No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Taxonomy of Phacus oscillans (Euglenaceae) and its close relatives-balancing morphological and molecular features
Abstract
The establishment of epitypes (together with emended diagnoses) for seven species of Phacus Dujardin: Phacus oscillans Klebs, Phacus parvulus Klebs, Phacus pusillus Lemmermann, Phacus skujae Skvortzov, Phacus inflexus (Kisselew) Pochmann, Phacus polytrophos Pochmann and Phacus smulkowskianus (Zakryś) Kusber was achieved thanks to literature studies, verification of morphological diagnostic features (cell size, cell shape), as well as molecular characters (SSU rDNA). Within the group of the investigated Phacus species, usually well distinguished morphologically, inter-specific 18S rDNA sequence similarity was 95.1-99.0%, whereas intra-specific 18S rDNA sequence similarity was 99.1-99.9%. Some of the phylogenetic relationships between the seven species have not been resolved, but the topology obtained indicates their assignment into two sister clades. The first clade is composed of two sister groups – P. parvulus and P. pusillus, while the second constitutes an assemblage of the remaining five species, between which the relationships remain unresolved.
... Errors in identification have been frequent, possibly as a result of morphological changes that depend on environmental conditions. Although several Phacus species have been morphologically well distinguished, Kosmala et al. (2007) and Karnkowska-Ishikawa et al. (2010) considered molecular signatures to be necessary for identification of closely related species. Even at the generic level, P. horridus was originally attributed to the genus Phacus due to its flat and leaf-like shape, but it was later transferred to the genus Lepocinclis Pertyi based on molecular data (Bennett and Triemer 2012). ...
... Linton et al. (2010) again emended the diagnosis of the genera Phacus and Lepocinclis based solely on molecular sequences, transferring Euglena limnophila and Lepocinclis salina to the genus Phacus. According to Kosmala et al. (2007) and Karnkowska-Ishikawa et al. (2010), taxonomic studies of both small and relatively large Phacus species have shown that these species are well defined molecularly and morphologically. ...
... However, the NJ strain of P. pleuronectes differed from the other three strains due to five nt differences in Helix 43. Karnkowska-Ishikawa et al. (2010) also used a molecular signature (helix E23_2 of the cytoplasmic SSU rRNA sequence) as a key characteristic for the investigation of seven small Phacus species: P. oscillans, P. parvulus, P. pusillus, P. skujae, P. inflexus, P. polytrophos, and P. smulkowskianus. In the case of P. skujae Daeri010910E strain had 18 exceptions in helix E23_2 when compared to other strains within the species. ...
The photosynthetic euglenoid genus Phacus is commonly found in freshwater; it is characterized by a rigid to semi-rigid cell, usually flat with numerous small discoid chloroplasts without pyrenoids. To understand the phylogenetic relationships among Phacus species, we used combined cytoplasmic SSU and LSU rDNA and plastid-encoded SSU and LSU rDNA sequence data from 82 strains, including seven Lepocinclis, three Discoplastis, one Eutreptia, and two Eutreptiella strains, as well as morphological data. The combined molecular dataset was analyzed using Bayesian and maximum likelihood methods. The resulting tree revealed that the genus Phacus was not monophyletic and fully resolved the phylogenetic relationships among eight lineages that were congruent with unique morphological characters in each clade. Molecular phylogeny and detailed morphological data led to the descriptions of seven new species: P. brevisulca, P. claviformis, P. hordeiformis, P. longisulca, P. minimus, P. paraorbicularis and P. viridioryza. The new species were well supported as independent species and formed close relationships with small Phacus species and P. orbicularis in the tree. In addition, the new species had unique molecular signatures and showed high genetic diversity. Although the strains of P. orbicularis sensu Hübner were morphologically very similar, the phylogenetic analyses and genetic diversity suggested that P. orbicularis sensu Hübner should be divided into two subclades.This article is protected by copyright. All rights reserved.
... Green euglenids display a limited number of diagnostic features, thus species recognition is often arguable (Karnkowska-Ishikawa et al., 2010Kim and Shin, 2014;Łukomska-Kowalczyk et al., 2015). Currently, an increasing number of species is being represented in sequence databases, thus phylogenetic relationships of taxa become resolved and supported (Kim et al., 2015;Łukomska-Kowalczyk et al., 2020a;Łukomska-Kowalczyk et al., 2020b). ...
... The factors impeding species assignment of the rest of the reads, belonging mainly to three genera: Colacium, Trachelomonas and Phacus, could have been various. One of them is probably low genetic variability of 18S rDNA sequences in some parts of the phylogenetic tree of autotrophic euglenids, for example in the Phacus oscillans clade (Karnkowska-Ishikawa et al., 2010;Kim and Shin, 2014) or the Phacus anomalus clade (Łukomska-Kowalczyk et al., 2020b), where most of the reads assigned as Phacus sp. are placed. Furthermore, in the whole genus Colacium, ranges of its interspecific and intraspecific variability significantly overlap (Łukomska-Kowalczyk et al., 2016), On the other hand, an incomplete database and errors in the taxonomic assignment of some reference sequences are considered to be the main issues that can hamper metabarcoding studies (Pawlowski et al., 2018;Sawaya et al., 2019;Fan et al., 2020). ...
Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species‐level identification of almost 90% of them. Fifty species were detected by metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB‐based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time, and generated costs were taken into consideration. After examination of the forementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation. This article is protected by copyright. All rights reserved.
... Guiry and Guiry 2020). The number of species changes as taxonomic verifications (based on morphological and DNA sequence data) are ongoing (Kosmala et al. 2007, Karnkowska-Ishikawa et al. 2010, Linton et al. 2010, Bennett and Triemer 2012, Kim and Shin 2014, Łukomska-Kowalczyk et al. 2015. As a result, our understanding of the phylogenetic relationships among them is also constantly changing. ...
... Cells small (18-23 9 7.5-12 µm), cylindrical, slightly flattened, narrowing at both ends, terminate with a blunt papilla (see Karnkowska-Ishikawa et al., 2010). ...
Morphological and molecular features were analyzed for species of Phacus to better understand the phylogenetic relationships among them and establish the taxonomy; the phylogenetic analyses were based on nSSU rDNA; the research resulted in 55 new sequences. The study included species available in algae collections and those isolated directly from the environment in Poland and Czech Republic. As a result, the obtained phylogenetic tree of Phacus includes 50 species, out of which 7 are represented on the tree for the first time (Phacus anacoelus, P. anomalus, P. curvicauda, P. elegans, P. lismorensis, P. minutus and P. stokesii) and many have been taxonomically verified. For all verified species, diagnostic descriptions were amended, the naming was reordered and epitypes were designated.
... During the last ten years, several revisions were made in the number of euglenoid genera, e.g. Euglena sensu lato (Bennet et al., 2014, Karnkowska-Ishikawa et al., 2011, 2013, 11 Kosmala et al., 2009, Linton et al., 2010, Triemer et al., 2006), Lepocinclis (Kosmala et al., 2005), Monomorphina (Kosmala et al., 2007b, Nudelman et al., 2005) and Phacus ( Karnkowska-Ishikawa, et al., 2010, Kosmala et al., 2007a, Łukomska-Kowalczyk, 2015. The question about cryptic species diversity is studied and discussed in several works, Kim et al. (2013a, b) described quite a high number of cryptic species in the genus Monomorphina and Cryptoglena;Kim & Shin (2014) studied the cryptic diversity in the genus Phacus with the description of seven new species and the work about morphological and genetic diversity of Euglena deses group with an emphasis on cryptic species was published by Kim et al. (2016). ...
... During the last ten years, several revisions were made in the number of euglenoid genera, e.g. Euglena sensu lato (Bennet et al., 2014, Karnkowska-Ishikawa et al., 2011, 2013, Kosmala et al., 2009, Linton et al., 2010, Triemer et al., 2006), Lepocinclis (Kosmala et al., 2005), Monomorphina (Kosmala et al., 2007b, Nudelman et al., 2005) and Phacus ( Karnkowska-Ishikawa, et al., 2010, Kosmala et al., 2007a, Łukomska-Kowalczyk, 2015. The question about cryptic species diversity is studied and discussed in several works, Kim et al. (2013a, b) described quite a high number of cryptic species in the genus Monomorphina and Cryptoglena;Kim & Shin (2014) studied the cryptic diversity in the genus Phacus with the description of seven new species and the work about morphological and genetic diversity of Euglena deses group with an emphasis on cryptic species was published by Kim et al. (2016). ...
This thesis is focused on study of photosynthetic euglenophytes (Euglenoida,
Euglenophyceae, Euglenales) in the Czech Republic and Poland. In the
introductory part, euglenoids are presented as a group of organisms along with
their taxonomy, ecological role and their inhabited biotopes together with
information about their distribution on global and local scales. The results and
implications for the euglenoid ecology, distribution and practical protection are
shown in the rest of the thesis. Main results are based on a long-term research
(2007-2014) using several literature sources in combination with field sampling,
which brings data about taxonomy, ecology and rarity of 284 taxa of the Czech
Republic’s algal flora with two new records of rare and interesting euglenoid
taxa, Trachelomonas bituricensis var. lotharingia and Trachelomonas saccasii.
The results of projects published in this thesis are focused on the study of (1)
euglenoid ecology connected with small and shallow water bodies (former claypit
pond in the eastern Poland, small mesotrophic pond in the southern part of
the Czech Republic) which brings interesting data about euglenoids’ ecological
preferences; (2) taxonomic conclusions about common euglenoid species,
Trachelomonas caudata, occurring in natural populations, where results show
that several morphologically similar species probably form a part of “caudatae
complex” and they are synonymous with T. caudata. Aggregate data on ecology
and the distribution of euglenoids in the Czech Republic are used in the Red List
of these algae as the beginning of the pilot work of the Red List of microscopic
algae as a guideline for the practical protection of biotopes.
... All rights reserved. genus Lepocinclis (Kosmala et al. 2005), for the genus Phacus (Kosmala et al. 2007a, Karnkowska-Ishikawa et al. 2010, Kim and Shin 2014) and for the genus Euglena (Kosmala et al. 2009, Karnkowska-Ishikawa et al. 2011, 2012). Sequences from Stromobomonas and Trachelomonas were assigned to the clades described by (Ciugulea et al. 2008), since taxonomic verification was not carried out for these two genera. ...
... A similar situation also occurs in diatoms (Hamsher et al. 2011, Zimmermann et al. 2011), Dinoflagellata (Stern et al. 2012), Foraminifera (Pawlowski & Lecroq 2010) and fungi (Schoch et al. 2012), where COI gene has sufficient variability, but amplification is problematic. Amplification of various fragments of 18S rDNA for most autotrophic euglenid species is easy as suggested by previous experience (i.e., Kosmala et al. 2005; Kosmala et al. 2007a Kosmala et al. , 2007b Karnkowska-Ishikawa et al. 2010). On the other hand, 18S rDNA sequences of euglenids are fast evolving and highly variable compared to other eukaryotes, preventing specific primers from amplifying non-euglenid sequences. ...
Autotrophic euglenids (Euglenophyceae) are common and abundant group of microbial eukaryotes in freshwater habitats. They have a limited number of features, which can be observed using light microscopy, thus species identification is often problematic. Establishing a barcode for this group is therefore an important step towards the molecular identification of autotrophic euglenids. Based on the literature we selected verified species and used a plethora of available methods to validate two molecular markers: COI and 18S rDNA (the whole sequence and three fragments separately) as potential DNA barcodes. Analyses of the COI gene were performed based on the dataset of 43 sequences (42 obtained in the present study) representing 24 species and the COI gene was discarded as a DNA barcode mainly due to a lack of universal primer sites. For 18S rDNA analyses we used dataset containing 263 sequences belonging to 86 taxonomically verified species. We demonstrated that the whole 18S rDNA is too long to be useful marker, but from the three shorter analysed variable regions we recommend variable regions V2V3 and V4 of 18S rDNA as autotrophic euglenid barcodes due to their high efficiency (above 95% and 90% respectively). This article is protected by copyright. All rights reserved.
... It is the highest intraspecies genetic diversity of nSSU rDNA noted for autotrophic euglenids so far; however, it is comparable to the previous estimations in the Phacus genus (intraspecies: 0-4.9%; interspecies: 1-18.8%; Shin 2014, Łukomska-Kowalczyk et al. 2015) as well as in other genera of autotrophic euglenids (Kosmala et al. 2007a,b, 2009, Karnkowska-Ishikawa et al. 2010, Kim et al. 2012. ...
Although Lepocinclis ovum is recognized as a cosmopolitan and common species, and Lepocinclis globulus is the type species of the genus Lepocinclis, their correct identification is nearly impossible. The reason is that over 30 morphologically similar taxa appear in the literature, but no good diagnostic features exist to distinguish most of them. Using environmental sampling and nuclear SSU rDNA sequencing, we delimited species within the group of Lepocinclis ovum‐like taxa. Morphological and molecular features were analyzed for taxa isolated from Poland and two cultured strains from algae collections. In the case of environmental sampling, DNA was obtained from a small number of cells (20‐400) isolated with a micropipette without setting up laboratory cultures (52 isolates), and phylogenetic analyses were based on the variation in nSSU rDNA. Apart from L. ovum and L. globulus, 13 other species were distinguished and four taxa (Lepocinclis conica comb. nov., L. fominii comb. nov., L. gracilicauda comb. nov., and L. pseudofominii nom. nov.) had their taxonomic ranks changed. For all verified species, diagnostic descriptions were amended and epitypes designated. The only exception was L. ovum, for which the epitype was questioned and thus, a new candidate for the epitype is suggested for future adoption.
... morphospecies). Cryptic species have been recognized in ciliates [5,6], dinoflagellates [7,8], testate amoebae [9][10][11], heterotrophic flagellates [4] and several groups of algae, including euglenids [12][13][14], eustigmatophytes [15], green algae [16,17], coccolithophorids [18], and diatoms [19][20][21]. Thus, the concept of cryptic (usually genetically different) species has been examined in a diverse range of protists. ...
The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide, from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rRNA gene divergences (up to 42.4%). Some strains grow best at salinities from 75 to 125‰ and represent halophiles. All but one of these belong to two geographically heterogeneous clusters that form a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rRNA gene phylogenies, unlike most previous analyses based on two sequences.
... Some other filamentous taxa such as Oscillatoria princeps vaucher ex gomont (1892: 206) in Mühlsteinova et al. (2018) and Drouetiella lurida (gomont) Mai & Johansen in Mai et al. (2018: 27) have also been epitypified. the practice of epitypification is employed not only for cyanobacteria, but for other algal groups as well, including euglenaceae (Karnkowska-Ishikawa et al. 2010, Karnkowska-Ishikawa et al. 2012, eustigmataceae (Kryvenda et al. 2018), andKlebsormidiophyceae (rindi et al. 2017). an epitype can be a specimen or an illustration selected to serve as an interpretative type when the holotype, lectotype, or previously designated neotype, or all original material associated with a validly published name, cannot be identified for the purpose of the precise application of the name to a taxon (ICN, article 9.9). ...
Strains with complete morphological match to Pleurocapsa fuliginosa and P. minor were isolated from Oahu, with another strain matching P. minor isolated from a wet rock face in Utah. Phylogenetically these baeocyte and pseudofilament producing strains fell in a single well-supported clade among a number of pleurocapsalean strains. They were sister to a clade of baeocyte-producing strains that lack the ability to form psuedofilaments and likely belong in an as-yet-to-be-described genus. Strains putatively named Pleurocapsa are scattered throughout the Pleurocapsales and Chroococcales, indicating a need for clear definition of the genus so that revisionary work and alpha-level taxonomy can move forward. To satisfy this need, P. fuliginosa HA4302-MV1 and P. minor HA4230-MV1 were chosen as neotype and epitype, respectively, establishing the genus based on molecular sequence data. In addition to the distinctive morphology of the genus, all Pleurocapsa species for which 16S-23S ITS regions are available have an unusually long, branched D5 helix at the termination of the ITS region. The sister clade of strains that lack the ability to form pseudofilaments also possess an unusually long and branched D5 helix as well, suggesting that this feature of the ITS region may be a family-level synapomorphy.
... With the advent of molecular sequencing, the division of taxa between Phacus and Lepocinclis have been validated and a new genus Discoplastis was erected to accommodate several species formerly belonging to the genus Euglena and characterized by numerous small plastids without pyrenoids and strong metaboly of the cell 26 . Genus Phacus and Lepocinclis are species-rich and have been intensively studied on the species-level in the last decade, and several new species have been described [27][28][29][30][31] . In contrast, genus Discoplastis comprises only two species 26 . ...
Photosynthetic euglenids (Euglenophyta) are a monophyletic group of unicellular eukaryotes characterized by the presence of plastids, which arose as the result of the secondary endosymbiosis. Many Euglenophyta plastid (pt) genomes have been characterized recently, but they represented mainly one family – Euglenaceae. Here, we report a comparative analysis of plastid genomes from eight representatives of the family Phacaceae. Newly sequenced plastid genomes share a number of features including synteny and gene content, except for genes mat2 and mat5 encoding maturases. The observed diversity of intron number and presence/absence of maturases corroborated previously suggested correlation between the number of maturases in the pt genome and intron proliferation. Surprisingly, pt genomes of taxa belonging to Discoplastis and Lepocinclis encode two inverted repeat (IR) regions containing the rDNA operon, which are absent from the Euglenaceae. By mapping the presence/absence of IR region on the obtained phylogenomic tree, we reconstructed the most probable events in the evolution of IRs in the Euglenophyta. Our study highlights the dynamic nature of the Euglenophyta plastid genome, in particular with regards to the IR regions that underwent losses repeatedly.
... ), Lepocinclis (Kosmala et al. 2005, Bennet & Triemer 2012), Monomorphina (Nudelman et al. 2005, Kosmala et al. 2007b, Kim et al. 2013b) and Phacus (Kosmala et al. 2007a ,Karnkowska-Ishikawa et al. 2010, Łukomska-Kowalczyk et al. 2015 ...
This study brings results of a floristic survey of photosynthetic euglenoids. Data in this survey come from a floristic examination of more than 200 localities during the years 2008–2014 in combination with the literature data recorded from the end of 19th century to the present. In this work, 284 euglenoid taxa which belong to the genera Colacium (6 taxa), Cryptoglena (2 species), Discoplastis (1 species), Euglena (48 taxa), Euglenaformis (1 species), Euglenaria (3 species), Lepocinclis (36 taxa), Monomorphina (7 species), Phacus (71 taxa), Strombomonas (16 taxa) and Trachelomonas (93 taxa) are listed. Four categories of rarity were designed—common (52 taxa), rare (44 taxa), very rare (120 taxa) and data deficient (68 taxa). In checklist, ecological characteristics (colonized habitats, life strategy, level of rarity) of taxa are shown. Number of species is compared with several works from European countries (Hungary, Great Britain, Poland, Romania, Slovak Republic, Slovenia and Ukraine). Taxonomic notes and new combinations reflecting recent works based on molecular-morphology are made and discussed. Results of this study bring next part to the knowledge of the Czech Republic algal flora.
... The advent of DNA sequencing combined with careful morphological investigation allowed some of the taxonomic confusions to be resolved. Many species have been verified, and new taxa have been described to accommodate the observed molecular and morphological diversity Kosmala et al. 2005Kosmala et al. , 2007aKosmala et al. , 2007bKosmala et al. , 2009Karnkowska-Ishikawa et al. 2010Kim et al. 2013aKim et al. , b, 2014Kim et al. 2016;Linton et al. 2010;Łukomska-Kowalczyk et al. 2015;Shin and Triemer 2004;Zakryś 1997;Zakryś et al. 2002Zakryś et al. , 2004Zakryś et al. , 2013. ...
Euglenids are a group of >1500 described species of single-celled flagellates with diverse modes of nutrition, including phagotrophy and photoautotrophy. The group also encompasses a clade of specialist “primary” osmotrophs (Aphagea) and, very likely, one group of phagotrophs that are ectosymbiont-supporting anaerobes (Symbiontida). Almost all euglenids are free-living. The (usually) one or two emergent flagella have thick paraxonemal (paraxial) rods and originate in a deep pocket/reservoir, while the cell surface is almost always supported by a pellicle of parallel proteinaceous strips underlain by microtubules. Cells with 4–12 strips are rigid; most of those with more strips (typically ~20–40) have them arranged helically and exhibit active cell deformation called “euglenid motion” or “metaboly.” Most phagotrophic euglenids are surface-associated bacterivores or eukaryovores that employ a flagellar gliding motility; they are abundant in marine and freshwater sediments. Photoautotrophic species (Euglenophyceae) constitute a single subclade within euglenids and have a plastid (chloroplast) of secondary endosymbiotic origin, with three bounding membranes. The plastid is typically green, with chlorophylls a + b, and was derived from a chloroplastidan alga related to the Pyramimonadales. Photoautotrophic euglenids move primarily by swimming, and most (members of the taxon Euglenales, e.g., Euglena) have a single emergent flagellum and are generally restricted to fresh and brackish waters.
... The advent of DNA sequencing combined with careful morphological investigation allowed some of the taxonomic confusions to be resolved. Many species have been verified, and new taxa have been described to accommodate the observed molecular and morphological diversity Kosmala et al. 2005Kosmala et al. , 2007aKosmala et al. , 2007bKosmala et al. , 2009Karnkowska-Ishikawa et al. 2010Kim et al. 2013aKim et al. , b, 2014Kim et al. 2016;Linton et al. 2010;Łukomska-Kowalczyk et al. 2015;Shin and Triemer 2004;Zakryś 1997;Zakryś et al. 2002Zakryś et al. , 2004Zakryś et al. , 2013. ...
Euglenids are a group of >1500 described species of single-celled flagellates with diverse modes of nutrition, including phagotrophy and photoautotrophy. The group also encompasses a clade of specialist “primary” osmotrophs (Aphagea) and, very likely, one group of phagotrophs that are ectosymbiont-supporting anaerobes (Symbiontida). Almost all euglenids are free-living. The (usually) one or two emergent flagella have thick paraxonemal (paraxial) rods and originate in a deep pocket/reservoir, while the cell surface is almost always supported by a pellicle of parallel proteinaceous strips underlain by microtubules. Cells with 4–12 strips are rigid; most of those with more strips (typically ~20–40) have them arranged helically and exhibit active cell deformation called “euglenid motion” or “metaboly.” Most phagotrophic euglenids are surface-associated bacterivores or eukaryovores that employ a flagellar gliding motility; they are abundant in marine and freshwater sediments. Photoautotrophic species (Euglenophyceae) constitute a single subclade within euglenids and have a plastid (chloroplast) of secondary endosymbiotic origin, with three bounding membranes. The plastid is typically green, with chlorophylls a + b, and was derived from a chloroplastidan alga related to the Pyramimonadales. Photoautotrophic euglenids move primarily by swimming, and most (members of the taxon Euglenales, e.g., Euglena) have a single emergent flagellum and are generally restricted to fresh and brackish waters.
... geniculata), but interspecies divergence ranged from 7.6% (between E. geniculata and E. pseudochadefaudii) to 5.9% (between E. pseudostellata and E. viridis; Kosmala et al. 2009). According to Karnkowska-Ishikawa et al. (2010), relatively small Phacus species displaying clearly distinguishable morphologies showed lower molecular divergence than Euglena species; the nr SSU rDNA sequence divergence among them ranged from 4.8% (between Phacus polytrophos ASW08018 and P. pusillus CCAC0096) to 0.9% (between P. oscillans and P. smulkowskianus ACOI1226). Molecular divergence between species within the genus Monomorphina, however, ranged from 13.8% (between M. pyrum SAG1244-5 and M. aenigmatica CCAP1261/9) to 10.0% (between M. pyrum ACOI2583 and M. pseudopyrum CCAC0093). ...
... Five of the species they recognized were new. Their study builds on others who have used molecular sequence criteria to diagnose euglenid species (Marin et al., 2003;Kosmala et al., 2007Kosmala et al., , 2009Karnkowska-Ishikawa et al., 2010;Kim et al., 2010;Linton et al., 2010). In addition to euglenids, new cryptic species of green algae have also been described based primarily on molecular evidence, but sometimes with congruent support from SEM (Fawley et al., 2011). ...
A total of 27 strains of Oculatella were isolated, characterized and sequenced, and analysed phylogenetically with an additional environmental clone from the Atacama Desert and 10 strains isolated and sequenced by others. The strains were clearly separated based upon phylogenetic analyses conducted with a concatenated alignment of the 16S rRNA and 16S-23S ITS region of the ribosomal operons in the genus Oculatella. Differences in secondary structure of the conserved domains of the ITS region, as well as comparative analysis of P-distance among ITS regions, served to separate the strains into distinct taxonomic units. Seven new
species of Oculatella were described, including four from arid to semi-arid soils (O. atacamensis, O. mojaviensis, O. coburnii, O. neakameniensis) and three from more mesic habitats, including a temperate lake (O. hafneriensis), a desert waterfall (O. cataractarum) and a Hawaiian sea cave (O. kauaiensis). The soil forms show statistically significant morphological differences, but the ranges overlap to a degree that they are not diagnosable by morphology, and these four cryptic species are characterized here using molecular characters. The more mesic species, including the type species from Mediterranean hypogea, O. subterranea, are all morphologically distinct from each other and from all four soil taxa. This report is the first to use solely molecular criteria to distinguish cryptic species of cyanobacteria.
... This has led to a history of taxonomic duplications and re-descriptions, as well as the formulation of artificial classification schemes. Recently, the advent of molecular phylogenies has helped to resolve some of those taxonomic confusions (Bennett et al. 2014;Karnkowska-Ishikawa et al. 2010Kosmala et al. 2005;Linton et al. 2010;Marin et al. 2003;Milanowski et al. 2006;Triemer et al. 2006;Zakry s et al. 2002). ...
Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear-encoded genes (nSSU, nLSU, hsp90), one chloroplast-encoded gene (cpSSU) and one nuclear-encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well-defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.This article is protected by copyright. All rights reserved.
... Prodromus sinic a řas (Poulíčková et al., 2004) je seznamem taxonů, ve kterém není řešena platnost a synonymika jmen. Taxonomické korekce byly provedeny podle: a) molekulárních prací (Marin et al., 2003); b) molekulárně-morfologických prací (Kosmala et al., 2005, Kosmala et al., 2007a, Kosmala et al., 2007b, Kosmala et al., 2009, Karnkowska-Ishikawa et al., 2010); c) floristicko-taxonomických prací (Conforti, 1999, Couté & Tell, 2006, Da et al., 2009, Kim et al., 2000, Wołowski, 1998, Wołowski, 2002, Wołowski & Hindák, 2004, Zakryś, 1986); ...
... geniculata), but interspecies divergence ranged from 7.6% (between E. geniculata and E. pseudochadefaudii) to 5.9% (between E. pseudostellata and E. viridis; Kosmala et al. 2009). According to Karnkowska-Ishikawa et al. (2010), relatively small Phacus species displaying clearly distinguishable morphologies showed lower molecular divergence than Euglena species; the nr SSU rDNA sequence divergence among them ranged from 4.8% (between Phacus polytrophos ASW08018 and P. pusillus CCAC0096) to 0.9% (between P. oscillans and P. smulkowskianus ACOI1226). Molecular divergence between species within the genus Monomorphina, however, ranged from 13.8% (between M. pyrum SAG1244-5 and M. aenigmatica CCAP1261/9) to 10.0% (between M. pyrum ACOI2583 and M. pseudopyrum CCAC0093). ...
A morphological and molecular examination of the genus Monomorphina was conducted on 46 strains isolated mainly from Korea. The strains were divided into two types based on morphological data: Monomorphina aenigmatica and M. pyrum ‐ like species. Phylogenetic analysis based on a combined data set of nuclear SSU and LSU and plastid SSU and LSU rDNA showed that the strains could be divided into eight clades: Clade A of M. aenigmatica, Clade B of the isolates (M. pyropsis) from Michigan, USA, Clade C of M. pseudopyrum, Clade D of the isolates (M. pyroria) from Bremen, Germany, Clade E of M. soropyrum, Clade F of M. pyriformis, Clade G of M. parapyrum, and Clade H of M. pyrum. Six of these clades came from strains that would be considered M. pyrum sensu Kosmala et Zakryś, one of which could be recognized as a traditional species (M. pyrum) and five were designated as new species; each species had unique molecular signatures at nr SSU rDNA helix 17 and 17′ and spacer E23_14′‐E23_15. The species of Monomorphina had a wide range of genetic diversity with interspecies sequence similarity of 85.6%–97.1% and intraspecies similarity of 96.4%–99.9%. Our results suggested that genetic diversity found in the M. pyrum complex justifies the recognition of a minimum of eight species within this genus, based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.
... In algae, 18S rDNA, together with other sequences, have been used in phylogenetic analysis of many organisms within Chlorophyceae (Wilcox et al., 1992;Friedl and O'Kelly, 2002;Hoham et al., 2002;Rindi et al., 2009) , Raphidophyceae (Cavalier-Smith andChao, 1996), and Pelagophyceae (Bailey and Andersen, 1999). In euglenoids, 18S rDNA sequences have been used in most published studies (Montegut-Felkner and Triemer, 1997;Linton et al., 1999Linton et al., , 2010Preisfeld et al., 2000;Sittenfeld et al., 2002;Brosnan et al., 2003;Marin et al., 2003;Shin and Triemer, 2004;Kosmala et al., 2005Kosmala et al., , 2007Kosmala et al., , 2009Milanowski et al., 2006;Triemer et al., 2006;Karnkowska-Ishikawa et al., 2010;Kim et al., 2010). Chloroplast SSU rDNA (16S rDNA), although less common, has also been used in molecular phylogenies of euglenoids (Milanowski et al., 2001(Milanowski et al., , 2006Kosmala et al., 2009;Kim et al., 2010). ...
During a survey for marine microalgal resources, we isolated a rare marine euglenoid from the coastal waters of Qingdao, China in 2009, and established a pure culture. Electron microscopic and molecular phylogenetic (18S rDNA and 16S rDNA sequences) analyses revealed a close affinity with Eutreptiella gymnastica, a bloom-forming species. Different culture conditions were monitored to understand optimal E. gymnastica growth characteristics. The optimal growth conditions in a batch culture of this isolate were 20°C, 160 μmol photons/(m2·s) of white light, and a salinity of 10–31. Nutrient experiments demonstrated that growth increased dramatically with a phosphorus concentration greater than 72 μmol/L. Understanding the effect of culture conditions on E. gymnastica may help understanding the blooming mechanism of this alga in its natural environment.
... These sequences were attached to the diagnostic descriptions (Kosmala et al. 2007a,b, Karnkowska-Ishikawa et al. 2010). In this work, we departed from the above rule. ...
The establishment of epitypes (together with the emended diagnoses) for three species of Euglenaria Karnkowska, E. W. Linton et Kwiatowski [Eu. anabaena (Mainx) Karnkowska et E. W. Linton; Eu. caudata (Hübner) Karnkowska et E. W. Linton; and Eu. clavata (Skuja) Karnkowska et E. W. Linton] and two species of Euglena Ehrenberg [E. granulata (Klebs) Schmitz and E. velata Klebs] was achieved due to literature studies, verification of morphological diagnostic features (cell size, cell shape, number of chloroplasts, the presence of mucocysts), as well as molecular characters (SSU rDNA). Now all these species are easy to identify and distinguish, despite their high morphological similarity, that is, spindle-shaped (or cylindrically spindle-shaped) cells and parietal, lobed chloroplasts with a single pyrenoid, accompanied by bilateral paramylon caps located on both sides of the chloroplast. E. granulata is the only species in this group that has spherical mucocysts. E. velata is distinguished by the largest cells (90–150 μm) and has the highest number of chloroplasts (>30). Eu. anabaena has the fewest chloroplasts (usually 3–6), and its cells are always (whether the organism is swimming or not) spindle-shaped or cylindrically spindle-shaped, in contrast to the cells of Eu. clavata, which are club-shaped (clavate) while swimming and only after stopping change to resemble the shape of a spindle or a cylindrical spindle; Eu. clavata has numerous chloroplasts (15–20). Eu. caudata is characterized by asymmetrical spindle-shaped (fusiform) cells, that is, with an elongated rear section and a shorter front section; the number of chloroplasts normally ranges from 7 to 15.
... The last 10 years have seen much taxonomic reclassification of these organisms, based on morphological and molecular data. As a result, the number of previously recognized species has been greatly reduced (Zakryś, 1997;Zakryś et al., 1997Zakryś et al., , 2002Zakryś et al., , 2004Shin & Triemer, 2004;Kosmala et al., 2005Kosmala et al., , 2007aKosmala et al., , 2007bKosmala et al., , 2009Karnkowska-Ishikawa et al., 2010, 2011, 2013 and some new species have been described based solely on molecular data (Kosmala et al., 2007a(Kosmala et al., , 2009). Among the green euglenoids, as is the case with many other groups of organisms, it has become increasingly difficult to find a new species that is clearly distinct morphologically. ...
In this paper, we describe a new photosynthetic euglenoid species, Euglenaria clepsydroides Zakryś, sp. nov., found in Poland. A large population of this species exists in a few, small, eutrophic bodies of water inside the Masurian Landscape Park (covering a part of the Masurian Lake District in Poland). The characteristic and atypical (hourglass-like) cell shape sets it well apart from the other species that have been described up to now. This atypical cell shape has so far been observed only in three species – Lepocinclis constricta, Euglena undulata and Euglena gymnodinioides – whose other morphological characteristics, such as the number and morphology of chloroplasts, the lack of mucocysts, and nuclear SSU rDNA sequence data, exclude the possibility that they could be close relatives of Euglenaria clepsydroides. On the phylogenetic tree, the new species is situated within the Euglenaria clade. While it is a sister group of the clade that includes representatives of Euglenaria anabaena, the two species are clearly morphologically distinct.
... Our research fully supports observations made by Pringsheim (1956) and many other authors (including Ehrenberg 1835, 1838, Klebs 1883, Lemmermann 1910, Johnson 1944, Chu 1946, Gojdics 1953, Huber-Pestalozzi 1955, Pringsheim 1956, Popova 1966, regarding the high morphological diversity among E. deses with respect to the size and shape of the cells, the size and shape of the chloroplasts, and the presence and the number of large paramylon grains, at the same time showing that these characteristics have no diagnostic significance. The high diversity of the morphological forms of E. deses occurring in nature is not surprising, since it may be the result of adaptation to life in rapidly changing and diverse habitat conditions, something that numerous authors have suggested when referring to other euglenoid species (Pringsheim 1956, Popova 1966, Zakryś and Kucharski 1996, Zakryś et al. 2002, 2004, Kosmala et al. 2005, 2007a,b, 2009, Karnkowska-Ishikawa et al. 2010, and many others). For this reason and based on phylogenetic analyses, morphological studies, and literature analysis, it is logical to recognize only three species in the ''E. ...
For this study, we have examined the literature and the morphological diversity, as well as analyzed the nuclear SSU rDNA sequences of two very common and cosmopolitan species formerly known as Euglena deses Ehrenb. and Euglena intermedia (G. A. Klebs) F. Schmitz. Our studies have shown that there is evidence for distinguishing only one species (E. deses). Here, we define new diagnostic features for E. deses, namely, periplast ornamentation (the presence of small papillae—discovered for the first time in this species) and the lateral location of the anterior canal opening, from which the flagellum emerges. We also designate the epitype and emend the diagnosis for E. deses.
Although Strombomonas verrucosa has been the type of the genus name for almost 100 years, its lack of clear diagnostic traits has rendered morphological distinction from its congeners almost impossible. As such, a study was conducted combining previously unused morphological data (chloroplast characters) with molecular data (sequences of nuclear SSU, LSU and plastid‐encoded SSU rDNA) and extensive literature review. The study focused on environmental samples obtained from Poland and China and resulted in 51 new sequences representing three molecular markers (17 nSSU, 16 nLSU and 18 cpSSU rDNA). Revised delimitations of the genus Strombomonas and its type S. verrucosa are presented that include new and detailed diagnostic characters. In addition to the type, we recognize nine species: S. acuminata , S. borystheniensis , S. eurystoma , S. fluviatilis , S. gibberosa , S. maxima , S. ovalis , S. schauinslandii , S. triquetra . Three of these are incorporated into a phylogeny for the first time ( S. fluviatilis , S. gibberosa , S. schauinslandii ). To improve the efficiency of DNA isolation from loricate cells, a protocol utilising a chelating resin for DNA isolation – following the lead of diatomologists – has been adjusted for Euglenaceae and is also presented.
Photosynthetic euglenoids represent a large group of flagellates, which could be found in most freshwater, marine and brackish habitats, but also in extreme environments with low pH or in moist soil. The existence of this group has been known for a relatively long led to the description of wide morphological variability. In my contribution, I briefly summarize the possible causes of this morphological variability (effect of the environment and phenotypic plasticity during ontogenesis) and current knowledge about the taxonomy of these protist organisms, showing the most recent changes and descriptions of new genera.
A number of heterocytous, mat-forming, tapering cyanobacteria in the Rivulariaceae have recently been observed in both the Atlantic and Pacific coasts in the rocky intertidal and supratidal zones. These belong to the genera Nunduva, Kyrtuthrix, and Phyllonema, and have been the subject of several recent papers. Herein, two new species of Nunduva (N. komarkovae, N. sanagustinensis) and two new species of Kyrtuthrix (K. munecosensis, K. totonaca) are characterized and described from the coasts Mexico. Genetic separation based on the 16S-23S ITS region was pronounced (>10% in all comparisons). Morphological differences between all existing species in these two genera were also observed, but the group is morphologically complex and these taxa are considered pseudocryptic. Nunduva and Kyrtuthrix remain morphologically and phylogenetically separate even with the addition of new species. However, how long will this remain the case? Many new genera and species of cyanobacteria have recently been described. Will the taxonomy of cyanobacteria eventually become saturated? Will we start to see multiple populations for the same cryptic species, or will future taxonomists collapse multiple species into fewer species, or multiple genera into single genera. The description of even more Nunduva and Kyrtuthrix species causes us to pause and evaluate the future of cyanobacterial taxonomy. These same questions are faced by algal taxonomists studying other phyla, and the resolution may ultimately be similar.
Soil cyanobacteria are crucial biological components of soil crusts and carry out many functions in dryland ecosystems. Despite this importance, their taxonomy and population genetics remain poorly known. We isolated 42 strains of simple filamentous cyanobacteria previously identified as Pseudophormidium hollerbachianum from 26 desert locations in the North and South America and characterized these strains using a total evidence approach, i.e., using both morphological and molecular data to arrive at taxonomic decisions. Based on a phylogenetic analysis of 16S rRNA gene sequences, we propose and characterize Myxacorys gen. nov. with two new species Myxacorys chilensis, the generitype, and M. californica. We also found distinct 16S-23S ITS sequence variability within species in our dataset. Especially interesting was the presence of two distinct lineages of M. californica obtained from locations in close spatial proximity (within a few meters to kms from each other) suggesting niche differentiation. The detection of such unrecognized lineage-level variability in soil cyanobacteria has important implications for biocrust restoration practices and conservation efforts. This article is protected by copyright. All rights reserved.
Thirteen phytoflagellates, ten of them euglenophytes, are described and documented for the “Hohe Garbe” in the nature reserve “Aland-Elbe-Niederung” at the lowlands of the River Elbe.
Eleven flagellate species are new for Saxony-Anhalt (Germany). The occurrences are discussed with respect to flood plain ecology. Phacus warszewiczii is depicted for Germany for the first time.
Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and cell movement. Euglenids exhibit diverse modes of nutrition, including phagotrophy and photosynthesis. Photosynthetic species (Euglenophyceae) constitute a single subclade within euglenids. Their plastids embedded by three membranes arose as the result of a secondary endosymbiosis between phagotrophic eukaryovorous euglenid and the Pyramimonas-related green alga. Within photosynthetic euglenids three evolutionary lineages can be distinguished. The most basal lineage is formed by one mixotrophic species, Rapaza viridis. Other photosynthetic euglenids are split into two groups: predominantly marine Eutreptiales and freshwater Euglenales. Euglenales are divided into two families: Phacaceae, comprising three monophyletic genera (Discoplastis, Lepocinclis, Phacus) and Euglenaceae with seven monophyletic genera (Euglenaformis, Euglenaria, Colacium, Cryptoglena, Strombomonas, Trachelomonas, Monomorphina) and polyphyletic genus Euglena. For 150 years researchers have been studying Euglena based solely on morphological features what resulted in hundreds of descriptions of new taxa and many artificial intra-generic classification systems. In spite of the progress towards defining Euglena, it still remains polyphyletic and morphologically almost undistinguishable from members of the recently described genus Euglenaria; members of both genera have cells undergoing metaboly (dynamic changes in cell shape), large chloroplasts with pyrenoids and monomorphic paramylon grains. Model organisms Euglena gracilis Klebs, the species of choice for addressing fundamental questions in eukaryotic biochemistry, cell and molecular biology, is a representative of the genus Euglena.
Two populations of Rivularia-like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase-Escalante National Monument, a desert park-land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae. This article is protected by copyright. All rights reserved.
This research aims to create a list and make a description of Phacus species found in polytypic ponds around Ekaterinburg in accordance with recent taxonomy changes. We used traditional methods (plankton nets) of collecting samples from water reservoirs to trap and concentrate the plankton in focus for our study. We analyzed species’ composition of the genus Phacus in various water reservoirs in Ekaterinburg and its vicinity. As a result, 17 species and one subspecies were identifi ed according to the new genus taxonomy. All discovered species are new for Middle Ural. Descriptions and pictures of every recorded Phacus species are provided.
This report describes the discovery of the rare euglenoid taxon Trachelomonas bituricensis var. lotharingia in a small mesotrophic pond in the Czech Republic. Only limited data are available on the distribution of this taxon as same as for typical variety of Trachelomonas bituricensis, even though this taxon is morphologically very well defined. I provide a brief discussion of the taxonomic validity of this taxon based only on morphological features, which are characteristic for the taxonomy of the genus Trachelomonas. This finding is completely new for the algal flora of the Czech Republic. This report provides new information about the worldwide distribution of this taxon and its ecology.
Euglenoids form a diverse group of eukaryotic organisms that may have arisen a billion years or more before the origins of plants and animals. They are largely unicellular flagellates with only one genus, and they form colonies. There are nearly 2,900 nominal species for the major photosynthetic taxa, but, of these, only about 800 are accepted as taxonomically valid. Modern phylogenetics has caused numerous changes in euglenoid taxonomy, which keeps the number of accepted species in constant transition. The majority of photosynthetic taxa live in freshwater, and only a few taxa are found in seas and oceans. The most common habitats are eutrophic small water bodies (ditches, canals, ponds). This chapter provides a classification of the freshwater representatives of the Euglenophyceae, with descriptions of their morphology, reproduction, and ecology, as well as color photographs and line drawings of the taxa and a key to genera.
Although Phacus longicauda is the type species of the genus Phacus and one of the most common species among autotrophic euglenids, its correct identification is nearly impossible. Over 30 morphologically similar taxa appear in the literature, but there are no good diagnostic features to distinguish them. Using environmental sampling and whole genome amplification, we delimited species within the Phacus longicauda complex. Morphological and molecular characters were analysed for 36 strains isolated from environmental samples (mainly from Poland). DNA was obtained from a small number of cells (20-30) isolated with a micropipette from every sample, i.e., without setting up laboratory cultures, and phylogenetic analyses were based on variation in nSSU rDNA. Apart from Phacus longicauda, three other species: Phacus circumflexus, Phacus helikoides and Phacus tortus were distinguished. Phacus cordata comb. nov. Zakryś et M. Łukomska and Phacus rotunda comb. nov. Zakryś et M. Łukomska had their taxonomic ranks changed and two species new for science, Phacus cristatus sp. nov. Zakryś et M. Łukomska and Phacus crassus sp. nov. Zakryś et M. Łukomska, were described. For all verified species diagnostic descriptions were amended and epitypes designated. This article is protected by copyright. All rights reserved.
The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one-factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t-test, p < 0.05), than those for interspecies variations (>2.9% and >26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples.This article is protected by copyright. All rights reserved.
The photosynthetic euglenoid genus Cryptoglena is differentiated from other euglenoid genera by having a longitudinal sulcus, one chloroplast, two large trough‐shaped paramylon plates positioned between the chloroplast and pellicle, and lack of metaboly. The genus contains only two species. To understand genetic diversity and taxonomy of Cryptoglena species, we analyzed molecular and morphological data from 25 strains. A combined data set of nuclear SSU and LSU and plastid SSU and LSU rRNA genes was analyzed using Bayesian, maximum likelihood, maximum parsimony, and distance (neighbor joining) methods. Although morphological data of all strains showed no significant species‐specific pattern, molecular data segregated the taxa into five clades, two of which represented previously known species: C. skujae and C. pigra, and three of which were designated as the new species, C. soropigra, C. similis, and C. longisulca. Each species had unique molecular signatures that could be found in the plastid SSU rRNA Helix P23_1 and LSU rRNA H2 domain. The genetic similarity of intraspecies based on nr SSU rDNA ranged from 97.8% to 100% and interspecies ranged from 95.3% to 98.9%. Therefore, we propose three new species based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.
The paper comprises descriptions of 35 Euglena species including 3 new species: Euglena navicula sp.
nov., .E gymnodinioides sp. nov., E. smulkowskial?a sp. nov. lt also coritains decriptions of 5 varieties,
including2newones: EuglenamesniliDeflandreetDusivar.majorvar.nov.,E. desesEhr.vat.digrata
var. nov. Also a review of all available Polish papers on taxonomy and occurrence of Euglena spp.
in Poland is included. Three new subgenera: Euglena, Calliglena, Discoglena of the genus Euglena are established.
Guidelines for submitting commentsPolicy: Comments that contribute to the discussion of the article will be posted within approximately three business days. We do not accept anonymous comments. Please include your email address; the address will not be displayed in the posted comment. Cell Press Editors will screen the comments to ensure that they are relevant and appropriate but comments will not be edited. The ultimate decision on publication of an online comment is at the Editors' discretion. Formatting: Please include a title for the comment and your affiliation. Note that symbols (e.g. Greek letters) may not transmit properly in this form due to potential software compatibility issues. Please spell out the words in place of the symbols (e.g. replace “α” with “alpha”). Comments should be no more than 8,000 characters (including spaces ) in length. References may be included when necessary but should be kept to a minimum. Be careful if copying and pasting from a Word document. Smart quotes can cause problems in the form. If you experience difficulties, please convert to a plain text file and then copy and paste into the form.
Kusber, W.-H.: A study on Phacus smulkowskianus (Euglenophyceae) — a rarely reported taxon found in waters of the Botanic Garden Berlin-Dahlem. — Willdenowia 28: 239–247. 1998. — ISSN 0511-9618. The morphological variation and ecology of a rarely reported but widely distributed flagellate, previously referred to as Phacus similis and Euglena smulkowskiana, was studied in detail during one year in a pond of the Botanic Garden Berlin-Dahlem. Its taxonomy and nomenclature are discussed and the new combination Phacus smulkowskianus is made.
Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum-likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine-bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.
Verification of morphological diagnostic features and the establishment of three epitypes for three species of Phacus Dujardin—Phacus pleuronectes (O. F. Müll.) Dujardin, Phacus orbicularis Hübner, and Phacus hamelii Allorge et Lefèvre—was performed based on literature studies and analysis of morphological (cell shape, cell size, and periplast ornamentation) as well as molecular (18S rDNA) characters. Periplast ornamentation was recognized as a main diagnostic character, distinguishing P. orbicularis from P. pleuronectes and P. hamelii. Phacus orbicularis has struts running perpendicular to the longitudinal axis of the strips, while P. pleuronectes and P. hamelii do not. On the SSU rDNA tree, obtained by the Bayesian method, P. orbicularis, P. pleuronectes, and P. hamelii belong to three distinct clades. Some of the phylogenetic relationships are not resolved, but there are at least three Phacus species (P. hamatus, P. platyaulax, P. longicauda; for taxonomic authors, see Introduction) that are more closely related to P. orbicularis than is P. pleuronectes. Phacus hamelii is more closely related to P. ranula and the assemblage of several species of Phacus, which have small cells, than to P. orbicularis or P. pleuronectes.
We investigated the similarity of a single Euglena myxocylindracea strain, isolated originally by Bold and MacEntee, to several Euglena geniculata strains on both morphological and DNA levels. We found the three DNA stretches, consisting of fragments coding for the parts of cytoplasmic and chloroplast small subunit rRNA, and the internal transcribed spacer (ITS2) of cytoplasmic rDNA, with the combined length of 4332 nucleotides, are identical in E. myxocylindracea and E. geniculata, strain SAG 1224-4b. Morphological differences between E. myxocylindracea and any E. geniculata strain examined were well within the range of E. geniculata variability as well. The only difference behind the distinction of E. myxocylindracea from E. geniculata is the presence of the second chloroplast in the latter. However, we were able to induce the appearance of the second chloroplast in the cells of E. myxocylindracea and its disappearance in the cells of E. geniculata by changing the composition of the culture media. We therefore conclude that E. myxocylindracea Bold and MacEntee should be regarded as an environmental form of E. geniculata Dujardin. For the first time the morphology of E. geniculata chloroplasts was shown as revealed by confocal laser microscopy.
An X-Windows-based graphic user interface is presented which allows the seamless integration of numerous existing biomolecular programs into a single analysis environment. This environment is based on a core multiple sequence editor that is linked to external programs by a user-expandable menu system and is supported on Sun and DEC work stations. There is no limitation to the number of external functions that can be linked to the interface. The length and number of sequences that can be handled are limited only by the size of virtual memory present on the workstation. The sequence data itself is used as the reference point from which analysis is done, and scalable graphic views are supported. It is suggested that future software development utilizing this expandable, user-defined menu system and the I/O linkage of external programs will allow biologists to easily integrate expertise from disparate fields into a single environment.
The program MRBAYES performs Bayesian inference of
phylogeny using a variant of Markov chain Monte Carlo.
Availability: MRBAYES, including the source code, documentation,
sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Contact: johnh{at}brahms.biology.rochester.edu
No abstract available.
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new
system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing
the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows
the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional
multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order
of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to
be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments
or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with
a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled
on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for
x86 PCs, and Macintosh PowerMac.
The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
Almost complete sequences of plastid SSU rDNA (16S rDNA) from 17 species belonging to the order Euglenales (sensu Nemeth, 1997; Shi et al., 1999) were determined and used to infer phylogenetic relationships between 10 species of Euglena, three of Phacus, and one of each of Colacium, Lepocinclis, Strombomonas, Trachelomonas and Eutreptia. The maximum-parsimony (MP), maximum-likelihood (ML) and distance analyses of the unambiguously aligned sequence fragments imply that the genus Euglena is not monophyletic. Parsimony and distance methods divide Euglenaceae into two sister groups. One comprises of representatives from the subgenera Phacus, Lepocinclis and Discoglena (sensu Zakryś, 1986), whereas the other includes members of Euglena and Calliglena subgenera (sensu Zakryś, 1986), intermixed with representatives of Colacium, Strombomonas and Trachelomonas. In all analyses subgenera Euglena--together with Euglena polymorpha (representative of the subgenus Calliglena)--and Discoglena--together with Phacus and Lepocinclis--form two well-defined clades. The data clearly indicate that a substantial revision of euglenoid systematics is very much required, nevertheless it must await while more information can be gathered, allowing resolution of outstanding relationships.
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
In this issue of PLoS Biology, Hebert et al. (2004) have set out to test the resolution and performance of “DNA barcoding,” using a single mtDNA gene, cytochrome c oxidase I (COI), for a sample of North American birds. Before turning to details of this study, it is useful as context to consider the following questions: What is DNA barcoding, and what does it promise? What is new about it? Why is it controversial? What are the potential pitfalls?
Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings--Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Eight new taxa of Euglenophyta are described in this paper. They were collected from several provinces in China and respectively
namedEuglena allorgei var.exsulcata, E. pisciformis var.globosa, E. tortilis. Lepocinclis glabra var.papillata, Phacus pisiformis, Ph. strombuliformis, Ph. trimarginatus var.truncatus andAstasia angusta.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Morphological and molecular studies, as well as original literature reexamination, necessitate establishment of five Euglena species with a single axial, stellate chloroplast [Euglena viridis (O. F. Müller) Ehrenberg 1830, Euglena pseudoviridis Chadefaud 1937, Euglena stellata Mainx 1926, Euglena pseudostellata sp. nov., and Euglena cantabrica Pringsheim 1956], three species with two chloroplasts (Euglena geniculata Dujardin ex Schmitz 1884, Euglena chadefaudii Bourrelly 1951, and Euglena pseudochadefaudii sp. nov.), and one species with three chloroplasts (Euglena tristella Chu 1946). The primary morphological features, allowing distinction of the considered species are the presence and the shape of mucocysts, as well as the number of chloroplasts. Spherical mucocysts occur in E. cantabrica and E. geniculata, while spindle-shaped mucocysts are present in E. stellata, E. pseudostellata, E. chadefaudii, E. pseudochadefaudii, and E. tristella. No mucocysts are observed in E. viridis and E. pseudoviridis. Two new species (E. pseudochadefaudii sp. nov. and E. pseudostellata sp. nov.) differ from the respective species, E. chadefaudii and E. stellata, only at the molecular level. Molecular signatures and characteristic sequences are designated for nine distinguished species. Emended diagnoses for all and delimitation of epitypes for seven species (except E. viridis and E. tristella) are proposed.
Eighteen new 16S rDNA and 16 new 18S rDNA sequences from 24 strains, representing 23 species of photoautotrophic euglenoids, were obtained in nearly their entire length. Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on separate data (39 sequences of 16S rDNA and 58 sequences of 18S rDNA), as well as on combined data sets (37 sequences). All methods of sequence analysis gave similar results in those cases in which the clades received substantial support. However, the combined data set produced several additional well-supported clades, not encountered before in the analyses of green euglenoids. There are three main well-defined clades (A, B/C/D, and G) on trees from the combined data set. Clade G diverges first, while clades A and B/C/D form sister groups. Clade A consists of Euglena species sensu stricto and is divided into three sub-clades (A1, A2, and A3). Clade A3 (composed of E. deses and E. mutabilis) branches off first; then, two sister clades emerge: A1 (composed of E. viridis-like species) and A2 (consisting of E. agilis and E. gracilis species). Clade B/C/D consists of the Strombomonas, Trachelomonas, Cryptoglena, Monomorphina, and Colacium genera. Clade G comprises Phacus and Lepocinclis, as well as the Discoglena species of Euglena, with Discoglena branching off first, and then Phacus and Lepocinclis emerging as sister groups.
We studied the morphological diversity and analyzed the small subunit rDNA sequences of two taxa formerly known as Euglena spirogyra Ehr. and Euglena fusca (Klebs) Lemmermann. Our studies confirmed that the two should have the rank of a species, namely Lepocinclis spirogyroides (Ehr.) Marin et Melkonian and Lepocinclis fusca (Klebs) Kosmala et Zakryś comb. nov. (Euglenophyceae). We are defining new diagnostic features for these species, namely the size and the shape of the cells and the shape of the papillae, as well as designating epitypes for them.
Abstract— Branch support is quantified as the extra length needed to lose a branch in the consensus of near-most-parsimonious trees. This approach is based solely on the original data, as opposed to the data perturbation used in the bootstrap procedure. If trees have been generated by Farris's successive approximations approach to character weighting, branch support should be examined in terms of weighted extra length needed to lose a branch. The sum of all branch support values over the tree divided by the length of the most parsimonious tree[s] provides a new index, the total support index. This index is a measure of tree stability in terms of supported resolutions, which is of prime importance in cladistic analysis.
A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid-containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well-supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well-supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well-supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well-supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage.
Euglena viridis (subgenus Euglena) serves as the type species for the genus Euglena. In this study, molecular phylogenetic analyses using a small subunit (SSU) and a combined SSU–partial large subunit rDNA data set for members of the genus Euglena showed that strains identified as E. viridis on the basis of morphology are distributed between two separate nonsister clades. Although all the E. viridis strains examined were morphologically indistinguishable and possessed spherical mucocysts and stellate chloroplasts with one paramylon center, there was a high degree of sequence divergence between the E. viridis strains in different clades, making this a cryptic species. Like E. viridis, all taxa from the subgenus Euglena are characterized by having one or more stellate chloroplasts with paramylon grains clustered around the center of the chloroplast. These additional taxa were divided into four clades in all the molecular analyses. Strains of Euglena stellata formed two nonsister clades whose members had a single aggregate chloroplast with paramylon center and spindle-shaped mucocysts. A geniculata clade included species with one or two stellate chloroplasts with paramylon centers and spherical mucocysts, and the cantabrica clade had members with one stellate chloroplast with paramylon center and spherical mucocysts often arranged in spiral rows. Interspersed among these were three additional clades bearing taxa from the subgenus Calliglena that contains members with discoid plastids and pyrenoids that may or may not be capped with paramylon. These taxa formed a laciniata clade, mutabilis clade, and gracilis clade. This study demonstrates that E. viridis and E. stellata are cryptic species that can only be distinguished at the molecular level. Because E. viridis is the designated type species for the genus Euglena, we designated an epitype for E. viridis.
So-called DNA barcodes have recently been proposed to answer the problem of specimen identification and to quantify global biodiversity. We show that this proposition is wanting in terms of rationale, methodology and interpretation of results. fit addition to falling short of all its stated goals, the method abandons the benefits of morphological Studies in favor of a limited molecular identification system that would ultimately impede our understanding of biodiversity. (C) The Willi Hennig Society 2004.
Morphological studies of 16 strains belonging to the genus Monomorphina revealed a single, parietal, orbicular chloroplast in their cells. The chloroplast has a tendency to be perforated and disintegrates in
aging populations and thus may appear to be many chloroplasts under the light microscope. A single
chloroplast in the cells of Cryptoglena skujae is also parietally located and highly perforated. It never
forms a globular and closed structure, but is open from the side of the furrow, resembling the letter C.
We have verified the Monomorphina pyrum group (M. pyrum–like) on the basis of phylogenetic analysis
of SSU rDNA and morphological data. The strain CCAC 0093 (misidentified as M. reeuwykiana) diverges first on the SSU rDNA phylogenetic tree. The rest of the M. pyrum–like strains form a tight cluster, ubdivided into several smaller ones. Because morphological differences between the M. pyrum–like strains including the strain CCAC 0093) do not conform to the tree topology, we suggest that they all (except the strain CCAC 0093) belong to M. pyrum.We designate a new species, M. pseudopyrum, for the strain CCAC 0093, solely on the basis of molecular characters. We also suggest that M. reeuwykiana and similar species should stay in Phacus and Lepocinclis unless detailed molecular and morphological studies show otherwise. Emended diagnoses of the genera Monomorphina and Cryptoglena and the species M. aenigmatica are also proposed, as well as the delimitation of an epitype for M. pyrum, the type species for the genus Monomorphina.
Taxonomy underpins all biological research, with implications for many basic scientific and applied fields. Insights into the stability or change of animal and plant guilds require species identification on a broad scale and biodiversity questions have become a major public issue. But this comes at a time when taxonomy is facing a crisis, because ever fewer specialists are available. Here, we explore the possibility of using DNA-based methodology to overcome these problems. The utility of DNA sequences for taxonomic purposes is well established. However, all current taxonomic approaches intend to use DNA, at best, as an auxiliary criterion for identifying a species or a taxon, but have not given it a central role. We propose a scheme in which DNA would be the scaffold of a taxonomic reference system, whilst maintaining the importance of the morphological information associated with whole specimens.
DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
In this paper we present a new method for analysing molecular evolution in homologous genes based on a general stationary Markov process. The elaborate statistical analysis necessary to apply the method effectively has been performed using Monte Carlo techniques. We have applied our method to the silent third position of the codon of the five mitochondrial genes coding for identified proteins of four mammalian species (rat, mouse, cow and man). We found that the method applies satisfactorily to the three former species, while the last appears to be outside the scope of the present approach. The method allows one to calculate the evolutionarily effective silent substitution rate (vs) for mitochondrial genes, which in the species mentioned above is 1.4 X 10(-8) nucleotide substitutions per site per year. We have also determined the divergence time ratios between the couples mouse-cow/rat-mouse and rat-cow/rat-mouse. In both cases this value is approximately 1.4.
A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process. By using matrix algebra theory, the theoretical foundation of Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984) methods was provided. Extensive computer simulation was used to compare the accuracy and effectiveness of various methods for estimating the evolutionary distance between two nucleotide sequences. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414-422, 1982), and Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) are preferable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutionary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269-285, 1984) method is superior to others.
When novel gene sequences are discovered, they are usually identified, classified, and annotated based on aggregate measures of sequence similarity. This method is prone to errors, however. Phylogenetic analysis is a more accurate basis for gene classification and ortholog identification, but it is relatively labor-intensive and computationally demanding. Here we report and demonstrate a rapid new method for gene classification based on phylogenetic principles. Given the phylogeny of a minimal sample of gene family members, our method automatically identifies amino acids that are phylogenetically characteristic of each class of sequences in the family; it then classifies a novel sequence based on the presence of these characteristic attributes in its sequence. Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time.
Sequence comparisons and a revised classification of the Euglenophyceae were based on 92 new SSU rDNA sequences obtained from strains of Euglena, Astasia, Phacus, Trachelomonas, Colacium, Cryptoglena, Lepocinclis, Eutreptia, Eutreptiella and Tetreutreptia. Sequence data also provided molecular signatures for taxa from genus to class level in the SSU rRNA secondary structure, revealed by a novel approach (search for non-homoplasious synapomorphies) and used for taxonomic diagnoses. Photosynthetic euglenoids and secondary heterotrophs formed a clade, designated as Euglenophyceae (emend.) with two orders: Euglenales and Eutreptiales. The mostly marine Eutreptiales (Eutreptia, Eutreptiella; not Distigma) comprised taxa with two or four emergent flagella (the quadriflagellate Tetreutreptia was integrated within Eutreptiella). The Euglenales (freshwater genera with < or = one emergent flagellum) formed nine clades and two individual branches (single strains); however, only two clades were congruent with traditional genera: Trachelomonas (incl. Strombomonas) and Colacium. Euglena was polyphyletic and diverged into four independent clades (intermixed with Astasia, Khawkinea and Lepocinclis) and two individual branches (e.g. E. polymorpha). Phacus was also subdivided into Phacus s. str. and two combined lineages (mixed with Lepocinclis spp. or Cryptoglena). In consequence, Euglena (s. str.), Phacus and other genera were emended and one lineage (mixed Phacus/Lepocinclis-clade) was recognized as the previously neglected genus Monomorphina Mereschkowsky (1877). The sister clade of Phacus s. str. (mixed Euglena/Lepocinclis-clade) was identified as Lepocinclis Perty (emended).
Society has a growing need for credible taxonomic information in order to allow us to conserve, manage, understand, and enjoy the natural world. At the same time support for tax- onomy and collections is failing to keep pace. Funds nominally allocated to taxonomy go largely to reconstruct molecular phylogenies, while thousands of species are threatened by im- minent extinction. Ecologists working in the tropics have felt this lack of taxonomic knowl- edge as an impediment that inhibits their ability to analyze community-level phenomena. It is time to evaluate the sources of this impediment and address them. Taxonomy must facilitate, not obstruct biodiversity studies and conservation. Existing taxonomic practices have served us well for centuries, but are clearly inadequate for the chal- lenge at hand. The taxonomic community must rally around a common vision, critically evalu- ate its needs, set an ambitious research agenda, embrace emerging technologies, and univocally communicate its aspirations. This will require a major change in approach, engaging individual scholars, professional societies, and institutions. Molecular data, abundant and inexpensive, have revolutionized phylogenetics but not diminished the importance of traditional work. Mor-
Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of 'species' fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional 'species'. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re-analysis and meta-analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high-throughput sequencing methodologies, however, place the idea of a universal, multi-locus molecular barcoding system in the realm of the possible.
DNA barcoding has revealed unrecognized species in several animal groups. In this study we have employed DNA barcoding to examine Hyalella, a taxonomically difficult genus of amphipod crustaceans, from sites in the southern Great Basin of California and Nevada, USA. We assessed the extent of species diversity using a species screening threshold (SST) set at 10 times the average intrapopulation cytochrome c oxidase subunit I (COI) haplotype divergence. Despite the fact that this threshold approach is more conservative in delineating provisional species than the phylogenetic species concept, our analyses revealed extraordinary levels of cryptic diversity and endemism. The SST discriminated two provisional species within Hyalella sandra, and 33 provisional species within Hyalella azteca. COI nucleotide divergences among these provisional species ranged from 4.4% to 29.9%. These results have important implications for the conservation of life in desert springs - habitats that are threatened as a result of groundwater over-exploitation.
Introduction to general state-space Markov chain theory. In W. R. Gilks, S. Richardson, and D. J. Spiegelhalter (Eds.), Markov Chain Monte Carlo in Practice, Chapter 4, pp. 59-74. London: Chapman and Hall. Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000). Codon- substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431-449. Yang, Z. and B. Rannala (1997). Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Molecular Biology and Evolution 1, 717-724. Yang, Z. H. (1993). Maximum-likelihood-estimation of phylogeny from DNA- sequences when substitution rates differ over sites. Molecular Biology and Evolution I0(6), 1396-1401. Zuckerkandl, E. (1987). On the molecular evolutionary clock. Journal of Molec- ular Evolution 26, 34-46. Zuckerkandl, E. and L. Pauling (1962). Molecular disease, evolution, and genic heterogeneity. In M. Kasha and B. Pullman (Eds.), Horizons in Biochem- istry, pp. 189-225. Ne
Przyczynek do znajomos polskich euglenin
- R Dre_ Zepolski
Dre_ zepolski, R. 1925. Przyczynek do znajomos polskich euglenin. [Supplement a ` la connaisance des Euglé de la Pologne]. Kosmos 50:173–250 (in Polish with French summary).
Eugleninae Die Sü Deutschlands, O ¨ sterreichs und der Schweiz, H. 2: flagellatae II
- E Lemmermann
Lemmermann, E. 1913. Eugleninae. In Pascher, A. [Ed.] Die Sü Deutschlands, O ¨ sterreichs und der Schweiz, H. 2: flagellatae II. Verlag von Gustav Fisher, Jena, Germany, pp. 115–74.
Diagnosen neuer Algen aus Zentralasien
- Kisselew
Kisselew, J. A. 1931. Diagnosen neuer Algen aus Zentralasien. Trans. Uzbekistan Inst. Trop. Med. 1:1–85.
Euglenophyta Pigmentadas de la Argen-tina
- V Tell
- G Conforti
Tell, V. & Conforti, G. 1986. Euglenophyta Pigmentadas de la Argen-tina. J. Cramer in der Gebrü der Borntraeger Verlegsbuch-handlung, Berlin-Stuttgart, Germany, 31 pp.
AutoDecay 4.0.2. A program distributed by the author
- T Eriksson
Eriksson, T. 1998. AutoDecay 4.0.2. A program distributed by the author. Department of Botany, Stockholm University, Stock-holm, Sweden.