Pyrolysis mass spectrometry characterisation and numerical taxonomy ofAeromonas spp.

Reference strains (2) and 29 isolates ofAeromonas spp. from clinical material and environmental specimens were characterised in traditional biochemical tests, and in pyrolysis mass spectrometry, which gives data reflecting whole-cell composition. Numerical taxonomic analyses of the data sets were compared with conventional identification at species level, and pathogenic potential, as inferred from the origin of the isolates. Clustering with conventional test reaction patterns showed, for each of the species represented, a clearly defined core group of typical isolates, surrounded by a halo of aberrant strains. One further cluster comprised strains intermediate betweenA. caviae andA. hydrophila, and one strain was grossly atypical in both analyses. Clustering from pyrolysis data corresponded less well with species identification. Broadly, the biochemical division between core and halo strains was supported in pyrolysis forA. caviae andA. sobria, but the main group ofA. hydrophila in pyrolysis comprised strains clustering in the core and halo groups of this species, and three strains intermediate betweenA. hydrophila andA. caviae in biochemical tests. Two further pyrolysis clusters comprised core and halo strains ofA. hydrophila. However, pyrolysis clustering correlated well with inferred pathogenicity, showing four clusters of probable pathogens, six clusters of probable nonpathogens, and one two member cluster of doubtful status. Most strains that clustered in the species haloes, or in species-intermediate groups in biochemical tests, were non-human isolates, or were isolated in the absence of symptomatic infection. The correlation of inferred pathogenicity with biochemical clustering was poorer than that with pyrolysis clustering.Abbreviations CTRP conventional test reaction pattern - PyMS pyrolysis mass spectrometry     

Phylohydrax (Rubiaceae-Spermacoceae)—a new genus to accommodate the African and Madagascan“Hydrophylax” species

Hydrophylax, a genus of maritime strand or dune plants, was previously thought to comprise three species, one from India, Sri Lanka and Thailand (H. maritima), and two from Africa and Madagascar (H. carnosa and H. madagascariensis respectively). Evidence is presented that the African and Madagascan species are better placed into a separate genus (Phylohydrax). Differential characters betweenH. maritima andP. carnosa—P. madagascariensis, the relationships between the three species, and the affinities ofPhylohydrax andHydrophylax to otherSpermacoceae are discussed in detail.     

Evaluation of random amplified polymorphic DNA for species identification and phylogenetic analysis inStylosanthes (Fabaceae)

Random amplified polymorphic DNA (RAPD) was assessed for its suitability as a tool to be used in the identification of taxa from the genusStylosanthes (Fabaceae, Papilionoideae, Aeschynomeneae). Five random primers were used to fingerprint accessions from seven species in the genus, and generated RAPD profiles that were species-specific. Data were used to examine evolutionary relationships between taxa, employing both clustering and ordination techniques, and the results were compared with those from a previous cladistic analysis of chloroplast DNA (cpDNA) restriction fragments. Both multivariate approaches indicated relationships that were generally similar to those obtained by RFLP analysis of cpDNA. However, while cluster analysis grouped together all accessions within species, ordination placed certain accessions ofS. humilis, S. macrocephala andS. capitata into separate groups. Experiments to test the assumed homology of comigrating RAPDs estimated 85.7% homology for accessions within species, and 53.8% homology for accessions between species. The value of RAPD data in systematics is discussed.     

Unique repetitive sequences of 170 bp inChlorella

Summary Cot analysis ofChlorella DNA revealed that the genome of the unicellular green alga contained a small amount of repetitive sequences (at most 15% of the total DNA). Short repetitive sequences (SRS) of 170 bp produced by enzymatic digestion of algal DNA with eitherHaeIII,HinfI, orPstI, were found by polyacrylamide gel electrophoresis, and their copy number was estimated to be a few hundred (about 2% of the total repetitive sequences). All three members showed high sequence homology and could be be unified into one family, HaeIII family. The family was divided further into two subfamilies,HinfI- (HaeIII-andHinfI-SRS) andPstI-(PstI-SRS) subfamilies, based on small sequence differences among the members. TheHaeIII family had characteristic structural features, including a considerable number of small unique sequence units (purine-CC) and both direct and inverted repeats, and were organized in tandem arrays in the genome.     

Experimental hybridization between catfishes of the families Clariidae and Pangasiidae in Thailand

Synopsis Hybrids between the clariid speciesClarias macrocephalus andC. batrachus and the pangasiid speciesPangasius sutchi were obtained by hormone injection of brood stock and artificial fertilization. Pure parental crosses as well as all possible hybrid combinations were obtained. Fertility, hatchability, and post-yolk absorption survival was high (66–99%) in all pure parental crosses and in all crosses between the two species ofClarias. In crosses betweenClarias andPangasius fertilization was also very high (68–97%) but hatchability varied from 11 to 23% and post-yolk absorption survival from 0% inPangasius sutchi ×Clarias batrachus to about 50% inPangasius sutchi ×Clarias macrocephalus . The longest-lived hybrids ofPangasius andClarias were those ofPangasius sutchi ×Clarias macrocephalus which survived until the experiment was prematurely terminated due to contaminated food after 4 1/2 months, at which point they had grown to total lengths of 8–14cm. The hybrids comprised four morphotypes, two relativelyPangasius-like and two relativelyClarias-like, but all markedly different from the parental species.     

Geographic structuring of chloroplast DNA genotypes inTiarella trifoliata (Saxifragaceae)

Tiarella trifoliata comprises varietieslaciniata, trifoliata, andunifoliata, and is distributed from southeastern Alaska to northern California. We analyzed restriction site variation of chloroplast DNA (cpDNA) using 23 endonucleases in 76 populations representing the entire geographic range of the species and the three recognized varieties. We also employed comparative restriction site mapping of PCR-amplified chloroplast DNA fragments using 16 restriction endonucleases. This species exhibits low cpDNA restriction site variation. No differentiation is evident among varieties of this species based on cpDNA data; some plants of each variety were characterized by each of the two major cpDNA types detected. The two major cpDNA clades, which differ by only a single restriction site mutation, are geographically structured. A northern clade comprises populations from Alaska to central Oregon; most populations analyzed from southern Oregon and California form a southern clade. Populations that possess the typical northern cpDNA type also occur disjunctly to the south at high elevations in the Siskiyou—Klamath Mountain area of southern Oregon and northern California. Conversely, the southern cpDNA type is found disjunctly to the north in the Olympic Peninsula of Washington. Both geographic areas characterized by disjunct cytoplasms are considered glacial refugia.Tiarella trifoliata joins two other species,Tolmiea menziesii andTellima grandiflora, in having well-demarcated northern and southern cpDNA lineages. All three species have similar life-history traits and geographic distributions. We suggest that glaciation may have played a major role in the formation of the cpDNA discontinuities present in these three taxa. The pronounced relationship between cpDNA variation and geographic distribution suggests the potential applicability of intraspecific phylogeography to plants via the analysis of intraspecific cpDNA variation. These three examples also join a rapidly growing data base which indicates that cytoplasms are often geographically structured within species and species complexes.     

Morphological and molecular comparisons ofCampsis grandiflora andC. radicans (Bignoniaceae), an eastern Asian and eastern North American vicariad species pair

Morphological and molecular comparisons were made forCampsis grandiflora (Thunb.)K. Schumann (Bignoniaceae) from eastern Asia andC. radicans (L.)Seemann from eastern North America. Chloroplast DNA (cpDNA) variation was surveyed with 20 restriction endonucleases. The cpDNA divergence between the two vicariad species was 2.44%, which is the highest reported among North Temperate disjunct taxa and one of the highest reported for infrageneric taxa. Detailed morphological comparisons also suggest a high level of divergence. Cluster analyses based on 22 morphological characters and 39 OTUs revealed two distinct groups corresponding with the two species. The average taxonomic distance between the two species was 1.806. Analyses of variance (ANOVA) revealed that 12 of the 18 quantitative characters differed significantly ( 0.01) betweenC. grandiflora andC. radicans. Divergence time based on cpDNA data was estimated as 24.4 million years. The Bering land bridge hypothesis was favored over the North Atlantic land bridge hypothesis based on the estimated divergence time and the geological history of the North Temperate region. The high levels of morphological and cpDNA divergence are not consistent with morphological stasis, which has been proposed as a common mode of evolution for North Temperate disjunct taxa.     

An ultrastructural comparison betweenSpermatozopsis andDunaliella (Chlorophyceae)

The ultrastructure of the type species of the genusDunaliella, D. salina, has been reinvestigated in an attempt to clarify the relationships betweenDunaliella andSpermatozopsis. Dunaliella salina differs in the following ultrastructural characters fromSpermatozopsis (as exemplified byS. similis Preisig etMelkonian): presence of a distinctive surface coat covering the plasmalemma; presence of a prominent pyrenoid (with pairs of thylakoids partially entering the pyrenoid matrix); dictyosomes parabasal; endoplasmic reticulum closely underlying the plasmalemma around most of the cell; contractile vacuoles absent; cell form ovoid to elongated and not spirally twisted; mitochondrial profiles near the flagellar apparatus. Differences in the ultrastructure of the flagellar apparatus: basal body angle more or less fixed; distal connecting fibre cross-striated; system II fibre (rhizoplast) present, associated with mitochondrial profile; system I fibre underlying two-stranded microtubular root; mating structure present. These ultrastructural differences justify distinction between the two taxa at generic level. The problematical status of freshwater species ofDunaliella is briefly discussed.     

5S and 5.8S ribosomal RNA evolution in the suborder tetrahymenina (Ciliophora: Hymenostomatida)

Summary The nucleotide sequences of the 5S and 5.8S rRNAs of eight strains of tetrahymenine ciliates have been determined. The sequences indicate a clear distinction betweenTetrahymena paravorax and its suggested conspecificT. vorax, but leave the taxonomic distinction betweenT. vorax andT. leucophrys in doubt. The rRNA sequences of sixTetrahymena species and of three other species of the suborder Tetrahymenina have been used to deduce evolutionary schemes in which ancestral rRNA sequences and changes are proposed. These schemes suggest the predominant acceptance of GA and CT transitions in the 5S rDNA during the evolution of the suborder.     

Seed oil fatty acid patterns of theAconitum-Delphinium-Helleborus complex (Ranunculaceae)

Many members ofRanunculaceae contain unusual fatty acids in their seed oils. This leads to rather typical genus-specific fatty acid patterns or fingerprints in these seed oils. The members of theDelphinioideae and/orHelleboroideae, however, do not contain highly unusual fatty acids. Nevertheless, their seed oil fatty acid fingerprints are also fairly typical and genus-specific, and the patterns found are rather consistent throughout several species of one genus. It was found that species ofAconitum do not contain fatty acids with 20 carbon atoms.Delphinium, Consolida, Helleborus, Nigella and others do contain C₂₀ fatty acids. In allHelleborus species, for example, there was a consistent C₂₀ fatty acid pattern of 20:020:120:2>20:3. Species ofNigella andGaridella contain high levels,Helleborus low levels, of 20:2n-6 in their seed oils.Delphinium andAconitum both contain low levels of 18:3n-3, whereasHelleborus spp. consistently show high levels of this fatty acid. The genus-specific fatty acid patterns found are discussed, and a correlation with the subfamily and tribe affiliation of the genera investigated here is attempted.     

A physical and genetic map of theCorynebacterium glutamicum ATCC 13032 chromosome

A combined physical and genetic map of theCorynebacterium glutamicum ATCC 13032 chromosome was constructed using pulsed-field gel electrophoresis (PFGE) and hybridizations with cloned gene probes. Total genomic DNA was digested with the meganucleasesSwaI (5-ATTTAAAT-3),PacI (5-TTAATTAA-3), andPmeI (5-GTTTAAAC-3) yielding 26, 27, and 23 fragments, respectively. The chromosomal restriction fragments were then separated by PFGE. By summing up the lengths of the fragments generated with each of the three enzymes, a genome size of 3082 +/- 20 kb was determined. To identify adjacentSwaI fragments, a genomic cosmid library ofC. glutamicum was screened for chromosomal inserts containingSwaI sites. Southern blots of the PFGE gels were hybridized with these linking clones to connect theSwaI fragments in their natural order. By this method, about 90% of the genome could be ordered into three contigs. Two of the remaining gaps were closed by cross-hybridization of blottedSwaI digests using as probesPacI andPmeI fragments isolated from PFGE gels. The last gap in the chromosomal map was closed by hybridization experiments using partialSwaI digestions, thereby proving the circularity of the chromosome. By hybridization of gene probes toSwaI fragments separated by PFGE about 30 genes, including rRNA operons, IS element and transposon insertions were localized on the physical map.     

Evolution of thedec-1 eggshell locus inDrosophila. I. Restriction site mapping and limited sequence comparison in themelanogaster species subgroup

Summary We have analyzed 18 kb of DNA in and upstream of thedefective chorion-1 (dec-1) locus of the eight known species of themelanogaster species subgroup ofDrosophila. The restriction maps ofD. simulans, D. mauritiana, D. sechellia, D. erecta, andD. orena are shown to have basically the restriction map ofD. melanogaster, whereas the maps ofD. teissieri andD. yakuba were more difficult to align. However, the basic amount of DNA and sequence arrangement appear to have been conserved in these species. A small deletion of varying length (65–200 bp) is found in a repeated sequence of the central transcribed region ofD. melanogaster, D. simulans, andD. erecta. Restriction site mapping indicated that thedec-1 gene is highly conserved in themelanogaster species subgroup. However, sequence comparison revealed that the amount of nucleotide and amino acid substitution in the repeated region is much larger than in the 5 translated region. The 5 flanking region showed noticeable restriction site polymorphisms between species. Based on calculations from the restriction maps a dendrogram was derived that supports earlier published phylogenetic relationships within themelanogaster species subgroup except that theerecta-orena pair is placed closer to themelanogaster complex than toD. teissieri andD. yakuba.     

Chloroplast DNA study of the generaAmbrosia s.l. andHymenoclea (Asteraceae): Systematic implications

The relationship ofAmbrosia (ragweed) andFranseria has long been debated. Their treatment as separate genera has been repeatedly challenged. In this study, chloroplast DNA restriction site variation was examined for species from bothAmbrosia andFranseria as well as taxa from the closely related genusHymenoclea. The chloroplast genomes of members of these three genera were examined using 21 restriction endonucleases and the restriction mutations were used to construct phylogenetic trees. Wagner and Dollo parsimony as well as weighted parsimony were employed to compare the different phylogenies. The results support a close relationship betweenAmbrosia andFranseria, but indicate that the two groups are well separated. Compared toFranseria, Ambrosia is a much more strongly supported group, and the results indicate thatHymenoclea is closer toFranseria than toAmbrosia. The cpDNA phylogeny was used as a framework to examine evolutionary trends in morphology and secondary chemistry.     

Differential abundance of simple repetitive sequences in species ofBrassica and relatedBrassicaceae

SixBrassica species, known as the triangle of U, and four species from related genera were characterized by DNA fingerprinting with simple repetitive oligonucleotide probes. Our results show that CT-, TCC-, and GTG-repeat motifs are equally abundant in the genomes of the sixBrassica species. In contrast, GATA-, GGAT-, and GACA-multimers are unevenly distributed among different species. As judged from the number and strength of hybridization signals, the highest copy number of all three motifs occurs inBrassica nigra, while the lowest is observed inB. oleracea. The abundance of GATA-and GACA-repeats varies in a coordinate way. The amphidiploid genomes ofB. juncea, B. carinata, andB. napus each harbour intermediate amounts of (GATA)₄ and (GACA)₄-detected repeats as compared to their diploid progenitors, thus supporting the concept of the U triangle. GATA-, GACA-, and GGAT-repeats were also abundant inEruca sativa andSinapis arvensis, but not inRaphanus sativus andSinapis alba. These results support the idea thatBrassica nigra is more closely related toSinapis arvensis than to otherBrassica species such asB. rapa andB. oleracea.     

Phylogeny and habitat adaptations within a monophyletic group of wetland moss genera (Amblystegiaceae)

Genus level phylogenetic patterns within a monophyletic group of wetland mosses consisting ofTomentypnum, Hamatocaulis, Scorpidium, Conardia, Calliergon, Warnstorfia, Straminergon, andLoeskypnum (Amblystegiaceae) are cladistically analysed, usingPalustriella and partlyCratoneuron as outgroups. The ingroup consists of two clades, one withTomentypnum, Hamatocaulis andScorpidium, the other with the other ingroup genera. The second clade gets completely resolved only with the inclusion of habitat data. The adaptation to relatively dry wetland habitats probably evolved in the ancestor ofStraminergon andLoeskypnum, the species ofCalliergon andWarnstorfia, which are more ancestral, growing in wetter habitats. The more primitive taxa of the ingroup, as well asPalustriella species, occur in relatively mineral-rich habitats and adaptations to poorer habitats occurred several times in the two clades.     

Distribution of a 375 bp repeat sequence inAllium (Alliaceae) as revealed by FISH

Information about evolutionary relationships between species of the genusAllium is desirable in order to facilitate breeding programmes. One approach is to study the distribution of repetitive DNA sequences among species thought on taxonomic grounds, to be closely related. We have used fluorescent in-situ hybridisation (FISH) to examine seven species within sect.Cepa of the genus (A. altaicum, A. cepa, A. fistulosum, A. galanthum, A. pskemense, A. oschaninii andA. vavilovii), one species from sect.Rhizirideum (A. roylei), two species from sect.Allium (A. sativum andA. porrum) and one species from sect.Schoenoprasum (A. schoenoprasum). Each species was probed using a 375 bp repeat sequence isolated fromA. cepa (Barnes & al. 1985), which was generated and labelled by polymerase chain reaction (PCR). No signals were detected in anyAllium species not belonging to sect.Cepa with the exception ofA. roylei, whose designation in sect.Rhizirideum is now questioned. Within sect.Cepa the probe was found to hybridize to the terminal regions of the chromosome arms of all the species examined. In addition a number of interstitial bands were detected. Use of FISH reveals a more detailed map of the location of the repeat sequences than has previously been obtained by C-banding and other staining procedures. The distribution of the terminal and interstitial sites when compared, allow us to identify three species groups namely,A. altaicum andA. fistulosum; A. cepa, A. roylei, A. oschaninii andA. vavilovii; andA. galanthum andA. pskemense.     

Patterns of Fish Movement on Eastern Tasmanian Rocky Reefs

We assessed small-scale movement patterns of fishes on three eastern Tasmanian reefs by divers visually resighting 1040 individuals of 16 species marked with unique colour-coded tags. With the possible exception of the monacanthid Acanthaluteres vittiger, common species showed high fidelity to site, with individuals generally resighted <100m from the initial tagging site and remaining near the tagging site throughout the 1 year duration of study. The wrasses Pictilabrus laticlavius and Notolabrus tetricus were more sedentary than Notolabrus fucicola and the monacanthids Meuschenia australis and Meuschenia freycineti. Body length, sex, water temperature and time since tagging had little influence on distance moved compared to variation between individuals, other than movement distance increasing with body length for N. tetricus. Movement patterns were generally consistent at all three sites, although mean distance moved by N. fucicola was double at Swanport and Return Point compared to Lobster Point. N. tetricus but not P. laticlavius emigrated from areas artificially cleared of macroalgae. The sedentary nature of most small- to medium-sized reef fish species, particularly labrids, indicates that relatively small (1km diameter) marine protected areas should generally provide conservation benefits for these fishes but few `spillover' benefits in surrounding areas.     

Taxonomic evaluations of the genusPinus (Pinaceae) based on electrophoretic data of salt soluble and insoluble seed storage proteins

Electrophoretic studies on seed storage proteins of various gymnosperm species showed that both salt soluble and insoluble protein fractions give taxonomic information. Among species of the genusPinus evident differences are found between the subgeneraHaploxylon (Strobus) andDiploxylon (Pinus). In sect.Strobus the two subsectt.Strobi andCembrae are readily distinguished fromP. bungeana (sect.Parrya) which appears to fall in an intermediate position between haploxyl and diploxyl pines. Among the species of subg.Diploxylon, mountain pines show very similar protein patterns in agreement with their recent speciation (Quaternary).     

Tamarin polyspecific associations: Forest utilization and stability of mixed-species groups

Niche separation is likely to play a key role in the formation of mixed-species groups. Saddle-backed tamarins (Saguinus fuscicollis) were studied at three sites with different primate communities in northern Bolivia: (1) with red-bellied tamarins,S. labiatus; (2) with emperor tamarins,S. imperator; and (3) without a congeneric species. The degree of association is higher betweenS. labiatus andS. fuscicollis than betweenS. imperator andS. fuscicollis and is related to differences in forest utilization between associating pairs. Niche separation is found to be greater betweenS. labiatus andS. fuscicollis than betweenS. fuscicollis andS. imperator. The mean height and habitat utilization ofS. fuscicollis does not differ greatly across the three sites, nor does the height of tamarins in and out of association. It is concluded that combined with differences in body size and dietary overlap, vertical segregation plays an important role in tamarin polyspecific associations (increasing the potential of both foraging and anti-predatory benefits) and that this is not a consequence of vertical displacement ofS. fuscicollis by its dominant congeners.