Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.

https://pubag.nal.usda.gov/pubag/downloadPDF.xhtml?id=102&content=PDF

Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences

DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.

DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.

http://people.uncw.edu/pawlikj/2008AquatBotNagle.pdf

The habitat function of mangroves for terrestrial and marine fauna: a review

The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and a 192-kb megaplasmid that contains the majority of genes responsible for solvent production. Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of gene order, which has not been seen in comparisons of other genomes with similar, or, in some cases closer, phylogenetic proximity. This conservation allows the prediction of many previously undetected operons in both bacteria. However, the C. acetobutylicum genome also contains a significant number of predicted operons that are shared with distantly related bacteria and archaea but not with B. subtilis. Phylogenetic analysis is compatible with the dissemination of such operons by horizontal transfer. The enzymes of the solventogenesis pathway and of the cellulosome of C. acetobutylicum comprise a new set of metabolic capacities not previously represented in the collection of complete genomes. These enzymes show a complex pattern of evolutionary affinities, emphasizing the role of lateral gene exchange in the evolution of the unique metabolic profile of the bacterium. Many of the sporulation genes identified in B. subtilis are missing in C. acetobutylicum, which suggests major differences in the sporulation process. Thus, comparative analysis reveals both significant conservation of the genome organization and pronounced differences in many systems that reflect unique adaptive strategies of the two gram-positive bacteria.

Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum

Aims: Vegetation classification consistent with the
Braun-Blanquet approach is widely used in Europe for applied
vegetation science, conservation planning and land management.
During the long history of syntaxonomy, many concepts and names
of vegetation units have been proposed, but there has been no
single classification system integrating these units. Here we
(1) present a comprehensive, hierarchical, syntaxonomic system
of alliances, orders and classes of Braun-Blanquet syntaxonomy
for vascular plant, bryophyte and lichen, and algal communities
of Europe; (2) briefly characterize in ecological and
geographic terms accepted syntaxonomic concepts; (3) link
available synonyms to these accepted concepts; and (4) provide
a list of diagnostic species for all classes. LocationEuropean
mainland, Greenland, Arctic archipelagos (including Iceland,
Svalbard, Novaya Zemlya), Canary Islands, Madeira, Azores,
Caucasus, Cyprus. Methods: We evaluated approximately 10000
bibliographic sources to create a comprehensive list of
previously proposed syntaxonomic units. These units were
evaluated by experts for their floristic and ecological
distinctness, clarity of geographic distribution and compliance
with the nomenclature code. Accepted units were compiled into
three systems of classes, orders and alliances
(EuroVegChecklist, EVC) for communities dominated by vascular
plants (EVC1), bryophytes and lichens (EVC2) and algae (EVC3).
Results: EVC1 includes 109 classes, 300 orders and 1108
alliances; EVC2 includes 27 classes, 53 orders and 137
alliances, and EVC3 includes 13 classes, 24 orders and 53
alliances. In total 13448 taxa were assigned as indicator
species to classes of EVC1, 2087 to classes of EVC2 and 368 to
classes of EVC3. Accepted syntaxonomic concepts are summarized
in a series of appendices, and detailed information on each is
accessible through the software tool EuroVegBrowser.
Conclusions: This paper features the first comprehensive and
critical account of European syntaxa and synthesizes more than
100 yr of classification effort by European phytosociologists.
It aims to document and stabilize the concepts and nomenclature
of syntaxa for practical uses, such as calibration of habitat
classification used by the European Union, standardization of
terminology for environmental assessment, management and
conservation of nature areas, landscape planning and education.
The presented classification systems provide a baseline for
future development and revision of European syntaxonomy.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/avsc.12257

Vegetation of Europe: hierarchical floristic classification system of vascular plant, bryophyte, lichen, and algal communities

/pdf/phylogenetic-relationships-in-3a5e1i5yug.pdf

Phylogenetic relationships in

Phylogenetic relationships of all 10 recognized taxa of the genus Monanthes which is endemic to the Canary Islands and Salvage Islands, were investigated using the four data sets: morphology, sequences of the chloroplast DNA trnL (UAA) — trnF (GAA) intergenic spacer, ITS2 sequences of the nuclear ribosomal region and Random Amplified Polymorphic DNAs (RAPDs). In contrast to the molecular data, the morphological data were internally inconsistent which probably resulted from parallel or convergent evolution of morphological characters. The molecular data sets indicated that the genus is not monophyletic due to inclusion of the annual M. icterica which is the putative sister taxon of Aichryson, that M. polyphylla is the sister taxon of the perennial species of the genus, that M. muralis from Hierro is of allotetraploid origin and that M. lowei, M. minima, M. brachycaulos, M. laxiflora, M. anagensis and M. muralis from La Palma are closely related. Combined ITS2 sequences, trnL — trnF sequences and morphological data indicated that the relationships among three types of perennial growth forms, i.e. tiny rosettes, small, branched shrubs and diffuse branches shrublets, are highly dependent on the outgroup used. After deletion of the most distant outgroup and a taxon of alleged hybrid origin (M. muralis) relationships among the growth forms of Monanthes still could not be consistently resolved.

/pdf/phylogenetic-relationships-in-monanthes-crassulaceae-based-2pvrg6jiio.pdf

G.-J. Wijers

Papers

Phylogenetic relationships in

Phylogenetic relationships in Monanthes (Crassulaceae) based on morphological, chloroplast and nuclear DNA variation