Evolutionary relationships in the genus Bordetella

The nucleotide sequence of the pertussis toxin operon of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica, has shown that the last two species contain many common mutations and are likely to derive from a common ancestor (Arico and Rappuoli, 1987). To elucidate further the evolutionary relationships between the Bordetella species, we have cloned and sequenced the promoter region and the gene coding for the S1 subunit of pertussis toxin from additional B. pertussis strains, such as the type strain BP 18323 and two recent clinical isolates, namely strain BP 13456 from Sweden and strain BP SA1 from Italy. While the strains BP SA1 and BP 13456 are shown to differ from the published B. pertussis sequences by only one base pair, the type strain BP 18323 contains a total of 11 base-pair substitutions. Remarkably, 9 of the 11 substitutions found in BP 18323 are also common to B. parapertussis and B. bronchiseptica, strongly suggesting that this strain derives from the same ancestor as B. parapertussis and B. bronchiseptica. Computer analysis of the sequence data allows the construction of an evolutionary ‘tree’ showing that the B. pertussis strains are very homogeneous and significantly distant from B. parapertussis and B. bronchiseptica. Therefore the proposed conversion from B. parapertussis to B. pertussis appears highly improbable.     

Evolutionary trends in the genus Bordetella

The genus Bordetella comprises seven species with pathogenic potential for different host organisms. This article attempts to review our current knowledge about the systematics and evolution of this important group of pathogens, their relationship to environmental microorganisms and about molecular mechanisms of host adaptation.     

Evolutionary trees for the genus Bordetella

Recent data on enzyme electrophoretic mobility and DNA sequences for pertussis toxin allow the construction of evolutionary trees for various strains belonging to the genus Bordetella. In contrast to previous analyses, these data can be seen to support the separate clustering of Bordetella pertussis strains, in agreement with the traditional classification based on other phenotypic characteristics. An earlier argument placing the divergence of B. pertussis and B. parapertussis before 1912 does not follow from the evolutionary trees proposed here, which also have different implications for several other claims concerning the evolution of these strains.     

Evolutionary relationships within the Neotropical, eusporangiate fern genus Danaea (Marattiaceae)

Genera within the eusporangiate fern family Marattiaceae have long been neglected in taxonomic and systematic studies. Here we present the first phylogenetic hypothesis of relationships within the exclusively Neotropical genus Danaea based on a sampling of 60 specimens representing 31 species from various Neotropical sites. We used DNA sequence data from three plastid regions (atpB, rbcL, and trnL-F), morphological characters from both herbarium specimens and live plants observed in the field, and geographical and ecological information to examine evolutionary patterns. Eleven representatives of five other marattioid genera (Angiopteris, Archangiopteris, Christensenia, Macroglossum, and Marattia) were used to root the topology. We identified three well-supported clades within Danaea that are consistent with morphological characters: the "leprieurii" clade (containing species traditionally associated with the name D. elliptica), the "nodosa" clade (containing all species traditionally associated with the name D. nodosa), and the "alata" clade (containing all other species). All three clades are geographically and ecologically widely distributed, but subclades within them show various distribution patterns. Our phylogenetic hypothesis provides a robust framework within which broad questions related to the morphology, taxonomy, biogeography, evolution, and ecology of these ferns can be addressed.     

Evolutionary trends of microsatellites during the speciation process and phylogenetic relationships within the genus Secale

Eleven weedy or wild species or subspecies of the genus Secale L. were compared with a set of cultivated rye accessions, based on inter-simple sequence repeat (ISSR) markers to analyze their phylogenetic relationships. A total of 846 bands were amplified from reactions using 12 screening primers, including 79 loci with a mean of 10.1 alleles per locus. The number of amplified bands for each primer ranged from 12 to 134, with a mean of 70.5 amplified bands per primer. The presence and distribution of amplified bands in different accessions demonstrate that a rapid evolutionary trend of microsatellite repeats occurred during the speciation process from the perennial wild form to annual cultivated rye. In addition, variation, amplification, and deletion of microsatellites in genomes revealed phylogenetic relationships in the genus Secale. Analysis of the presence, number, and distribution of amplified bands in genomes, as well as the comparison with genetic similarity (GS) indices based on ISSR, indicate that Secale strictum subsp. africanum (Stapf) Hammer, Secale strictum anatolicum (Boiss.) Hammer, Secale sylvestre Host, and Secale strictum subsp. strictum (C. Presl) Hammer emerged in succession from a common ancestor of Secale following geographic separation and genetic differentiation. The annual weedy rye evolved from S. strictum subsp. strictum, which was domesticated as present-day cultivated rye. Data from ISSR analyses separated all investigated accessions of the genus Secale into three distinct groups. These results support the division of the genus Secale into three species: the annual wild species S. sylvestre; the perennial wild species S. strictum, including several differential subspecies forms such as strictum, africanum, and anatolicum; and S. cereale, including cultivated and weedy rye as subspecies forms.     

IgA protease activity of microbes in the genus Bordetella

Monoclonal IgA paraproteins of subclasses 1 and 2, isolated from the sera of myeloma patients, were incubated for 4, 24, 48 and 72 hours with B. pertussis, B. parapertussis, B. bronchiseptica cultures, as well as Haemophilus influenzae strain. The fragmentation of IgA was studied by immunielectrophoresis with antisera to alpha-chain, to Fab alpha + Fc alpha, to Fab alpha and with antisera to light chains corresponding to the type of paraprotein. B. pertussis and B. parapertussis were found to have subclass-unspecific IgA protease which splitted off a cathode fragment, similar to Fab-fragment and, probably, corresponding to the variable domain of alpha-chain (Fv), after 48-hour incubation. Similar IgA protease was detected in H. influenzae, found to have classical IgA1 protease as well. All Bordetella species under study splitted off anode components from IgA paraproteins of both subclasses. These components, containing the determinants of heavy and light IgA chains, were either IgA - alpha I-antitrypsin complexes or some IgA fragments with high electrophoretic motility. None of the strains under study splitted monoclonal IgG.     

Species relationships in the genus Tulipa

The relationships of diploid and polyploid species belonging to the sub-section Eriostemones of the genus Tulipa have been investigated from the point of view of chromosome morphology, relative DNA values, and meiotic pairing properties. Karyotype morphology is basically the same for all species and eight principal chromosome classes can be distinguished. The range of DNA values obtained by Feulgen cytophotometry for the diploid species is relatively small and provides little assistance in ascertaining the pattern of ploidy involved in the evolution of the group. Partial asynapsis and reverse loop pairing in several of the diploids at pachytene reveals a degree of structural differentiation which may be the outcome of hybridity between species. Significantly, these anomalies are rarely encountered at the equivalent tetraploid levels and a scheme is proposed to account for this behaviour.     

Chromosome relationships in the genus Salmo

Chromosome numbers and polymorphisms in rainbow trout, Atlantic salmon, and brown trout are described. The karyotypes of these three species are compared with each other and with those of other salmonid fish from the genera Salmo, Salvelinus, and Oncorhynchus. Karyotype evolution from a postulated ancestral tetraploid is discussed.     

Lysogeny and conversion characteristics of microbes in the genus Bordetella

The genomes of B. pertussis bacteriophages 134 and 41405 and B. bronchiseptica bacteriophage 214 have been studied. As revealed by the methods of heteroduplex and restriction analyses, the populations of these bacteriophages are heterogeneous and their DNAs differ in size and location of inserts. The study carried out with the use of blot hybridization techniques has shown that in lysogenic cells the genome is not integrated into the chromosome, but exists as an autonomous plasmid replicon. Only partial incorporation of the phage genome into the recipient chromosome takes place in the process of conversion, the phage genome continuing its existence as an autonomous replicon.     

Evolutionary history of the genus Trisopterus

The group of small poor cods and pouts from the genus Trisopterus, belonging to the Gadidae family, comprises four described benthopelagic species that occur across the North-eastern Atlantic, from the Baltic Sea to the coast of Morocco, and the Mediterranean. Here, we combined molecular data from mitochondrial (cytochrome b) and nuclear (rhodopsin) genes to confirm the taxonomic status of the described species and to disentangle the evolutionary history of the genus. Our analyses supported the monophyly of the genus Trisopterus and confirmed the recently described species Trisopterus capelanus. A relaxed molecular clock analysis estimated an Oligocene origin for the group (∼30 million years ago; mya) indicating this genus as one of the most ancestral within the Gadidae family. The closure and re-opening of the Strait of Gibraltar after the Messinian Salinity Crisis (MSC) probably triggered the speciation process that resulted in the recently described T. capelanus.     

Evolutionary relationships among members of the genus Chlamydia based on 16S ribosomal DNA analysis.

Nucleotide sequences from strains of the four species currently in the genus Chlamydia, C. pecorum, C. pneumoniae, C. psittaci, and C. trachomatis were investigated. In vitro-amplified RNA genes of the ribosomal small subunit from 30 strains of C. pneumoniae and C. pecorum were subjected to solid-phase DNA sequencing of both strands. The human isolates of C. pneumoniae differed in only one position in the 16S rRNA gene, indicating genetic homogeneity among these strains. Interestingly, horse isolate N16 of C. pneumoniae was found to be closely related to the human isolates of this species, with a 98.9% nucleotide similarity between their 16S rRNA sequences. The type strain and koala isolates of C. pecorum were also found to be very similar to each other, possessing two different 16S rRNA sequences with only one-nucleotide difference. Furthermore, the C. pecorum strains truncated the 16S rRNA molecule by one nucleotide compared to the molecules of the other chlamydial species. This truncation was found to result in loss of a unilaterally bulged nucleotide, an attribute present in all other eubacteria. The phylogenetic structure of the genus Chlamydia was determined by analysis of 16S rRNA sequences. All phylogenetic trees revealed a distinct line of descent of the family Chlamydiaceae built of two main clusters which we denote the C. pneumoniae cluster and the C. psittaci cluster. The clusters were verified by bootstrap analysis of the trees and signature nucleotide analysis. The former cluster contained the human isolates of C. pneumoniae and equine strain N16. The latter cluster consisted of C. psittaci, C. pecorum, and C. trachomatis. The members of the C. pneumoniae cluster showed tight clustering and strain N16 is likely to be a subspecies of C. pneumoniae since these strains also share some antigenic cross-reactivity and clustering of major outer membrane protein gene sequences. C. psittaci and strain N16 branched early out of the respective cluster, and interestingly, their inclusion bodies do not stain with iodine. Furthermore, they also share less reliable features like normal elementary body morphology and plasmid content. Therefore, the branching order presented here is very likely a true reflection of evolution, with strain N16 of the species C. pneumoniae and C. psittaci forming early branches of their respective cluster and with C. trachomatis being the more recently evolved species within the genus Chlamydia.     

Detection of Bordetella bronchiseptica strains containing the main agglutinogens of all species of the genus Bordetella

The study of 26 B. bronchiseptica strains with typical morphological and biochemical properties resulted in the detection of 8 strains having the main specific agglutinogens of 3 Bordetella species (serovars) in different combinations. The presence of the agglutinogens was confirmed in the agglutination test and the agglutinin adsorption test with the use of monospecific antisera to the main agglutinogens. The comparison of natural B. bronchiseptica serovars and artificial convertants (resulting from the conversion of B. parapertussis by B. pertussis phages) revealed their identical biochemical activity, their capacity for causing necrosis when injected intradermally into rabbits and for the formation of two types of colonies, differing in size and serological activity. In contrast to B. parapertussis convertants, B. bronchiseptica serovars had no lysogenic properties and were sensitive to B. pertussis and B. bronchiseptica phages.     

Evolutionary relationships between morphology, performance and habitat openness in the lizard genus Niveoscincus (Scincidae: Lygosominae)

Correlations between an animal's morphology and ecological parameters such as habitat characteristics emphasize the intimate link between phenotype and the environment, but are often difficult to interpret because the functional consequences of morphological variation are frequently unknown. We provide one of the few studies relating limb morphology, functional capabilities, and habitat in reptiles. We tested the hypothesis that species occupying open microhabitats would possess relatively longer limbs and faster sprint speeds than those occurring in more closed microhabitats. A number of morphological characteristics relevant to locomotion were quantified, including the length of the bones of the fore- and hindlimbs and body size. A phylogenetic analysis was then used to examine the evolutionary relationships between morphology, locomotor performance and microhabitat openness in seven species of Niveoscincus and one species of the closely related genus Pseudemoia. A significant evolutionary relationship was established between sprinting ability, morphology, and the openness of the microhabitat occupied by a species. The phylogenetic analysis demonstrated an evolutionary trend in Niveoscincus of species occupying open microhabitats (e.g. N. greeni, N ocellatus) being large with long limbs and high sprinting ability, while those occupying closed microhabitats (e.g. N coventryi, P. entrecasteauxii) art smaller with short limbs and much slower maximum sprint speeds.     

Limitation of phage multiplication by microbes of the genus Bordetella

Possible causes limiting the multiplication of Bordetella phages or inducing their restriction, such as the influence of lysogenic immunity and the restriction-modification (R-M) system or the incompatibility of the receptor apparatus, have been studied. The limitation of the multiplication of phages by some B. bronchiseptica and B. pertussis strains has been shown to be due to the presence of the R-M system and lysogenic immunity. In five B. bronchiseptica strains and two B. pertussis strains site-specific endonucleases (restrictases) with Hind III specificity have been detected. One B. bronchiseptica strain without the R-M system has been detected. B. bronchiseptica strains producing site-specific endonucleases are practically nonpathogenic for humans, grow in common culture media and selectively produce only one restrictase, type Hind III, which guarantees from the admixture of other specific endonucleases. The B. parapertussis strains under study (altogether 100 strains) have not been found to limit the multiplication of Bordetella test phages. The absence of site-specific endonucleases has also been confirmed biochemically. These strains are recommended as indicator strains for the multiplication of Bordetella phages.