A revision of the Paeonia suffruticosa complex (Paeoniaceae)

The taxonomical concept of the Paeonia suffruticosa complex i.e. Sect. Moutan Subsect. Vaginatae, has changed greatly since 1990. Six species and four subspecies have been described as new and two subspecies raised to specific level. Five species and two subspecies are recognized in the present revision, viz. P. suffruticosa subsp. suffruticosa and subsp. yinpingmudan, P. jishanensis, P. qiui, P. ostii, P. rockii subsp. rockii and subsp. taibaishanica. P. yananensis, P. ridleyi, P. spontanea, P. moutan subsp. atava, P. suffruticosa subsp. atava, P. rockii subsp. linyanshanii and P. ostii var. lishizhenii are treated as synonyms. P. papaveracea and P. baokangensis are proposed to be interspecific hybrids. A key to the recognized species and subspecies is provided. Biological features of the species are described and their distributions are mapped. The relationships between species are inferred and the origins of commonly cultivated tree peonies ( P. suffruticosa and P. ostii ) are discussed.     

Reproductive isolation of two sympatric subspecies ofJuniperus phoenicea (Cupressaceae) in southern Spain

The phenology, reproductive cycle and cone crop of two sympatric subspecies ofJuniperus phoenicea (Cupressaceae) were studied during three consecutive years in southern Spain. The flowering pattern of each subspecies was constant during this period: inJ. phoenicea subsp.turbinata flowering was always in October–November, whileJ. phoenicea subsp.phoenicea flowered in February–March. There was no overlap between the flowering periods of the two taxa. The reproductive cycle of the two subspecies was similar, though there were some important differences because of their flowering times. Male cone development in both subspecies occurred in autumn, but the male cones ofJ. phoenicea subsp.phoenicea did not shed pollen until the end of February. InJ. phoenicea subsp.turbinata, the gap between pollination and fertilisation was seven months while inJ. phoenicea subsp.phoenicea it was only three months, fertilisation taking place at the same time in the two taxa. Post-fertilisation events were similar in the two subspecies, leading to a cycle of two years inJ. phoenicea subsp.turbinata and a shorter one of about 20 months inJ. phoenicea subsp.phoenicea. Alternating good and slight seed cone crops were found in both taxa during the three years studied, the good crops of one subspecies coinciding with the slight crops of the other one. Although the proximity of the two subspecies and method of pollination could make hybridisation between the taxa possible, the different flowering seasons prevent hybridisation isolating them reproductively.     

Assessment of Daucus carota L. (Apiaceae) subspecies by chemotaxonomic and DNA content analyses

For a clearer distinction between the four subspecies of Daucus carota native from Portugal (subsp. carota, subsp. maximus, subsp. gummifer and subsp. halophilus), morphological features of the fruits, DNA content analyses by flow cytometry, and chemical characterization of the essential oils were undertaken.We found chemotaxonomic evidences to consider D. carota subsp. maximus as a separate species rather than a subspecies of D. carota. This separation is based on the morphometric analysis of the fruits and in the high levels of asarone present only in the essential oil of the subsp. maximus. The remaining subspecies are difficult to distinguish from each other based on the morphology of the fruits and in DNA content. However, based on the essential oils, it was possible to distinguish the subspecies halophilus from the other two (subsp. gummifer and subsp. carota) because of its high content of elemicin, with the other two having high levels of geranyl acetate.Based on these results, the subspecies maximus is proposed as a different species (Daucus maximus Desf.) and the taxonomic status of other three subspecies (subsp. carota, subsp. gummifer and subsp. halophilus) is maintained. Still, the latter three taxa need to be further studied for a more precise taxonomic characterization.     

Ribotyping to differentiate Fusobacterium necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme isolated from bovine ruminal contents and liver abscesses.

Differences in biological activities (hemagglutination, hemolytic, leukotoxic, and virulence) and ribotypes between the two subspecies of Fusobacterium necrophorum of bovine ruminal and liver abscess origins were investigated. Hemagglutination activity was present in all hepatic, but only some ruminal, strains of Fusobacterium necrophorum subsp. necrophorum. Ruminal F. necrophorum subsp. necrophorum had low leukotoxin titers yet was virulent in mice. Fusobacterium necrophorum subsp. funduliforme of hepatic or ruminal origin had no hemagglutination activity, had low hemolytic and leukotoxic activities, and was less virulent to mice. For ribotyping, chromosomal DNAs of 10 F. necrophorum subsp. necrophorum and 11 F. necrophorum subsp. funduliforme isolates were digested with restriction endonucleases (EcoRI, EcoRV, SalI, PstI, and HaeIII) and examined by restriction fragment length polymorphisms after hybridizing with a digoxigenin-labeled cDNA probe transcribed from a mixture of 16 and 23S rRNAs from Escherichia coli. The most discriminating restriction endonuclease enzyme for ribotyping was EcoRI. The presence or absence of two distinct bands of 2.6 and 4.3 kb differentiated the two subspecies. Regardless of the origin, only F. necrophorum subsp. necrophorum, a virulent subspecies, had a ca. 2.6-kb band, whereas F. necrophorum subsp. funduliforme, a less virulent subspecies, had a ca. 4.3-kb band. Ribotyping appears to be a useful technique to genetically differentiate the two subspecies of F. necrophorum.     

Comparison of the Biochemical Properties of Bacteroides melaninogenicus from Human Dental Plaque and Other Sites

A total of 45 strains of black-pigmented bacteroides, including Bacteroides melaninogenicus subsp. melaninogenicus, Bacteroides melaninogenicus subsp. intermedius and Bacteroides melaninogenicus subsp. asaccharolyticus , have been examined for morphological and physiological characteristics. They were also tested for the range of acidic metabolites, the typical basic amino acid of the mucopeptide, the base composition of DNA, the electrophoretic mobility of malate dehydrogenase and the susceptibility to certain antibiotics. The subspecies most commonly isolated from supragingival human dental plaque are B. melaninogenicus subsp. intermedius and B. melaninogenicus subsp. melaninogenicus . A list of tests for the differentiation of the three subspecies is given, but the separation of B. melaninogenicus subsp. asaccharolyticus from the other two subspecies of B. melaninogenicus is nevertheless recommended.     

Mycobacterium avium subsp. paratuberculosis and M. avium subsp. avium are independently evolved pathogenic clones of a much broader group of M. avium organisms

Mycobacterium avium comprises organisms that share the same species designation despite considerable genomic and phenotypic variability. To determine the degree and nature of variability between subspecies and strains of M. avium, we used multilocus sequencing analysis, studying 56 genetically diverse strains of M. avium that included all described subspecies. In total, 8,064 bp of sequence from 10 gene loci were studied, with 205 (2.5%) representing variable positions. The majority (149/205) of these variations were found among M. avium subsp. hominissuis organisms. Recombination was also evident in this subspecies. In contrast, there was comparatively little variability and no evidence of recombination within the pathogenic subspecies, M. avium subsp. paratuberculosis, M. avium subsp. avium, and M. avium subsp. silvaticum. Phylogenetic analysis showed that M. avium subsp. avium and M. avium subsp. silvaticum strains clustered together on one branch, while a distinct branch defined M. avium subsp. paratuberculosis organisms. Despite the independent origin of these pathogenic subspecies, an analysis of their rates of nonsynonymous (dN) to synonymous (dS) substitutions showed increased dN/dS ratios for both: 0.67 for M. avium subsp. paratuberculosis and 0.50 for M. avium subsp. avium/M. avium subsp. silvaticum, while the value was 0.08 for M. avium subsp. hominissuis organisms. In conclusion, M. avium subsp. hominissuis represents a diverse group of organisms from which two pathogenic clones (M. avium subsp. paratuberculosis and M. avium subsp. avium/M. avium subsp. silvaticum) have evolved independently.     

Geographic divergence in floral morphology and scent in Linanthus dichotomus (Polemoniaceae)

Floral reproductive morphology and scent are of primary importance to pollinators in guiding foraging decisions. We compared the floral scent and reproductive morphology between two subspecies of Linanthus dichotomus (Polemoniaceae) that are taxonomically distinguished by geography and flowering time: the vespertine L. dichotomus subsp. dichotomus and the diurnal L. dichotomus subsp. meridianus. Disparity in flowering time between the two subspecies is accompanied by differences in flower visitors. We collected floral volatiles using dynamic headspace methods and analyzed them using gas chromatography and mass spectroscopy. Together, the subspecies produced a total of 39 floral scent compounds. Subspecies differ in the quantitative pattern of volatiles that attract noctuid moths (e.g., lilac aldehydes) vs. a more general suite of visitors (e.g., phenylacetaldehyde), but not in overall scent emission rates. A discriminant function analysis correctly distinguished between the two subspecies based on scent samples 86% of the time. We measured seven reproductive morphological traits; a discriminant function analysis distinguished between the two subspecies based on morphological samples 81% of the time. We found significant differences between subspecies in scent but not in individual morphological traits. The evidence presented here is most consistent with a hypothesis of pollinator-mediated selection.     

Morphology and anatomy of the leaves of Bersama abyssinica Fresen. from Kenya and Uganda

The detailed morphology and anatomy of leaves of Bersama abyssinica collected in Kenya and Uganda is described. Certain differences are noted between the leaves of subsp. abyssinica and subsp. paullinioides and the significance of these is discussed. It is suggested that palisade ratio values might be a possible means of differentiating between the two subspecies.     

A revision of the genus Centranthus DC. (Valerianaceae)

Centranthus DC. is a mediterranean genus comprising 17 taxa (including 9 species and 7 subspecies). Two new subspecies, namely C. longiflorus subsp. atlanticus and C. calcitrapae subsp. trichocarpus , are described. Affinities within the genus are discussed and four species are newly circumscribed; five new infraspecific combinations are made. Vicariance is demonstrated with the aid of two dot maps.     

Hybridizations and genetic relationships among Lindernia species (Scrophulariaceae): L. procumbens and two subspecies of L. dubia

Lindernia procumbens and L. dubia are common annual weeds in flooded rice fields of Japan. Two subspecies of L. dubia, subsp. major and subsp. dubia, are usually recognized in Japan but they are both regarded as synonyms of L. dubia elsewhere. In a cluster analysis based on AFLP, most L. dubia subsp. major formed a separate cluster from L. dubia subsp. dubia although 11% of haplotypes classified using AFLP were not coincident with classification using the shape of leaf bases, which is the commonly used identification trait. Artificial F₁ plants between L. procumbens and L. dubia subsp. major, and between L. procumbens and L. dubia subsp. dubia did not produce seed. Forty percent of capsules produced by F₁ plants from these two subspecies were slimmer and 80% pollen were sterile in slimmer capsules. However, seed number of most F₁ capsules was not different from that of self-fertilized plants, suggesting that there was no complete reproductive isolation between the subspecies. Natural hybridization of these subspecies may have occurred but we are not aware of it because F₁ plants are rare and F₂ plants are indistinguishable from these subspecies.     

DNA-DNA hybridization and analysis of restriction endonuclease and rRNA gene patterns of atypical (catalase-weak/negative) Campylobacter jejuni from paediatric blood and faecal cultures.

Sixteen strains of atypical (catalase-weak or negative), hippurate-hydrolysing campylobacters from paediatric blood and faecal cultures were identified by DNA-DNA slot hybridization. All were closely related (greater than or equal to 67%) to Campylobacter jejuni and representative strains had G + C contents of 30 +/- 1 mol%. Numerical analysis of chromosomal DNA HaeIII digest patterns revealed two clusters of strains at the 55%S level corresponding to C. jejuni subsp. jejuni and C. jejuni subsp. doylei; most strains belonged to the latter subspecies. No two strains had identical patterns but within each subspecies two subgroups were identifiable, corresponding to Lior biotypes I and II. Southern blot hybridization analysis with a 16 + 23S rRNA cistron probe from Escherichia coli also showed differences between the various strains, and in a numerical analysis three groupings were formed at 70%S corresponding to C. jejuni subsp. jejuni Lior biotypes I and II, and C. jejuni subsp. doylei. Four of the subspecies doylei strains contained a 3.4-MDa plasmid. These analyses showed that catalase-negative C. jejuni subsp. jejuni were genomically distinguishable from C. jejuni subsp. doylei as were Lior biotypes within subsp. jejuni. Ability to produce catalase is not a feature common to all C. jejuni strains, and our results confirm that some strains of subspecies jejuni may be negative in that character although typical in other respects. DNA pattern heterogeneity was consistent with serological differences between strains.     

Screening of the antioxidative properties and total phenolic contents of three endemic Tanacetum subspecies from Turkish flora

Methanolic extracts of three different Tanacetum subspecies [Tanacetum densum (Lab.) Schultz Bip. subsp. sivasicum Hub-Mor and Grierson, Tanacetum densum (Lab.) Schultz Bip. subsp. eginense Heywood and Tanacetum densum (Lab.) Schultz Bip. subsp. amani Heywood] which are endemic to Turkish flora were screened for their possible antioxidant activities by two complementary test systems namely DPPH free radical scavenging and beta-carotene/linoleic acid. In DPPH system, the most active plant was T. densum subsp. amani with an IC(50) value of 69.30+/-0.37 microg/ml. On the other hand, T. densum subsp. sivasicum exerted greater antioxidant activity than those of other subspecies in beta-carotene/linoleic acid system (79.10%+/-1.83). Antioxidant activities of BHT, curcumine and ascorbic acid were also determined as positive controls in parallel experiments. Total phenolic constituents of the extracts of Tanacetum subspecies were performed employing the literature methods involving Folin-Ciocalteu reagent and gallic acid as standard. The amount of total phenolics was highest in subsp. sivasicum (162.33+/-3.57 microg/mg), followed by subsp. amani (158.44+/-2.17 microg/mg). Especially, a positive correlation was observed between total phenolic content and antioxidant activity of the extracts.     

DNA-DNA hybridization and analysis of restriction endonuclease and rRNA gene patterns of atypical (catalase-weak/negative) Campylobacter jejuni from paediatric blood and faecal cultures

Sixteen strains of atypical (catalase-weak or negative), hippurate-hydrolysing campylobacters from paediatric blood and faecal cultures were identified by DNA–DNA slot hybridization. All were closely related ( 67%) to Campylobacter jejuni and representative strains had G + C contents of 30 ± 1 mol%. Numerical analysis of chromosomal DNA Hae III digest patterns revealed two clusters of strains at the 55%S level corresponding to C. jejuni subsp. jejuni and C. jejuni subsp. doylei ; most strains belonged to the latter subspecies. No two strains had identical patterns but within each subspecies two subgroups were identifiable, corresponding to Lior biotypes I and II. Southern blot hybridization analysis with a 16 + 23S rRNA cistron probe from Escherichia coli also showed differences between the various strains, and in a numerical analysis three groupings were formed at 70%S corresponding to C. jejuni subsp. jejuni Lior biotypes I and II, and C. jejuni subsp. doylei . Four of the subspecies doylei strains contained a 3·4-MDa plasmid. These analyses showed that catalase-negative C. jejuni subsp. jejuni were genomically distinguishable from C. jejuni subsp. doylei as were Lior biotypes within subsp. jejuni . Ability to produce catalase is not a feature common to all C. jejuni strains, and our results confirm that some strains of subspecies jejuni may be negative in that character although typical in other respects. DNA pattern heterogeneity was consistent with serological differences between strains.     

Parallel Evolution Under Domestication and Phenotypic Differentiation of the Cultivated Subspecies of <Emphasis Type="Italic">Cucurbita pepo</Emphasis> (Cucurbitaceae)

Parallel Evolution under Domestication and Phenotypic Differentiation of the Cultivated Subspecies of Cucurbita pepo (Cucurbitaceae). Cucurbita pepo (pumpkin, squash, gourd, Cucurbitaceae) is an ancient North American domesticate of considerable economic importance. Based on molecular genetic polymorphisms, two cultivated lineages of this species, each consisting of very many edible–fruited cultigens, have been recognized, C. pepo subsp. pepo and C. pepo subsp. texana. However, the phenotypic commonalities and differences between these two subspecies have not as yet been systematically collected and organized. Among the evolutionary developments common to the two subspecies are the increased size of the plant parts, less plant branching, and premature loss of chlorophyll in the exocarp of the fruits. In both subspecies, bush growth habit, conferred by allele Bu, is common to the cultigens grown for consumption of the immature fruits, as is the deviation from the 1:1 ratio of fruit length to fruit width. A major characteristic differentiating between the edible–fruited cultigens of the respective subspecies are the longitudinal protrusions, in subsp. pepo, versus depressions, in subsp. texana, of the fruit surface corresponding with the subsurface primary carpellary vein tracts. Subsp. pepo also has larger fruits and larger and longer seeds. In addition, some alleles affecting stem color, leaf mottling, multiple flower bud production, and fruit characteristics are frequently occurring to nearly fixed in one subspecies but are rare to less common in the other.     

Ecotype differentiation and coexistence of two parapatric tetraploid subspecies of cocksfoot (Dactylis glomerata) in the Alps

Two tetraploid subspecies of Dactylis glomerata L., subsp. reichenbachii (Hausm.) Stebbins et Zohary and subsp. glomerata , occur in the French Alps. The former is confined to dolomitic, south-facing, alpine lawns above 2000 m, whereas the latter occurs in non-dolomitic habitats in subalpine meadows mainly below 1900 m. Previous studies of allozyme variation have shown that genetic introgression between the two subspecies occurs over large areas. By contrast, morphologically intermediate individuals only occur in an extremely narrow area, suggesting that the morphological and physiological differences between the two subspecies is of adaptive significance. A reciprocal clone transplant experiment was set up to examine (1) any genetic differences between subspecies indicative of ecotypic differentiation in relation to habitat characteristics and (2) the level of phenotypic plasticity in the two subspecies. Genetic differentiation was confirmed by a statistically significant taxon × site interaction effect in anova for all traits studied. The glomerata populations produced more tillers, longer leaves and higher culms in all sites, especially in their home environment. However, reichenbachii populations produced more seeds than the glomerata populations in the original reichenbachii environment, suggesting ecotypic differentiation between the two subspecies. This result might also explain why the glomerata subspecies is unable to colonize dolomitic habitats occupied by the reichenbachii subspecies. The reichenbachii populations showed less plasticity than the glomerata populations for leaf length and floriferous tiller number, a result which is discussed in the context of the response of plants from productive and non-productive habitats to environmental variation.     

Ribotyping of Fusobacterium necrophorum strains isolated from bovine and ovine hepatic abscesses

A microbiological study was made of 100 strains of Fusobacterium necrophorum isolated from hepatic abscesses in bovine and ovine herds. Differences between the biological activity and ribotypes within the two F. necrophorum subspecies were studied. Conventional methods identified 89 isolates as F. necrophorum subsp. necrophorum and 11 as F. necrophorum subsp. funduliforme. For ribotyping, 50 strains (35 F.n. subsp. necrophorum, 11 F.n. subsp. funduliforme and 4 reference strains) were digested with restriction endonucleases (HindIII, EcoRI and BamHI) and examined after hybridization with digoxigenin-labelled cDNA probe transcribed from a 16 and 23S rRNAs from Escherichia coli. The most discriminating restriction endonuclease enzymes for ribotyping were EcoRI and BamHI. The presence or absence of two distinct band of 5 kb (EcoRI) and 10.5 kb (BamHI) differentiated the two subspecies. This technique also revealed genetic differences between isolates which could be used in the epidemiological study of clinical processes caused by F. necrophorum.     

Divergence of Genomic Sequences between Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris

Relatedness between Lactococcus lactis subsp. cremoris and L. lactis subsp. lactis was assessed by Southern hybridization analysis, with cloned chromosomal genes as probes. The results indicate that strains of the two subspecies form two distinct groups and that the DNA sequence divergence between L. lactis subsp. lactis and L. lactis subsp. cremoris is estimated to be between 20 and 30%. The previously used phenotypic criteria do not fully discriminate between the groups; therefore, we propose a new classification which is based on DNA homology. In agreement with this revised classification, the L. lactis subsp. lactis and L. lactis subsp. cremoris strains from our collection have distinct phage sensitivities.     

A biosystematic investigation of the Asplenium lepidum complex

Twenty-nine populations of three closely related taxa, Asplenium lepidum, A. haussknecktii and A. samarkandense , have been raised together in cultivation. There is considerable inter-population variation, and the ranges of variation of the three species overlap. Cytogenetic investigation of artificial hybrids has shown that the three taxa are all allotetraploid and that they share the same diploid parents, A. aegaeum and A. ruta-muraria subsp. dolomiticum. Analysis of F1 and F2 hybrids between different populations indicates high inter-fertility.
The aggregate is re-defined as a single polymorphic species (A. lepidum) consisting of two subspecies (subsp. lepidum and subsp. haussknechtii) distinguished primarily by gland and sporangial characters. A. samarkandense is reduced to a variety of subsp. haussknechtii. It is suggested that the two subspecies have had separate geographical origins from different morphological variants of the same diploid parents, but the polymorphic nature of the aggregate is principally due to divergent evolution in small populations isolated on limestone mountains in southern Europe and western Asia.     

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T))

Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.