Taxonomic Ambiguity Research Articles

Molecular analysis of complete ssu to lsu rdna sequence in the harmful dinoflagellatealexandrium tamarense (korean isolate, HY970328M)

New PCR primers (N=18) were designed for the isolation of complete SSU to LSU rDNA sequences from the dinoflagellateAlexandrium tamarense. Standard PCR, employing each primer set selected for amplifications of less than 1.5 kb, successfully amplified the expected rDNA regions of A. tamarense (Korean isolate, HY970328M). Complete SSU, LSU rDNAs and ITS sequences, including 5.8S rDNA, were recorded at 1,800 bp, 520 bp and 3,393 bp, respectively. The LSU rDNA sequence was the first report inAlexandrium genus. No intron was found in the LSU rRNA coding region. Twelve D-domains within the LSU rDNA were put together into 1,879 bp (44.4% G+C), and cores into 1514 bp (42.8% G+C). The core sequence was significantly different (0.0867 of genetic distance, 91% sequence similarity) in comparison withProrocentrum micans (GenBank access. no. X16108). The D2 region was the longest in length (300 bp) and highly variable among the 12 D-domains. In a phylogenetic analysis using complete LSU rDNA sequences of a variety of phytoplankton,A tamarense was clearly separated with high resolution against other species. The result suggests that the sequence may resolve the taxonomic ambiguities ofAlexandrium genus, particularly of the tamarensis complex.

Integrated Method for Single-Cell DNA Extraction, PCR Amplification, and Sequencing of Ribosomal DNA from Harmful Dinoflagellates Cochlodinium polykrikoides and Alexandrium catenella

A simplified technique was developed for DNA sequence-based diagnosis of harmful dinoflagellate species. This protocol integrates procedures for DNA extraction and polymerase chain reaction (PCR) amplification into a single tube. DNA sequencing reactions were performed directly, using unpurified PCR products as the DNA template for subsequent sequencing reactions. PCR reactions using DNA extracted from single cells of Cocodinium polykrikoides and Alexandrium catenella successfully amplified the target ribosomal DNA regions. DNA sequencing of the unpurified PCR products showed that DNA sequences corresponded to the expected locus of ribosomal DNA regions of both A. catenella and C. polykrikoides (each zero genetic distance and 100% sequence similarity). Using the protocol described in this article, there was little DNA loss during the purification step, and the technique was found to be rapid and inexpensive. This protocol clearly resolves the taxonomic ambiguities of closely related algal species (such as Alexandrium and Cochlodinium), and it constitutes a significant breakthrough for the molecular analysis of nonculturable dinoflagellate species.

A simple molecular approach for identifying a rare Acronychia (Rutaceae) provides new insights on its multiple hybrid origins

Hybridization plays an important role in the evolution of plant diversity. Nonetheless, it is often difficult to clearly ascertain hybrid origin by assessing morphological characters alone. Acronychia littoralis (Rutaceae) is a recently described rare tree from littoral rainforests in eastern Australia. Two forms have been tentatively distinguished on the basis of different leaf morphology however, because of the variability of the discriminatory characters across populations (and in some cases across single individuals), compiling data on the exact distribution of each form has been a difficult process. To further complicate matters, some of these distinguishing morphological characters are intermediate between those of closely related, sympatric species. As a result, simple molecular techniques were developed to assist the development of adequate conservation and management strategies for A. littoralis and to better understand its evolutionary history. Sequence data from the ITS2 region were obtained and haplotype specific primers that distinguished the two forms and the related taxa were developed. Sequence data suggest that the two forms of A. littoralis are each of hybrid origin but both involve different parental taxa. The findings provide a perspective on the evolutionary dynamics of the local rainforest flora and highlight the need for phylogenetic evaluation of rare taxa where there is taxonomic ambiguity.

Identifying chironomids (Diptera: Chironomidae) for biological monitoring with PCR-RFLP.

Chironomids are excellent biological indicators for the health of aquatic ecosystems, but their use at finer taxonomic levels is hindered by morphological similarity of species at each life stage. Molecular markers have the potential to overcome these problems by facilitating species identification particularly in large-scale surveys. In this study, the potential of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach was tested to rapidly distinguish among chironomids within a geographic area, by considering chironomid species from Melbourne, Australia. By comparing molecular markers with diagnostic morphological traits, RFLP profiles of the cytochrome oxidase I (COI) region were identified that were specific to genera and some common species. These profiles were used to develop an RFLP-based key, which was validated by testing the markers on samples from several wetlands and streams. As well as allowing for rapid identification of species that are difficult to separate on morphological grounds, this approach also has the potential to resolve current taxonomic ambiguities.

Barley yellow dwarf virus: Luteoviridae or Tombusviridae?

Summary Barley yellow dwarf virus (BYDV), the most economically important virus of small grains, features highly specialised relationships with its aphid vectors, a plethora of novel translation mechanisms mediated by long-distance RNA interactions, and an ambiguous taxonomic status. The structural and movement proteins of BYDV that confer aphid transmission and phloem-limitation properties resemble those of the Luteoviridae, the family in which BYDV is classified. In contrast, many genes and cis-acting signals involved in replication and gene expression most closely resemble those of the Tombusviridae. BYDV is in genus Luteovirus, family Luteoviridae. BYDV includes at least two serotypes or viruses: BYDV-PAV and BYDV-MAV. The former BYDV-RPV is now Cereal yellow dwarf virus-RPV (CYDV-RPV). CYDV is in genus Polerovirus, family Luteoviridae. Genus Luteovirus shares many features with family Tombusviridae. Physical properties: approximately 25 nm icosahedral (T = 3) virions. One major (22 kDa) and one minor (50-55 kDa) coat protein. 5.6-5.8 kb positive sense RNA genome with no 5'-cap and no poly(A) tail. Most grasses. Most important in oats, barley and wheat. Also infects maize and rice. Yellowing and dwarfing in barley, stunting in wheat; reddening, yellowing and blasting in oats. Some isolates cause leaf notching and curling. Key attractions: Model for the study of circulative transmission of aphid-transmitted viruses. Plethora of unusual translation mechanisms. Evidence of recombination in recent evolutionary history creates taxonomic ambiguity. Economically important virus of wheat, barley and oats, worldwide. Useful websites/meetings: International symposium: 'Barley Yellow Dwarf Disease: Recent Advances and Future Strategies', CIMMYT, El Batan, Mexico, 1-5 September 2002, http://www.cimmyt.cgiar.org/Research/wheat/Conf_BYD_02/invitation.htm http://www.cimmyt.org/Research/wheat/BYDVNEWS/htm/BYDVNEWS.htm Aphid transmission animation: http://www.ppws.vt.edu/~sforza/tmv/bydv_aph.html.

Are most of the domoic acid-producing species of the diatom genus Pseudo-nitzschia cosmopolites?

Records from all oceans, most of them published during 1990–2000, and personal unpublished observations of nine Pseudo-nitzschia taxa known as potential domoic acid (DA) producers have been used to outline their geographical distribution. Pseudo-nitzschia seriata f. seriata as the only taxon was found in the North Atlantic Ocean exclusively. The records of P. multistriata were too few and the identification of P. turgidula from the North Atlantic too unreliable to provide an idea about their distribution. Pseudo-nitzschia pungens and the less frequently recorded P. fraudulenta, P. multiseries and P. australis appeared to be cosmopolites. The wide distribution of the apparently most efficient DA producers, P. australis and P. multiseries, is especially noteworthy. The records of P. delicatissima and P. pseudodelicatissima also indicate a cosmopolitan distribution although with the qualification of certain taxonomic and identification ambiguities. Hence, the question of whether most DA-producing Pseudo-nitzschia species are cosmopolites may be answered with a tentative “yes”.

Unravelling the taxonomic status of the genus Cynopterus (Chiroptera: Pteropodidae) in Sri Lanka by multivariate morphometrics and mitochondrial DNA sequence analysis

Summary The systematic and conservation status of the genus Cynopterus Cuvier, 1824, especially with regard to the status of C. sphinx Vahl, 1797 and C. brachyotis Muller, 1838, is still much in debate. The aim of this study was to conduct a comprehensive systematic study to resolve the taxonomic ambiguity of the Cynopterus species complex in Sri Lanka. Initially, a study was conducted to review the morphological variation within the species complex using multivariate statistical analysis with three character systems; sixteen measurements of cranial and dental, and 7 external characters were recorded for 364 adult specimens from Sri Lanka. Multivariate analysis using principal component analysis and canonical variate analysis of morphometric data indicated the presence of two different taxa (morphotypes) in Sri Lanka: A small morphotype related to C. brachyotis , a large morphotype related to C. sphinx . Within the morphotypes geographical sub populations were also found whose taxonomic status was ambiguous. To resolve this ambiguity and determine the precise identification of taxa, 23 samples from the morphotypes were examined for the mitochondrial DNA (mtDNA) sequence divergence in a 425 bp region of the cytochrome b gene. The sequence data revealed the presence of only two major mtDNA phylogenetic groups with a sequence divergence of 9.2 %, indicating that the species complex comprise only two distinct genetic species: The large morphotype which belonged to C. sphinx and the small morphotype which belonged to C. brachyotis . mtDNA sequence data supported the view that the sub populations are eco-morphotypes of C.sphinx. A total of seven mtDNA haplotypes were found in the Cynopterus species complex, five belonging to C. brachyotis and two belonging to C. sphinx . C. brachyotis was found only in the forest habitat.

Let's not Abandon Science for Advocacy: Reply to Berg and Berg.

Berg and Berg (2000) conduct an analysis of their unpublished allozyme data for populations of Amblema and report that as sample size increases the opportunity detect rare alleles increases. They argue that to discriminate among within a genus, one must quantify the degree of variation both among populations within each and among putative species and that the accuracy of the estimation of variation increases with sample size. We wholeheartedly agree. Indeed, our study was undertaken provide additional data address questions arising from just such a lack of comparative analysis and small sample size. Berg and Berg point out that sample sizes in our study of the freshwater mussels Megalonaias and Amblema were small and that small sample sizes may lead Type II statistical errors. We completely agree, but recognize that the alternative Type I error has serious consequences as well. Regrettably, small sample sizes are often the norm with that are being considered for federal listing as endangered, threatened, or of special concern, as was the case in our study. Where taxonomic evaluations are made, voucher specimens are absolutely necessary cross-check genetic data and validate specimen identifications (Lydeard & Roe 1998). Among molluscs, traditional morphological and conchological traits, often coupled with small sample sizes, have led a proliferation of named entities (e.g., Lea 1834). Recognition of ecophenotypic plasticity and evaluation of larger population samples and comparative material has led many of these names becoming synonymous. Molecular genetic approaches are often useful for addressing taxonomic ambiguity (Mulvey et al. 1998). Unfortunately, many people, perhaps Berg and Berg among them, view named entities as unassailable, especially in the context of conservation. This position is indefensible and counterproductive.

Crustacean biodiversity through the marine fossil record

Approximately 2,600 genera of marine crustaceans have been recognized in the fossil record, and crustaceans constitute the major component of marine arthropod diversity from the mid- Paleozoic to the Recent. Despite problems of sporadic fossil preservation and/or taxonomic ambiguity, some general statements can be made about the history of crustacean biodiversity, based on global taxonomic data bases. Ostracodes were the first major group to radiate, attaining high diversity during the Ordovician Period with other members of the Paleozoic evolutionary fauna; rates of extinction and responses to mass extinctions were also similar to those of groups within the Paleozoic fauna. Malacostracans and barnacles (cirripedes), the two other crustacean groups with important fossil records, had minor diversity throughout the Paleozoic Era. Both groups experienced diversification from the mid-Mesozoic to Recent with lower extinction rates, as characteristic members of the Modern evolutionary fauna.

Allozymic variation in tubificid oligochaetes from the Laurentian Great Lakes

Aquatic oligochaetes are an important component of the benthos in many freshwater habitats. Yet, virtually nothing is known about the population genetics of this group. Electrophoretic surveys of allozymic variation of selected members of the Family Tubificidae were conducted at six locations in the Laurentian Great Lakes of North America. Branchiura sowerbyi was the dominant member of the oligochaete fauna at two sites, and was found to be monomorphic at all enzyme loci that were examined. In contrast, members of the genus Limnodrilus, which included L. cervix, L. claparedianus, L. hoffmeisteri, L. maumeensis, and L. udekemianus showed considerable allozymic variation at several enzyme loci. L. udekemianus exhibited tri- and tetra-allelic heterozygous electromorph banding patterns at the monomeric Pgm locus, along with ‘unbalanced’ heterozygous patterns at both Pgm and the dimeric Pgi locus. Genetic distance analyses suggest that L. cervix, L. claparedianus, and L. maumeensis are closely-related (genetic identifies ranged from 0.92–0.85), and may represent subspecies rather than distinct species. Breeding studies need to confirm this assertion. This survey represents the first attempt to characterize allozymic variation of aquatic oligochaetes in North America. Additional work should focus on elucidating taxonomic ambiguities within this group via both morphological and biochemical genetic studies.

EVOLUTIONARY ANALYSIS OF THE LARGE SUBUNIT OF CARBOXYLASE (rbcL) NUCLEOTIDE SEQUENCE AMONG THE GRASSES (GRAMINEAE).

The full nucleotide sequences of the chloroplast encoded large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) are available for nine grass species and partial sequence data for one species. Relative rate tests of the "molecular clock" hypothesis suggest that rbcL evolved more rapidly in the lineage leading to Zea than in those leading to the other species. The estimated overall substitution rate for rbcL among these grasses is about 5 times 10-10 substitutions per site per year, or about one-half the synonymous rate. The nine full sequences were analyzed by the UPGMA, Wagner parsimony, maximum likelihood, and Fitch-Margoliash methods. The latter three methods produced trees with the same topology. This topology largely agrees with current taxonomic evidence regarding the relationships among these grasses. UPGMA produced a topology that conflicts more substantially with available taxonomic evidence. Statistical comparison of the three alternative topologies for the subfamilies Panicoideae, Pooideae and Bambusoideae failed to support one of these topologies over the others, reflecting the taxonomic ambiguities surrounding the relationships among these taxa. Phylogenetic analyses based on the partial sequences of all 10 species gave conflicting results with regard to the relationship between Hordeum and Triticum, both members of the tribe Triticeae. This indicates that rbcL sequences contain too little information to resolve relationships among genera within this tribe. Overall, the results suggest that rbcL sequence data can provide some new information concerning grass phylogeny, but that the amount of available data from this gene is too small to differentiate statistically among alternative topologies for the grasses. Conflicting results from parsimony, maximum likelihood, and Fitch-Margoliash methods proved useful in exploring the validity of assumptions underlying these methods.

Classical plant taxonomic ambiguities extend to the molecular level

The molecular evolution of cytochrome c from angiosperms is compared to that from vertebrates. On the basis of a cladistic analysis from 26 plant species, compared to that from 27 vertebrate species, we find that although the vertebrate sequences yield reasonably well-defined minimal trees that are congruent with the biological tree, the plant sequences yield multiple minimal trees that are not only highly incongruent with each other, but none of which is congruent with any reasonably biological tree. That is, the plant sequence set is much more homoplastic than that of the animal. However, as judged by the relative rate test, the extent of divergence, and degree of functional constraint, cytochrome c evolution in plants does not appear to differ from that of vertebrates.

Diameters and albedos of thirty-six asteroids

Radiometric diameters and albedos of 36 asteroids, most previously unmeasured by this technique, are reported. These objects were selected primarily to resolve taxonomic ambiguities resulting from the lack of albedo information. Of the sample of 36, most are of the common types C, S, and M, but also represented are types A, D, F, and P. One object, 214 Aschera, is of the rare E type (only the fourth of its kind known); 87 Sylvia is the largest known member of the P class; and albedo combined with Arizona eight-color data from Tholen (1983, Asteroid Taxonomy from Cluster Analysis of Photometry: Implications for Origin and Evolution of the Asteroid Belt. PhD dissertation, University of Arizona, Tucson) indicate that 336 Lacadiera is of type D, one of the few members of this class found in the main asteroid belt, and a prime candidate for future space missions.

Species of the Genus ScrupocellariaVAN BENEDEN (Bryozoa, Anasca) from Indian Waters

AbstractNine species of the genus Scrupocellaria VAN BENEDEN are figured and described in this paper. They are: Scrupocellaria maderensis BUSK. S. obtecta HASWELL. S. mansueta WATERS. S diadema BUSK. S. scruposa (LINNAEUS). S. spatulata (D'ORBIGNY). S. delilii (AUDOUIN). S. bertholettii (AUDOUIN). S. talonis OSBURN. The specimens were collected from the south west and south east coasts of India. Six species are described for the first time from Indian waters. Variations noticed in the morphology of the above species with those described elsewhere are assessed and discussed.A study of the genus from the available material shows that characters like the number of spines and nature of scuta show considerable intraspecific differences. Variation in spine number is a common occurrence and undue importance to spine number, especially in the case of tropical species, should be given with due caution. The history of S. bertholettii is really confusing especially in view of the creation of the var. tenuirostris. A comparative study of the type specimens would help to clarify the taxonomic ambiguity of this species.