Phylogenetic analysis supports horizontal transfer of P transposable elements

Nucleotide sequence comparisons were used to investigate the evolution of P transposable elements and the possibility that horizontal transfer has played a role in their occurrence in natural populations of Drosophila and other Diptera. The phylogeny of P elements was examined using published sequences from eight dipteran taxa and a new, partial sequence from Scaptomyza elmoi. The results from a number of different analyses are highly consistent and reveal a P-element phylogeny that contradicts the phylogeny of the species. At least three instances of horizontal transfer are necessary to explain this incongruence, but other explanations cannot be ruled out at this time.      

Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants

We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also includes the pantropical Grammitidaceae. The loxogrammoid lineage diverges first and is sister to a large clade comprising the three remaining species-rich lineages. One paleotropical clade includes the drynarioid and selligueoid ferns, whereas the second paleotropical clade includes the platycerioids, lepisoroids, microsoroids, and their relatives. The grammitids nest within the neotropical clade, although the sister taxon of this circum-tropic, epiphytic group remains ambiguous. Microsorum and Polypodium, as traditionally defined, were recovered as polyphyletic. The relatively short branch lengths of the deepest clades contrast with the long branch lengths leading to the terminal groups. This suggests that the polygrammoid ferns arose through an old, rapid radiation. Our analysis also reveals that the rate of substitution in the grammitids is remarkably higher relative to other polygrammoids. Disparities in substitution rate may be correlated with one or more features characterizing grammitids, including species richness, chlorophyllous spores, and an extended gametophytic phase.     

Mortality of Rocky Mountain elk in Michigan due to meningeal worm

Mortality from cerebrospinal parelaphostrongylosis caused by the meningeal worm (Parelaphostrongylus tenuis) has been hypothesized to limit elk (Cervus elaphus nelsoni) populations in areas where elk are conspecific with white-tailed deer (Odocoileus virginianus). Elk were reintroduced into Michigan (USA) in the early 1900s and subsequently greatly increased population size and distribution despite sympatric high-density (>or=12/km2) white-tailed deer populations. We monitored 100 radio-collared elk of all age and sex classes from 1981-94, during which time we documented 76 mortalities. Meningeal worm was a minor mortality factor for elk in Michigan and accounted for only 3% of mortalities, fewer than legal harvest (58%), illegal kills (22%), other diseases (7%), and malnutrition (4%). Across years, annual cause-specific mortality rates due to cerebrospinal parelaphostrongylosis were 0.033 (SE=0.006), 0.029 (SE=0.005), 0.000 (SE=0.000), and 0.000 (SE=0.000) for calves, 1-yr-old, 2-yr-old, and >or=3-yr-old, respectively. The overall population-level mortality rate due to cerebrospinal parelaphostrongylosis was 0.009 (SE=0.001). Thus, meningeal worm had little impact on elk in Michigan during our study despite greater than normal precipitation (favoring gastropods) and record (>or=14 km2) deer densities. Further, elk in Michigan have shown sustained population rates-of-increase of >or=18%/yr and among the highest levels of juvenile production and survival recorded for elk in North America, indicating that elk can persist in areas with meningeal worm at high levels of population productivity. It is likely that local ecologic characteristics among elk, white-tailed deer, and gastropods, and degree of exposure, age of elk, individual and population experience with meningeal worm, overall population vigor, and moisture determine the effects of meningeal worm on elk populations.     

Gymnogrammitis dareiformis is a polygrammoid fern (Polypodiaceae) – Resolving an apparent conflict between morphological and molecular data

 Maximum parsimony and maximum likelihood analyses of the combined data sets of two chloroplast genes, rbcL and rps4, demonstrate that nk;the monotypic genus Gymnogrammitis is part of the polygrammoid clade (Polypodiaceae + Grammitidaceae), and not the Davalliaceae as proposed in most studies. The genus forms a clade together with two Asiatic genera of the Polypodiaceae, Arthromeris and Selliguea. These last two genera have either simple or once-pinnate leaves, whereas Gymnogrammitis has highly divided (3- to 4-pinnate) blades. Two characters of this genus, the basic chromosome number of x=36 and the absence of indusia, support a relationship with the Polypodiaceae. Neither feature is found within Davalliaceae. Three morphological characters support the placement of Gymnogrammitis within the selligueoid lineage of Polypodiaceae: spores with a thick perine extending in microspines, sclerenchymatous strands in the rhizome, and non-clathrate rhizome scales. These results demonstrate that molecular and morphological data are phylogenetically congruent with the exception of blade dissection. Our study clearly shows the pitfalls of classifications based on single characters, and illustrates the importance of phylogenetic assessment of all taxonomic conclusions. Received November 22, 2001; accepted May 21, 2002 Published online: November 14, 2002 Addresses of the authors: Harald Schneider (e-mail: hschneid@duke.edu), Department of Biology, Duke University, Durham, North Carolina, 27708, USA; Current address: Albrecht-von-Haller Institut für Pflanzenwissenschaften der Universit?t G?ttingen, Abteilung Systematische Botanik, Untere Karspüle 2, D-37073 G?ttingen, Germany. Alan R. Smith, Ray Cranfill, University Herbarium, University of California, Berkeley, California 94720-2465, USA. Christopher H. Haufler, Terri Hildebrand, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA. Tom A. Ranker, University Museum and Department of Environmental, Population, and Organismic Biology, University of Colorado, Boulder, Colorado 80309, USA.     

Genetics, phylogenetics, and biogeography: Considering how shifting paradigms and continents influence fern diversity

About 25 years ago, a revolution began in evolutionary studies of seed-free vascular plants. Whereas common wisdom and laboratory-based observations had averred that minute spores and inbreeding of individual bisexual gametophytes diminished barriers to long distance migration, genetic analyses of sporophyte populations demonstrated outcrossing breeding systems that required two spores for each successful migration event. After those population-based discoveries, the processes controlling biogeographic patterns of ferns appeared to resemble those of seed plants, and vicariance took on renewed significance. More recently, data from DNA sequencing predicted that some of the most diverse extant fern families originatedafter the isolation of major land masses, and these new hypotheses also demanded fresh consideration of biogeographic assumptions. The Polypodiaceae yield phylogenetic insights through integration of DNA sequence analysis and biogeography. New evidence shows separate yet simultaneous radiations in the New and Old Worlds. By combining sequence data, vicariance, and a reassessment of morphological features, new family and generic boundaries are obtained. Contributors to this symposium discovered similar patterns in the systematics and biogeography of the seed-free vascular plants they studied. Although long distance migration remains an important factor in explaining fern distributions, local and recent radiations that result in species complexes are also significant in explaining fern biogeography.     

Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals

Background  

Vertebrate alpha (α)- and beta (β)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the α- and β-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil β-globin gene (ω) in the marsupial α-cluster, however, suggested that duplication of the α-β cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous α- and β-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus), to explore haemoglobin evolution at the stem of the mammalian radiation.     

Hierarchical analysis of variation in the mitochondrial 16S rRNA gene among Hymenoptera

Nucleotide sequences from a 434-bp region of the 16S rRNA gene were analyzed for 65 taxa of Hymenoptera (ants, bees, wasps, parasitoid wasps, sawflies) to examine the patterns of variation within the gene fragment and the taxonomic levels for which it shows maximum utility in phylogeny estimation. A hierarchical approach was adopted in the study through comparison of levels of sequence variation among taxa at different taxonomic levels. As previously reported for many holometabolous insects, the 16S data reported here for Hymenoptera are highly AT-rich and exhibit strong site-to-site variation in substitution rate. More precise estimates of the shape parameter (alpha) of the gamma distribution and the proportion of invariant sites were obtained in this study by employing a reference phylogeny and utilizing maximum-likelihood estimation. The effectiveness of this approach to recovering expected phylogenies of selected hymenopteran taxa has been tested against the use of maximum parsimony. This study finds that the 16S gene is most informative for phylogenetic analysis at two different levels: among closely related species or populations, and among tribes, subfamilies, and families. Maximization of the phylogenetic signal extracted from the 16S gene at higher taxonomic levels may require consideration of the base composition bias and the site-to-site rate variation in a maximum-likelihood framework.