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Phylogenetic Placement (phylogenetic + placement)
Selected AbstractsPHYLOGENETIC PLACEMENT OF AN UNUSUAL CORAL MUSHROOM CHALLENGES THE CLASSIC HYPOTHESIS OF STRICT COEVOLUTION IN THE APTEROSTIGMA PILOSUM GROUP ANT,FUNGUS MUTUALISMEVOLUTION, Issue 8 2009Bryn T. M. Dentinger The ,50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus Apterostigma cultivates a distantly related lineage comprised of the G2 and G4 groups. The G2 and G4 fungi were previously shown to form a monophyletic group sister to the thread-like coral mushroom family Pterulaceae. Here, we identify an enigmatic coral mushroom that produces both fertile and sterile fruiting structures as the closest free-living relative of the G4 fungi, challenging the monophyly of the Apterostigma -cultivated fungi for the first time. Both nonparametric bootstrap and Bayesian posterior probability support the node leading to the G4 cultivars and a free-living Pterula mushroom. These data suggest three scenarios that contradict the hypothesis of strict coevolution: (1) multiple domestications, (2) escape from domestication, (3) selection of single cultivar lineages from an ancestral mixed-fungus garden. These results illustrate how incomplete phylogenies for coevolved symbionts impede our understanding of the patterns and processes of coevolution. [source] PHYLOGENETIC PLACEMENT OF BOTRYOCOCCUS BRAUNII (TREBOUXIOPHYCEAE) AND BOTRYOCOCCUS SUDETICUS ISOLATE UTEX 2629 (CHLOROPHYCEAE),JOURNAL OF PHYCOLOGY, Issue 2 2004Hoda H. Senousy The phylogenetic placement of four isolates of Botryococcus braunii Kützing and of Botryococcus sudeticus Lemmermann isolate UTEX 2629 was investigated using sequences of the nuclear small subunit (18S) rRNA gene. The B. braunii isolates represent the A (two isolates), B, and L chemical races. One isolate of B. braunii (CCAP 807/1; A race) has a group I intron at Escherichia coli position 1046 and isolate UTEX 2629 has group I introns at E. coli positions 516 and 1512. The rRNA sequences were aligned with 53 previously reported rRNA sequences from members of the Chlorophyta, including one reported for B. braunii (Berkeley strain). Phylogenetic trees were constructed using distance, weighted maximum parsimony, and maximum likelihood, and their reliability was estimated using bootstrap analysis for distance and parsimony and Bayesian inference for likelihood. All methods showed, with high bootstrap or credibility support, that the four isolates of B. braunii form a monophyletic group whose closest relatives are in the genus Choricystis in the Trebouxiophyceae, whereas the previously reported B. braunii sequence is from a member of the Chlamydomonadales in the Chlorophyceae and isolate UTEX 2629 is a member of the Sphaeropleales in the Chlorophyceae. Polyphyly of these sequences was confirmed by Kishino-Hasegawa tests on artificial trees in which sequences were moved to a single lineage. [source] Reactive azo dye reduction by Shewanella strain J18 143BIOTECHNOLOGY & BIOENGINEERING, Issue 4 2006Carolyn I. Pearce Abstract A bacterial isolate designated strain J18 143, originally isolated from soil contaminated with textile wastewater, was shown to reduce intensely coloured solutions of the reactive azo dye, Remazol Black B to colourless solutions. Phylogenetic placement based on 16S rRNA gene sequence homology identified the bacterium as a Shewanella species. Based on results from analyses of the end products of dye decoloration of Remazol Black B and the simpler molecule, Acid Orange 7, using capillary electrophoresis, UV,visible spectrophotometry and liquid chromatography-mass spectrometry, we suggest that colour removal by this organism was a result of microbially mediated reduction of the chromophore in the dye molecules. Anaerobic dye reduction by Shewanella strain J18 143 was 30 times more efficient than the reduction carried out by aerated cultures. Whole cells used a range of electron donors for dye reduction, including acetate, formate, lactate, and nicotinamide adenine dinucleotide (NADH), with formate being the optimal electron donor. The impact of a range of process variables was assessed (including nitrate, pH, temperature, substrate concentration, presence of an extracellular mediator) and results suggest that whole cells of Shewanella J18 143 offer several advantages over other biocatalysts with the potential to treat azo dyes. © 2006 Wiley Periodicals, Inc. [source] Plumage-based phylogenetic analyses of the Merops bee-eatersIBIS, Issue 3 2004D. BRENT BURT I review previous systematic work on the family Meropidae and present phylogenetic hypotheses derived from my analyses of colour, pattern and shape variation in 30 plumage regions among species and subspecies in this family. Consistent patterns are seen across shallow portions of the trees. Uncertainty remains concerning the placement of several deep branches within this group's phylogeny. In particular, the phylogenetic placement of Meropogon forsteni and Merops breweri, M. ornatus, M. hirundineus and M. boehmi remains uncertain. The biogeographical patterns in the resultant trees are similar with either a Southeast Asian or African origin for the family, with most of the early diversification occurring in Africa, and with multiple independent subsequent invasions of non-African areas. [source] A phylogeny of Vetigastropoda and other "archaeogastropods": re-organizing old gastropod cladesINVERTEBRATE BIOLOGY, Issue 3 2010Stephanie W. Aktipis Abstract. The phylogenetic relationships among the "archaeogastropod" clades Patellogastropoda, Vetigastropoda, Neritimorpha, and Neomphalina are uncertain; the phylogenetic placement of these clades varies across different analyses, and particularly among those using morphological characteristics and those relying on molecular data. This study explores the relationships among these groups using a combined analysis with seven molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, cytochrome c oxidase subunit I [COI], myosin heavy-chain type II, and elongation factor-1, [EF-1,]) sequenced for 31 ingroup taxa and eight outgroup taxa. The deep evolutionary splits among these groups have made resolution of stable relationships difficult, and so EF-1, and myosin are used in an attempt to re-examine these ancient radiation events. Three phylogenetic analyses were performed utilizing all seven genes: a single-step direct optimization analysis using parsimony, and two-step approaches using parsimony and maximum likelihood. A single-step direct optimization parsimony analysis was also performed using only five molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, and COI) in order to determine the utility of EF-1, and myosin in resolving deep relationships. In the likelihood and POY optimal phylogenetic analyses, Gastropoda, Caenogastropoda, Neritimorpha, Neomphalina, and Patellogastropoda were monophyletic. Additionally, Neomphalina and Pleurotomariidae fell outside the remaining vetigastropods, indicating the need for further investigation into the relationship of these groups with other gastropods. [source] Sperm head morphology in 36 species of artiodactylans, perissodactylans, and cetaceans (Mammalia)JOURNAL OF MORPHOLOGY, Issue 2 2005Amy Downing Meisner Abstract Detailed descriptions of mammalian sperm morphology across a range of closely related taxa are rare. Most contributions have been generalized descriptions of a few distantly related mammalian species. These studies have emphasized a generalized ungulate sperm morphology, but have not underscored several important morphological differences in ungulate sperm, such as head shape. The present study is the first to document descriptions of sperm head morphology using cold field-emission scanning electron microscopy (FE-SEM) for a large number of closely related mammalian species. In total, the sperm of 36 species in three orders: Artiodactyla (even-toed ungulates), Cetacea (whales, porpoises, and dolphins), and Perissodactyla (odd-toed ungulates) were examined to gather new information relevant to the debate about the phylogenetic placement of cetaceans relative to terrestrial ungulates. In all species examined, the sperm heads were generally flattened and ovate in shape with a distinct apical ridge, although considerable variation in sperm head shape was detected, both within and between orders. In artiodactylans, the sperm head was uniformly flat in lateral view, whereas perissodactylan and cetacean sperm heads showed a distinct posterior thickening. In both artiodactylans and perissodactylans, the mitochondria were elongate and wound in a tight helix around the midpiece, whereas in cetaceans the mitochondria were rounded and appeared to be randomly arranged around the midpiece. Additionally, prominent ridges running along the anterior,posterior axis were observed in the postacrosomal region of the sperm head in four species of cetaceans. These ridges were not observed in any of the terrestrial ungulates examined. Pits or fenestrations were detected in the postacrosomal region in most artiodactylan species examined; these structures were not detected in perissodactylans or cetaceans. The equatorial segment of the acrosome was detected in the artiodactylan species examined, tentatively identified in perissodactylans, but not found in cetaceans. Its shape and location are described for relevant taxa. The presence of a recently reported substructure within the equatorial segment (the equatorial subsegment; Ellis et al. [2002] J Struct Biol 138:187,198) was detected in artiodactylans, and its shape is described for the species examined. © 2004 Wiley-Liss, Inc. [source] A NEW LYNGBYA SPECIES FROM AQUARENA SPRINGS, SAN MARCOS, TEXASJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Mills, J. T.1 & Johansen, J. R.2 1Department of Biology, St. Edwards University, Austin, TX 78704.USA; 2Department of Biology, John Carroll University, University Heights, OH 44118 USA A large Lyngbya species was isolated from Aquarena Springs, a series of freshwater, nonmineral springs flowing from the Edwards Aquifer that are impounded to form Spring Lake. The species grows in rather large, loosely formed clumps at a depth of 2-3 meters, and consists of sheathed filaments from 55 to 60 um in thickness containing a single trichome that ranges from 45-50 um in thickness in each sheath. The sheath is 5-6um thick. Our isolate is similar to Plectonema wollei Farlow ex Gomont, a large, thick sheathed morphospecies which has recently been placed in Lyngbya wollei (Farlow ex Gomont) Onodera et al. It is also similar to Blennothrix species, another large-trichomed genus with a distinctive form of false branching. However, the Lyngbya from Aquarena Springs shows no evidence of false branching of any type, forms loose clusters rather than mats, and is larger than any of the species currently described in any of the genera in question. When we sequenced the 16SrRNA and associated 16S-23S internal transcribed spacer (ITS), phylogenetic analysis indicated the taxon was most similar to Oscillatoria sanctae. However, there are so few taxa in the Oscillatoriaceae sensu stricto that have been sequenced, phylogenetic placement of the taxon by molecular analysis alone is not possible at present. Two different ITS configurations were obtained, one with both the tRNA "Ile" gene and the tRNA "Ala" gene, the other with no tRNA genes. Our work represents the first molecular analysis of any form in the large-trichomed Lyngbya clade. [source] Immigration, species radiation and extinction in a highly diverse songbird lineage: white-eyes on Indian Ocean islandsMOLECULAR ECOLOGY, Issue 12 2006BEN H. WARREN Abstract Molecular phylogenetic hypotheses of species-rich lineages in regions where geological history can be reliably inferred may provide insights into the scale of processes driving diversification. Here we sample all extant or recently extinct white-eye (Zosterops) taxa of the southwest Indian Ocean, combined with samples from all principal continental lineages. Results support a high dispersal capability, with at least two independent continental sources for white-eyes of the region. An early (within 1.8 million years ago) expansion into the Indian Ocean may have originated either from Asia or Africa; the three resulting lineages show a disparate distribution consistent with considerable extinction following their arrival. Africa is supported as the origin of a later expansion into the region (within 1.2 million years ago). On two islands, a pair of Zosterops species derived from independent immigrations into the Indian Ocean co-occur or may have formerly co-occurred, providing strong support for their origin by double-island colonization rather than within-island (sympatric or microallopatric) speciation. On Mauritius and La Réunion, phylogenetic placement of sympatric white-eyes allow us to rule out a scenario in which independent within-island speciation occurred on both islands; one of the species pairs must have arisen by double colonization, while the other pair is likely to have arisen by the same mechanism. Long-distance immigration therefore appears to be responsible for much of the region's white-eye diversity. Independent immigrations into the region have resulted in lineages with mutually exclusive distributions and it seems likely that competition with congeneric species, rather than arrival frequency, may limit present-day diversity. [source] Hybrid origin of a swordtail species (Teleostei: Xiphophorus clemenciae) driven by sexual selectionMOLECULAR ECOLOGY, Issue 3 2006AXEL MEYER Abstract The swordlike exaggerated caudal fin extensions of male swordtails are conspicuous traits that are selected for through female choice. Swords are one of only few examples where the hypothesis of a pre-existing bias is believed to apply for the evolution of a male trait. Previous laboratory experiments demonstrated that females prefer males with longer swords and even females from some swordless species show an affiliation for males of sworded species. Earlier phylogenetic studies based on maternally inherited mitochondrial DNA placed the sworded southern swordtail Xiphophorus clemenciae with swordless platies, contradicting its morphology-based evolutionary affinities. The analyses of new nuclear DNA markers now recover its traditional phylogenetic placement with other southern swordtails, suggesting that this species was formed by an ancient hybridization event. We propose that sexual selection through female choice was the likely process of hybrid speciation, by mating of platy females with males of an ancestral swordtail lineage. In artificial crosses of descendent species from the two potential ancestral lineages of X. clemenciae the hybrid and backcross males have swords of intermediate lengths. Additionally, mate choice experiments demonstrate that hybrid females prefer sworded males. These experimental lines of evidence make hybridization through xeno-specific sexual selection by female choice the likely mechanism of speciation. [source] Large subunit rDNA and rbcL gene sequence data place Petrohua bernabei gen. et sp. nov. in the Batrachospermales (Rhodophyta), but do not provide further resolution among taxa in this orderPHYCOLOGICAL RESEARCH, Issue 2 2007Morgan L. Vis SUMMARY The phylogenetic relationship among 12 previously described batrachospermalean taxa and a novel member of the order were investigated using the LSU and rbcL genes separately and in combination. The primary goal of this research was to establish the phylogenetic placement of a previously undescribed freshwater red alga from Chile. The results showed that the new entity with pseudoparenchymatous tube morphology is a member of the Batrachospermales and Petrohua bernabei gen. et sp. nov. is described herein. This is the first record to our knowledge of a Lemanea -like alga from Chile. It would appear that this thallus construction has evolved at least three times in the Batrachospermales and that the switch from a Batrachospermum -like construction to a pseudoparenchymatous construction may be a repeated adaptive response to turbulent waterfall habitats. In addition to providing information about a new freshwater red alga, this study sought to determine whether combining the data from two genes would produce a more robust phylogeny, particularly for intermediate nodes, to resolve familial relationships within the order. As with previous analyses, the Batrachospermales was resolved as a clade and support was high for relationships resolved among relatively recent nodes. Unfortunately, combining the LSU and rbcL data did not have the desired effect of more fully resolving intermediate nodes among the Batrachospermales. [source] | ||||||||||