysis of partial cox1 and partial nuclear 28S rDNA [57], and e. maximum likelihood analysis of partial cox1 and partial nad1 [58]. Scale bars in a. and b. indicate number of substitutions per site; c, d and e are drawn as cladograms with equal branch lengths to indicate topologies only as they are adapted from larger analyses. Further studies are required to elucidate the source(s) of incongruence between the amino acid and nucleotide estimates, but it may be the result of added homoplasy from the ribosomal genes, tRNA genes and non-coding regions included in the analysis. Whether the more sophisticated Bayesian model (mtZoa) used for the amino acid analysis has provided a more accurate estimate of interrelationships of Taenia, which requires further testing, additional sampling of nuclear genes, such as complete 18S and complete 28S rDNA [61], may be useful in providing 3 independent estimates (morphology, mitochondrial and nuclear DNA) of phylogeny. Parsimony mapping of morphological characters detailed by Hoberg et al. [6] onto the mtDNA amino acid phylogeny, using only the 7 Taenia species common to both studies, suggests 3 morphological characters might support nodes in the novel topology in Figure 1a; these included characters 11 (localization of the metacestode in the intermediate host), 19 (route of the vas deferens) and 20 (number of layers in the testes). However, a full assessment of the morphological data set, by means of an independent molecular-based phylogeny is premature without additional sampling of Taenia species.","divisions":[{"label":"title","span":{"begin":0,"end":19}},{"label":"p","span":{"begin":20,"end":943}},{"label":"p","span":{"begin":944,"end":1764}},{"label":"p","span":{"begin":1765,"end":4354}},{"label":"figure","span":{"begin":4355,"end":5099}},{"label":"label","span":{"begin":4355,"end":4363}},{"label":"caption","span":{"begin":4365,"end":5099}},{"label":"p","span":{"begin":4365,"end":5099}}],"tracks":[{"project":"2_test","denotations":[{"id":"20649981-10701570-10705690","span":{"begin":212,"end":213},"obj":"10701570"},{"id":"20649981-16371252-10705691","span":{"begin":429,"end":430},"obj":"16371252"},{"id":"20649981-16371252-10705692","span":{"begin":499,"end":500},"obj":"16371252"},{"id":"20649981-9576516-10705693","span":{"begin":1276,"end":1278},"obj":"9576516"},{"id":"20649981-18937885-10705694","span":{"begin":1439,"end":1441},"obj":"18937885"},{"id":"20649981-10961852-10705695","span":{"begin":1577,"end":1579},"obj":"10961852"},{"id":"20649981-15977909-10705696","span":{"begin":2922,"end":2924},"obj":"15977909"},{"id":"20649981-19874910-10705697","span":{"begin":3006,"end":3008},"obj":"19874910"},{"id":"20649981-16371252-10705698","span":{"begin":3441,"end":3442},"obj":"16371252"},{"id":"20649981-10701570-10705699","span":{"begin":4728,"end":4729},"obj":"10701570"},{"id":"20649981-9576516-10705700","span":{"begin":4823,"end":4825},"obj":"9576516"},{"id":"20649981-18937885-10705701","span":{"begin":4897,"end":4899},"obj":"18937885"},{"id":"20649981-10701570-10705702","span":{"begin":5810,"end":5811},"obj":"10701570"}],"attributes":[{"subj":"20649981-10701570-10705690","pred":"source","obj":"2_test"},{"subj":"20649981-16371252-10705691","pred":"source","obj":"2_test"},{"subj":"20649981-16371252-10705692","pred":"source","obj":"2_test"},{"subj":"20649981-9576516-10705693","pred":"source","obj":"2_test"},{"subj":"20649981-18937885-10705694","pred":"source","obj":"2_test"},{"subj":"20649981-10961852-10705695","pred":"source","obj":"2_test"},{"subj":"20649981-15977909-10705696","pred":"source","obj":"2_test"},{"subj":"20649981-19874910-10705697","pred":"source","obj":"2_test"},{"subj":"20649981-16371252-10705698","pred":"source","obj":"2_test"},{"subj":"20649981-10701570-10705699","pred":"source","obj":"2_test"},{"subj":"20649981-9576516-10705700","pred":"source","obj":"2_test"},{"subj":"20649981-18937885-10705701","pred":"source","obj":"2_test"},{"subj":"20649981-10701570-10705702","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ecd2","default":true}]}]}}