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PubMed2004

Accurate identification of closely related Dendrobium species with multiple species-specific gDNA probes.

About 63 species of Dendrobium are identified in China, making the identification of the origin of a particular Dendrobium species on the consumer market very difficult. We report evaluation of multiple species-specific probes screened from genomic DNA for closely related Dendrobium species identification, based on DNA array hybridization. Fourteen species-specific probes were screened from five closely related Dendrobium species, D. aurantiacum Kerr, D. officinale Kimura et Migo, D. nobile Lindl., D. chrysotoxum Lindl. and D. fimbriatum Hook., based on the SSH-Array technology we developed. Various commercial Dendrobium samples and unrelated samples were definitely identified. The specificity and accuracy of the multiple species-specific probes for species identification was assessed by identifying various commercial Dendrobium samples (Herba Dendrobii). Hybridization patterns of these multiple probes on digested genomic DNAs of Dendrobium species indicated that there are distinct polymorphic sequence fragment in the higher eukaryotes. This is the first report on detection and utilization of multiple species-specific probes of Dendrobium in whole genomic DNA, and this could be useful tools not only for a new technical platform for the closely related species identification but also for epidemiological studies on higher eukaryotes.

DNA↗
PubMed2004

Comparative inter-species pharmacokinetics of phenoxyacetic acid herbicides and related organic acids. evidence that the dog is not a relevant species for evaluation of human health risk.

Phenoxyacetic acids including 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-chloro-2-methylphenoxyacetic acid (MCPA) are widely utilized organic acid herbicides that have undergone extensive toxicity and pharmacokinetic analyses. The dog is particularly susceptible to the toxicity of phenoxyacetic acids and related organic acids relative to other species. Active renal clearance mechanisms for organic acids are ubiquitous in mammalian species, and thus a likely mechanism responsible for the increased sensitivity of the dog to these agents is linked to a lower capacity to secrete organic acids from the kidney. Using published data describing the pharmacokinetics of phenoxyacetic and structurally related organic acids in a variety of species including humans, inter-species comparative pharmacokinetics were evaluated using allometic parameter scaling. For both 2,4-D and MCPA, the dog plasma half-life (t(1/2)) and renal clearance (Clr; mL/h) rates did not scale as a function of body weight across species; whereas for all other species evaluated, including humans, these pharmacokinetic parameters reasonably scaled. This exceptional response in the dog is clearly illustrated by comparing the plasma t(1/2) at comparable doses of 2,4-D and MCPA, across several species. At a dosage of 5mg/kg, in dogs, the plasma t(1/2) for 2,4-D and MCPA were approximately 92-106 and 63 h, respectively, which is substantially longer than in the rat (approximately 1 and 6 h, respectively) or in humans (12 and 11 h, respectively). This longer t(1/2), and slower elimination in the dog, results in substantially higher body burdens of these organic acids, at comparable doses, relative to other species. Although these results indicate the important role of renal transport clearance mechanisms as determinants of the clearance and potential toxicity outcomes of phenoxyacetic acid herbicides across several species, other contributing mechanisms such as reabsorption from the renal tubules is highly likely. These findings suggest that for new structurally similar organic acids, a limited comparative species (rat versus dog) pharmacokinetic analysis early in the toxicology evaluation process may provide important insight into the relevance of the dog. In summary, the substantial difference between the pharmacokinetics of phenoxyacetic acids and related organic acids in dogs relative to other species, including humans, questions the relevance of using dog toxicity data for the extrapolation of human health risk.

Acetates↗
PubMed2002

Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus).

Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) and propose explicit protocols for each. We then compare species limits inferred from these approaches, using morphological and mtDNA data for the Yarrow's spiny lizard (Sceloporus jarrovii), a traditionally polytypic species from the southwestern United States and Mexico. All three approaches support division of S. jarrovii into five species, but only two species are the same among the three approaches. We find the greatest support for the five species that are delimited based on mtDNA data, and we argue that mtDNA data may have important (and previously unappreciated) advantages for species delimitation. Because different data and approaches can disagree so extensively, our results demonstrate that the methodology of species delimitation is a critical issue in systematics.

Animals↗
PubMed2004

A novel method for screening species-specific gDNA probes for species identification.

We report a method called SSH array which combines the suppression subtraction hybridization (SSH) and DNA array techniques to find species-specific DNA probes from genomic DNA (gDNA) for species identification. The method first obtains the differential gDNA fragments between two species by SSH and then hybridizes the differential gDNA fragments with arrays made of multiple whole genomes from several species to screen the unique gDNA fragments for one species. The screened unique gDNA fragments can be used as species-specific probes to differentiate the species they represent from all other species. We used five species of the genus Dendrobrium, D.aurantiacum Kerr, D.officinale Kimura et Migo, D.nobile Lindl., D.chrysotoxum Lindl. and D.fimbriatum Hook., as experimental materials to study the feasibility of the method. The results showed that the method could efficiently obtain different species-specific probes for each of the five species.

Animals↗
PubMedDate not supplied

[New species and sympatric relations of the chigger mite species group Talmiensis (Trombiculidae, Neotrombicula)].

A revision of chigger mites species being closely related to Neotrombicula talmiensis (Schluger, 1955) has been performed. 2 new species are described: N. pontica sp. n. from Krasnodar Territory (Western Caucasus) and N. sympatrica sp. n. from Krasnodar Territory, Daghestan, Tuva, Armenia, Kirghizia and Turkey (Rize Province). N. pontica sp. n. is closely related to N. carpathica Schluger et Vysotzkaya, 1970 and differs from this species by the larger number of idiosomal setae (NDV = = 75-99 against 63-77), shorter legs (Ip = 782-847 against 844-920, TaIII = 67-74 against 70-80), lesser m-t (0.180 against 0.192), slightly lesser scutum and slightly longer setae. N. sympatrica sp. n. is closely related to N. carpathica and differs from this species by the longer scutal and idiosomal setae (PL = 67-78 against 57-69, H = 65-75 against 57-68, Dmin = 43-52 against 39-48, Dmax = 61-70 against 54-64), longer legs (Ip = 892-973 against 844-920, TaIII = = 77-86 against 70-80) and lesser m-t (0.168 against 0.192). N. carpathica is reported for the first time from Northern Caucasus (Karachai-Cherkess Republic, Kabardino-Balkaria, North Ossetia); N. talmiensis is reported for the first time from Khakasia. Data on joint occurrence of 3 species are reported. The 3 types of sympatric pairs of the species have been found in the Western Caucasus: 1) N. pontica sp. n. and N. sympatrica sp. n., 2) N. sympatrica sp. n., and N. carpathica, 3) N. pontica sp. n., and N. carpathica. Differences between species in that localities, where the joint occurrence was recorded, have been analysed. Sympatric relations between N. sympatrica sp. n. and N. carpathica are characterized by increased value of some general diagnostic characters of these species, such as the length of idiosomal setae and length of legs. Different characters play main distinguishing role in different sympatric localities. Besides that, some local features appear in certain species of sympatric pairs (narrow scutum in 3 samples of N. carpathica, numerous idiosomal setae in 1 sample of N. sympatrica), that differs the populations of the sympatric pair, and also discriminates such aberrant group from other material of the same species. Functions produced by the method of discriminant analysis are proposed for the purpose of diagnostics in talmiensis group. Tests for assumptions of discriminant analysis, such as normality and homogeneity of variances, has been performed beforehand. Verifications of the functions on test samples demonstrated the good quality of its working. Key to species using discriminant functions has been constructed.

Animals↗
PubMed2002

Recurrent habitat disturbance and species diversity in a multiple-competitive species system.

To address how species interactions, dispersal and environmental disturbances interplay to affect the spatial distribution and diversity of species, we present a compartment model in which multiple species undergo competitive interaction of Lotka-Volterra type in a patchy environment arranged in a square lattice. Dispersal of species occurs between adjacent patches. Disturbances are periodically imposed on a central part of the environment in a belt-like block or an island-like block of various sizes where each species is killed for a certain time interval and then allowed to recover for the rest of a disturbance cycle. We deal with a case in which the local population dynamics within each patch is analytically determinable and has multiple locally stable equilibrium states in the absence of environmental disturbance. We further assume a trade-off between the reproductive rate of species and its dispersal ability. With these settings, we numerically examine how the spatio-temporal distributions of species are affected by changes in the pattern, size and duration of disturbances. The results demonstrate that: (1) in the undisturbed area, environmental disturbances could generate spatially segregated distributions of species; (2) in the disturbed area, species with higher dispersal abilities quickly invade and preferentially recover their population during the post-disturbance period, being temporarily relieved of competition from other species. These mechanisms collectively lead to increased species diversity in the whole habitat, functioning best when both the size and duration of disturbances are intermediate. In particular, the belt-like disturbance is more effective than the island-like disturbance in sustaining spatial heterogeneity for a wider range of duration of disturbance.

Animals↗
PubMed2006

Patterns of speciation in the Yucca moths: parallel species radiations within the Tegeticula yuccasella species complex.

The interaction between yuccas and yucca moths has been central to understanding the origin and loss of obligate mutualism and mutualism reversal. Previous systematic research using mtDNA sequence data and characters associated with genitalic morphology revealed that a widespread pollinator species in the genus Tegeticula was in fact a complex of pollinator species that differed in host use and the placement of eggs into yucca flowers. Within this mutualistic clade two nonpollinating "cheater" species evolved. Cheaters feed on yucca seeds but lack the tentacular mouthparts necessary for yucca pollination. Previous work suggested that the species complex formed via a rapid radiation within the last several million years. In this study, we use an expanded mtDNA sequence data set and AFLP markers to examine the phylogenetic relationships among this rapidly diverging clade of moths and compare these relationships to patterns in genitalic morphology. Topologies obtained from analyses of the mtDNA and AFLP data differed significantly. Both data sets, however, corroborated the hypothesis of a rapid species radiation and suggested that there were likely two independent species radiations. Morphological analyses based on oviposition habit produced species groupings more similar to the AFLP topology than the mtDNA topology and suggested the two radiations coincided with differences in oviposition habit. The evolution of cheating was reaffirmed to have evolved twice and the closest pollinating relative for one cheater species was identified by both mtDNA and AFLP markers. For the other cheater species, however, the closest pollinating relative remains ambiguous, and mtDNA, AFLP, and morphological data suggest this cheater species may be diverged based on host use. Much of the divergence in the species complex can be explained by geographic isolation associated with the evolution of two oviposition habits.

Animals↗
PubMed2006

Species traits and the form of individual species-energy relationships.

Environmental energy availability explains much of the spatial variation in species richness at regional scales. While numerous mechanisms that may drive such total species-energy relationships have been identified, knowledge of their relative contributions is scant. Here, we adopt a novel approach to identify these drivers that exploits the composite nature of species richness, i.e. its summation from individual species distributions. We construct individual species-energy relationships (ISERs) for each species in the British breeding avifauna using both solar (temperature) and productive energy metrics (normalized difference vegetation index) as measures of environmental energy availability. We use the slopes of these relationships and the resultant change in deviance, relative to a null model, as measures of their strength and use them as response variables in multiple regressions that use ecological traits as predictors. The commonest species exhibit the strongest ISERs, which is counter to the prediction derived from the more individuals hypothesis. There is no evidence that predatory species have stronger ISERs, which is incompatible with the suggestion that high levels of energy availability increase the length of the food chain allowing larger numbers of predators to exist. We find some evidence that species with narrow niche breadths have stronger ISERs, thus providing one of the few pieces of supportive evidence that high-energy availability promotes species richness by increasing the occurrence of specialist species that use a narrow range of resources.

Animals↗
PubMed2003

Gene flow across species boundaries in sympatric, sexually deceptive Ophrys (Orchidaceae) species.

Orchids of the genus Ophrys (Orchidaceae) are pollinated by male bees and wasps through sexual deception. The Ophrys sphegodes group encompasses several closely related species that differ slightly in floral morphology and are pollinated by different solitary bee species. Populations representing different species of the O. sphegodes group often flower simultaneously in sympatry. To test whether gene flow across the species boundaries occurs in these sympatric populations, or whether they are reproductively isolated, we examined the distribution of genetic variation within and among populations and species of this group. We collected at each of five different localities in southern France and Italy two sympatric, co-flowering Ophrys populations, representing six Ophrys species in total. The six microsatellite loci surveyed were highly variable. Genetic differentiation among geographically distant populations of the same species was lower than differentiation among sympatric populations of different species. However, the strength of genetic differentiation among species was among the lowest reported for orchids. Genotype assignment tests and marker-based estimates of gene flow revealed that gene flow across species boundaries occurred and may account for the low observed differentiation among species. These results suggest that sexual deceit pollination in Ophrys may be less specific than thought, or that rare mistakes occur.

Cluster Analysis↗
PubMed1985

Heterogeneity in the metabolism of the arachidonoyl molecular species of glycerophospholipids of rabbit alveolar macrophages. The interrelationship between metabolic activities and chemical structures of the arachidonoyl molecular species.

The relative incorporation of [3H]arachidonic acid (20:4) into individual molecular species containing 20:4 at the 2 position (18:1-20:4, 16:0-20:4 and 18:0-20:4 species) of diacyl and ether-linked glycerophosphocholine, glycerophosphoethanolamine and glycerophosphoinositol of rabbit alveolar macrophages has been measured by reversed-phase high-performance liquid chromatography (HPLC). The rate of incorporation of [3H]20:4 into the molecular species of glycerophospholipids was greatly influenced by their structures. The reversed-phase HPLC analysis allowed elucidation of the influence of structural differences, such as the nature of the polar head group, the fatty chain at the 1 position and the chemical form of the bond of the fatty chain attached at the 1 position on the uptake of [3H]20:4 by comparison of the specific radioactivities of arachidonoyl molecular species having the same structures, except that one of the three kinds of moiety was different. The specific radioactivities of the molecular species containing choline head groups were significantly higher than those containing ethanolamine and inositol moieties. The specific radioactivities of diacyl molecular species were considerably higher than those of ether-linked molecular species. The nature of the fatty chain attached at the 1 position also influenced the uptake of [3H]20:4 into glycerophospholipids. The arachidonoyl molecular species containing 18:1 at the 1 position were preferentially labelled with [3H]20:4 as compared to the corresponding 16:0-20:4 and 18:0-20:4 species either of diacyl or ether-linked glycerophospholipids. The present results suggest that the acyltransferase involved in the incorporation of 20:4 into glycerophospholipids has selectivity for the structures of glycerophospholipids and the order of selectivity of this enzyme for the arachidonoyl molecular species, deduced in the present experiments, was as follows: choline head group greater than ethanolamine and inositol groups, acyl bond greater than ether and vinyl ether bonds, 18:1 fatty chain greater than 16:0 and 18:0 fatty chains at the 1 position. Comparison of the metabolic activities of all major arachidonoyl molecular species of glycerophospholipids having a single structure is reported here for the first time.

Animals↗
PubMed1989

Proteeae species bacteriuria accompanying Proteeae species groin skin carriage in geriatric outpatients.

There have been numerous reports of Proteeae species urinary tract infections among elderly individuals. To explore a possible urinary carrier source of Proteeae species in this population, the frequency of aerobic gram-negative bacillus (AGNB) bacteriuria at the greater than or equal to 10(2)/ml level was determined in 67 ambulatory elderly outpatients classified as to Proteeae group (Morganella, Proteus, Providencia) groin carriage by a set of two skin cultures obtained at least 1 week apart. None had urethral catheters, symptomatic infections, skin ulcers, or recent antibiotic therapy. We found AGNB bacteriuria in 12 of 15 carriers (80%) and in 21 of 52 noncarriers (40%) (P = 0.009). Proteeae species bacteriuria occurred in eight carriers (53.3%) and six noncarriers (11.5%) (P = 0.001). At the 10(2) to 10(4)/ml level, Proteeae species were isolated in urine specimens from seven carriers (46.7%) and four noncarriers (7.7%) (P = 0.001). There was concordance of species of skin and urine Proteeae isolates in six carriers. By contrast, non-Proteeae AGNB bacteriuria at any level was present in four Proteeae species carriers (26%) and 15 noncarriers (28.8%) (P greater than 0.05). There was a 36.7% frequency of Proteeae species bacteriuria in nursing home residents, in contrast to 8.1% among those living in private homes; this parallels the greater frequency of Proteeae species groin carriage among nursing home residents in the study population. Low-level urinary colonization with Proteeae species accompanying Proteeae species groin skin colonization in elderly individuals is a hitherto unrecognized finding. This may account for the greater frequency of Proteeae species urinary infections in this population.

Aged↗
PubMed2003

[What the Prorocentrum species should be?--a review on identification of a Prorocentrum species from the East China Sea].

In the past decade, the Prorocentrum bloom was the most frequently occurred bloom in the East China Sea. It occurred every one year or two years, and covered huge areas. There were arguments on the identification of Prorocentrum bloom causative species. Some scientists thought the species being P. dentatum Stein, but the others thought that it was a new species, P. donghaiense Lu. For achieving the proper classification of the species, an "International Workshop on HAB Causative Species--Taxonomic View on a species of Prorocentrum in the East China Sea" was held in Shenzhen, China in November, 2002. By reviewing as much as available references, and by comparing the Prorocentrum specimen from the East China Sea with those from Japan, Korea and USA, scientists participated in this Workshop agreed that: 1) the specimens from Japanese and Korean waters, and from CCMP, USA were the same species; 2) the features of anterior projection and cell surface marking were similar to those of originally described P. dentatum Stein; 3) the major difference is the cell size. The specimens from the East China Sea were mostly less than 20 microns long, whereas the size of the original described P. deatatum was larger than 50 microns; 4) the minor difference is the shape of the cell end. The original described P. deatatum was with a pointed end, whereas the cells from the East China Sea were mostly with a rounded end. There was no final agreement for the species identification at the Workshop. By summing all views of scientists from the Workshop, the authors suggested that the bloom causative species of Prorocentrum in the East China Sea, as well as so-called species of P. dentatum from other East Asian waters, should be the same species. They are all P. donghaiense Lu.

China↗
PubMed1995

Relationship of membrane phospholipid composition, lactosylceramide molecular species, and the specificity of CMP-N-acetylneuraminate:lactosylceramide alpha 2,3-sialyltransferase to the molecular species composition of GM3 ganglioside.

The ceramide molecular species specificity of rat brain neuron CMP-N-acetylneuraminate:lactosylceramide alpha 2,3-sialyltransferase (LacCer alpha 2,3-ST) was determined using 19 molecular species of lactosylceramide incorporated into liposomes prepared with purified rat brain phospholipids. The neuron enzyme displayed a distinct molecular species specificity (which was different than the specificity of liver LacCer alpha 2,3-ST) based on both the long-chain base and the fatty acid composition of the lactosylceramide. Specifically, compared to the liver enzyme, relatively high activities were obtained with d18:1-16:0, d18:1-22:1, and d18:0-18:0 lactosylceramide molecular species. When the lipid composition of the neuron microsomal membranes was altered to resemble that of rat liver Golgi membrane lipids, the activities towards d18:1-16:0, d18:1-22:1, and d18:0-18:0 lactosylceramide molecular species were significantly (P < 0.01) reduced and the molecular species specificity of the neuron enzyme resembled that of liver LacCer alpha 2,3-ST. In the reciprocal experiment in which the lipid composition of the rat liver Golgi membranes was altered to resemble neuron microsomal membrane lipids, the molecular species specificity of liver LacCer alpha 2,3-ST was virtually identical to the specificity obtained with the native neuron enzyme. Analysis of the molecular species composition of lactosylceramide and GM3 in rat liver Golgi membranes revealed that the molecular species composition of rat liver Golgi membrane GM3 was precisely what would be expected based on the molecular species specificity of LacCer alpha 2,3-ST and the molecular species composition of lactosylceramide in the Golgi membrane.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Pacific Coast Iris species delimitation using three species definitions: biological, phylogenetic and genealogical

Morphological characters are used to discriminate the five Oregon species of the Pacific Coast irises (Iris series Californicae). In nearly every case, fixed differences were found between species, revealing that they are good phylogenetic species. However, when the biological species concept is applied, the whole series is found to be one biological species. Sequence data were generated from the chloroplast DNA region between the atpbeta and rbcL genes. For this 700 bp region, the maximum divergence observed in the series was one percent. These sequences, together with three restriction site characters, were used to produce a cladogram for multiple individuals of all species in the group. On the resulting consensus cladogram, the different individuals from each species do not cluster together. This could result from either introgressive hybridization or the retention of ancestral polymorphism. When the genealogical species concept is applied, only one species can be identified: the whole Series Californicae. There are therefore two natural levels at which taxa can be defined. It is recommended that the phylogenetic species be used as the taxonomic species in this group.Copyright 1998 The Linnean Society of London

Journal Article↗
PubMed1999

Molecular phylogeny of the Ceratosolen species pollinating Ficus of the subgenus Sycomorus sensu stricto: biogeographical history and origins of the species-specificity breakdown cases.

The 14 species of Ficus of the subgenus Sycomorus (Moraceae) are invariably pollinated by Ceratosolen species (Hym. Chalcidoidea), which in turn reproduce in the fig florets. They are distributed mostly in continental Africa, Madagascar, and the Mascarene and Comoro Islands, but 1 species extends its geographical range all over the Oriental region. Fig-pollinator relationships are usually strictly species specific, but exceptions to the 'one-to-one' rule occur within the group we studied. In order to understand both the biogeographical history of the Ceratosolen species associated with Ficus of the subgenus Sycomorus and the origins of the specificity breakdown cases, we have used cytochrome b sequences to reconstruct a phylogeny of the fig wasps. The results show that the pollinators from the Malagasy region and those from continental Africa form two distinct clades, which probably diverged after the crossing of the Mozambique Channel by an ancestral population. The Oriental wasp species show strong affinities with the African species. The two species-specificity exceptions are due to different evolutionary events. The occurrence of the two West African pollinators associated with F. sur can be explained by successive speciation events of the mutualistic partner without plant radiation. In contrast, we hypothesize that C. galili shifted by horizontal transfer from an unknown, presumably extinct, Ficus species to F. sycomorus after this native Malagasy fig species colonized Africa.

Animals↗
PubMed2003

Rapid and unequivocal differentiation of Candida dubliniensis from other Candida species using species-specific DNA probes: comparison with phenotypic identification methods.

Candida dubliniensis is a recently described opportunistic pathogen which shares many phenotypic characteristics with Candida albicans but which has been reported to rapidly acquire resistance to azole antifungal drugs. Therefore, differentiation of C. dubliniensis from C. albicans becomes important to better understand the clinical significance and epidemiologic role of C. dubliniensis in candidiasis. We compared phenotypic methods for the differentiation of C. dubliniensis from C. albicans (i.e. the ability to grow at elevated temperatures, colony color on CHROMagar Candida medium, and carbohydrate assimilation patterns) to amplify the results of a polymerase chain reaction (PCR) assay using universal fungal primers to the internal transcribed spacer 2 (ITS2) region of rDNA and species-specific DNA probes in an enzyme immunoassay format (PCR-EIA). DNA sequencing of the ITS1 rDNA region was also conducted. The C. dubliniensis ITS2 probe correctly identified all C. dubliniensis isolates without cross-reaction with any other Candida species tested (mean A(650 nm) +/- SE, C. dubliniensis probe with C. dubliniensis DNA, 0.372 +/- 0.01, n = 22; C. dubliniensis probe with other Candida species DNA, 0.001 +/- 0.02 n = 16, P < 0.001). All other Candida species tested (C. albicans, Candida glabrata, Candida krusei, Candida parapsilosis, and Candida tropicalis) were also correctly identified by the PCR-EIA without any detectable cross-reactions among species. Phenotypically, C. dubliniensis isolates demonstrated an increased sensitivity to heat compared to C. albicans isolates. At 42 degrees C, only 50% of C. dubliniensis isolates grew compared to 73% of C. albicans isolates and, at 45 degrees C, 91% of C. dubliniensis isolates failed to grow compared to 64% of C. albicans isolates. C. albicans was more likely to demonstrate a dark green or blue green colony color on CHROMagar Candida medium obtained from Becton Dickinson (i.e. 100% of C. albicans isolates were dark green or blue green versus 64% of C. dubliniensis isolates) whereas no difference in the percentage of C. albicans or C. dubliniensis isolates producing dark green or blue green colony color was detected using CHROMagar Candida medium from Hardy Diagnostics (82% for both species). The API 20C AUX carbohydrate assimilation system incorrectly identified C. dubliniensis as C. albicans in all but three cases: remaining isolates were misidentified as C. albicans/C. tropicalis, C. tropicalis/C. albicans, and Candida lusitaniae/C. albicans. In all, 82% of C. albicans isolates and 100% of C. dubliniensis isolates assimilated trehalose; the latter finding was opposite to that reported for C. dubliniensis in the API 20C AUX profile index. Xylose and alpha-methyl-D-glucoside assimilation, respectively, were negative for 100 and 95% of C. dubliniensis isolates and positive for 100 and 91% of C. albicans isolates, confirming earlier reports that assimilation results for xylose and alpha-methyl-D-glucoside may be helpful in the discrimination of these two species. However, conventional phenotypic species identification tests required days for completion, whereas the PCR-EIA could be completed in a matter of hours. In addition, identification of Candida species by ITS1 rDNA sequencing gave 100% correspondence to the results obtained by the PCR-EIA, confirming the specificity of the PCR-EIA method. These data indicate that although a combination of phenotypic methods may help differentiate C. dubliniensis from C. albicans to some extent, the PCR-EIA can provide a simple, rapid, and unequivocal identification of the most medically important Candida species in a single test.

Candida↗
PubMed2000

Species concepts and malaria parasites: detecting a cryptic species of Plasmodium.

Species of malaria parasite (phylum Apicomplexa: genus Plasmodium) have traditionally been described using the similarity species concept (based primarily on differences in morphological or life-history characteristics). The biological species concept (reproductive isolation) and phylogenetic species concept (based on monophyly) have not been used before in defining species of Plasmodium. Plasmodium azurophilum, described from Anolis lizards in the eastern Caribbean, is actually a two-species cryptic complex. The parasites were studied from eight islands, from Puerto Rico in the north to Grenada in the south. Morphology of the two species is very similar (differences are indistinguishable to the eye), but one infects only erythrocytes and the other only white blood cells. Molecular data for the cytochrome b gene reveal that the two forms are reproductively isolated; distinct haplotypes are present on each island and are never shared between the erythrocyte-infecting and leucocyte-infecting species. Each forms a monophyletic lineage indicating that they diverged before becoming established in the anoles of the eastern Caribbean. This comparison of the similarity, biological and phylogenetic species concepts for malaria parasites reveals the limited value of using only similarity measures in defining protozoan species.

Animals↗
PubMed2006

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi.

The claim that eukaryotic micro-organisms have global geographic ranges, constituting a significant departure from the situation with macro-organisms, has been supported by studies of morphological species from protistan kingdoms. Here, we examine this claim by reviewing examples from another kingdom of eukaryotic microbes, the Fungi. We show that inferred geographic range of a fungal species depends upon the method of species recognition. While some fungal species defined by morphology show global geographic ranges, when fungal species are defined by phylogenetic species recognition they are typically shown to harbour several to many endemic species. We advance two non-exclusive reasons to explain the perceived difference between the size of geographic ranges of microscopic and macroscopic eukaryotic species when morphological methods of species recognition are used. These reasons are that microbial organisms generally have fewer morphological characters, and that the rate of morphological change will be slower for organisms with less elaborate development and fewer cells. Both of these reasons result in fewer discriminatory morphological differences between recently diverged lineages. The rate of genetic change, moreover, is similar for both large and small organisms, which helps to explain why phylogenetic species of large and small organisms show a more similar distribution of geographic ranges. As a consequence of the different rates in fungi of genetic and morphological changes, genetic isolation precedes a recognizable morphological change. The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change.

Classification↗