ORIGINS AND AFFINITIES OF THE FILAMENTOUS GREEN ALGAL ORDERS CHAETOPHORALES AND OEDOGONIALES BASED ON 18S rRNA GENE SEQUENCES

The order Chaetophorales includes filamentous green algae whose taxonomic relationships to other chlorophycean orders is uncertain. Chaetophoralean taxa include filamentous species which are both branched and unbranched. Ultrastructural studies of zoospores have revealed similar flagellar apparatuses in a number of genera, including Uronema, Stigeoclonium, and Fritschiella, suggesting a close phylogenetic relationship among these taxa. The order Oedogoniales represents a second group of branched and unbranched filamentous green algae whose relationships to other chlorophycean orders also has been unclear. A possible close relationship between the Chaetophorales and Oedogoniales has been suggested. Using DNA sequences from the small-subunit ribosomal RNA gene (SSU rRNA) of several members of each order, we have examined the monophyly of the Chaetophorales and Oedogoniales, as well as the nature of their relationship to other chlorophycean orders. Our results show that chaetophoralean and oedogonialean taxa form separate monophyletic groups. Results also suggest that the two orders are not closely related to each other.     

Molecular analysis of Gigaspora (Glomales, Gigasporaceae)

This work presents a cooperative effort to integrate new molecular (isozyme and SSU analyses) characters into the morphological taxonomy of the genus Gigaspora (Glomales). Previous analyses of published Gigaspora SSU sequences indicated the presence of a few polymorphic nucleotides in the region delimited by primers NS71-SSU 1492'. In our study, the SSU of 24 isolates of arbuscular mycorrhizal (AM) fungi from the Gigasporaceae were amplified and the NS71-SSU 1492' region was directly sequenced. The corresponding sequences of four more isolates of AM fungi from Gigasporaceae, already published, were also included in our analyses. Three Gigaspora groups were identified on the basis of a 6 nucleotide-long 'molecular signature': Gigaspora rosea group ( G. rosea + G. albida ), Gigaspora margarita group ( G. margarita + G. decipiens ) and Gigaspora gigantea , which constituted a group by itself. The isozyme profiles (malate dehydrogenase, MDH) of 12 of these 28 isolates, and seven other isolates not sequenced, were compared. The results obtained further supported the grouping of isolates provided by the SSU analysis. Both SSU and MDH analysis indicated that two out of the 35 isolates had been misidentified, which was confirmed when their morphology was reassessed. The use of the Gigaspora intrageneric molecular signature as a quick, unambiguous and objective method to recognize Gigaspora isolates under any (field or laboratory) experimental conditions is suggested.     

Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora,Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al‐Adaid Lagoon in Qatar

The morphology, ontogenesis, and phylogenetic relationships of a halophile euplotid ciliates, Euplotes qatarensis nov. spec., isolated from the Khor Al‐Adaid Lagoon in Qatar were investigated based on live observation as well as protargol‐ and silver nitrate‐impregnated methods. The new species is characterised by a combination of features: the halophile habitat, a cell size of 50–65 × 33–40 μm, seven dorsal ridges, 10 commonly sized frontoventral cirri, two widely spaced marginal cirri, 10 dorsolateral kineties, and a double silverline pattern. The morphogenesis is similar to that of its congeners: (i) the oral primordium develops hypoapokinetally and the parental oral apparatus is retained; (ii) the frontoventral‐transverse field of five streaks gives rise to the frontal, ventral, and transverse cirri, but not to the cirri I/1 and the marginal cirri; (iii) the dorsal somatic ciliature develops by intrakinetal proliferation of basal bodies in two anlagen per kinety that are just anterior and posterior to the future division furrow; (iv) the caudal cirri are formed by the two rightmost dorsolateral kineties. The SSU rDNA sequence of E. qatarensis branches with full support in the Euplotopsis elegans–Euplotes nobilii–Euplotopsis raikovi clade. The closest related publicly available SSU rDNA sequence is the one of E. nobilii, with which E. qatarensis has 93.4% sequence similarity. Euplotes parawoodruffi Song & Bradbury, 1997 is transferred to the genus Euplotoides based on the absence of frontoventral cirrus VI/3.     

Do we need many genes for phylogenetic inference?

Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales+Spizellomycetales+Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis) and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha+Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize reconstruction artifacts.     

Characteristics and utility of nuclear-encoded large-subunit ribosomal gene sequences in phylogenetic studies of red algae

Primer sequences are described for amplifying and sequencing a large fragment (approximately 2500 b.p.) of the nuclear-encoded large-subunit ribosomal RNA gene (LSU) from red algae. In comparison to RuBisCo large-subunit gene (rbcL) and nuclear-encoded small-subunit ribosomal RNA gene (SSU) sequence data, LSU sequence data was intermediate in the number of phylogenetically informative positions and sequence divergence. Parsimony analysis of LSU sequences for 16 Gelidiales species resolved some nodes unresolved in rbcL and SSU parsimony trees. An analysis of LSU sequences from 13 species of red algae classified in 11 orders suggests that this gene may be useful in studies of higher-level relationships of red algae.     

Evolution of the diatoms: IX. Two datasets resolving monophyletic Classes of diatoms are used to explore the validity of adding short clone library sequences to the analysis

A previous study of available diatom sequences tested the value of multiple outgroups in analyses of the 18S ribosomal RNA gene aimed at recovering the three diatom Classes (Coscinodiscophyceae, Mediophyceae, Bacillariophyceae) as monophyletic groups. Of the 34 datasets tested in that study, three recovered these Classes and two of these are explored here in more detail. The major differences between these two datasets were the number of outgroups, the number of nucleotides selected for the analysis and the addition to the dataset of short clone library sequences, primarily from raphid pennate taxa. The addition of short sequences resulted in a smaller dataset in terms of total nucleotides analysed because of the filter selected in the ARB program to generate the final dataset for phylogenetic analysis. The 50% parsimony filter selects a base for the final dataset if that position is parsimony-informative in at least 50% of the sequences chosen for the analysis. Thus, with short sequences, fewer bases are available for selection in the final dataset. A final dataset with fewer nucleotides is produced from the original alignment than from a similar one with no filter applied. If no filter is applied, then a final dataset is produced with all full-length sequences. From these analyses, it was determined that the addition of short clone library sequences recovered sister relationships for certain raphid diatoms that go against conventional wisdom with regard to valve morphology. Thus, the smaller database caused some of the groupings to be unnatural. It was determined that the optimal resolution of the taxa in these datasets resulted from using only full length sequences and selected multiple outgroups. Results obtained from the reduced dataset would be a cause for concern with next generation sequencing in which short amplicons are used to identify taxa.     

Molecular Characterization of Gregarines from Sand Flies (Diptera: Psychodidae) and Description of Psychodiella n. g. (Apicomplexa: Gregarinida)

ABSTRACT. Sand fly and mosquito gregarines have been lumped for a long time in the single genus Ascogregarina and on the basis of their morphological characters and the lack of merogony been placed into the eugregarine family Lecudinidae. Phylogenetic analyses performed in this study clearly demonstrated paraphyly of the current genus Ascogregarina and revealed disparate phylogenetic positions of gregarines parasitizing mosquitoes and gregarines retrieved from sand flies. Therefore, we reclassified the genus Ascogregarina and created a new genus Psychodiella to accommodate gregarines from sand flies. The genus Psychodiella is distinguished from all other related gregarine genera by the characteristic localization of oocysts in accessory glands of female hosts, distinctive nucleotide sequences of the small subunit rDNA, and host specificity to flies belonging to the subfamily Phlebotominae. The genus comprises three described species: the type species for the new genus— Psychodiella chagasi ( Adler and Mayrink 1961 ) n. comb., Psychodiella mackiei ( Shortt and Swaminath 1927 ) n. comb., and Psychodiella saraviae ( Ostrovska, Warburg, and Montoya-Lerma 1990 ) n. comb. Its creation is additionally supported by sequencing data from other gregarine species originating from the sand fly Phlebotomus sergenti . In the evolutionary context, both genera of gregarines from mosquitoes ( Ascogregarina ) and sand flies ( Psychodiella ) have a close relationship to neogregarines; the genera represent clades distinct from the other previously sequenced gregarines.