Last of the human protists: the phylogeny and genetic diversity of Iodamoeba

Iodamoeba is the last genus of obligately parasitic human protist whose phylogenetic position is unknown. Iodamoeba small subunit ribosomal DNA sequences were obtained using samples from three host species, and phylogenetic analyses convincingly placed Iodamoeba as a sister taxon to Endolimax. This clade in turn branches among free-living amoeboflagellates of the genus Mastigamoeba. Two Iodamoeba ribosomal lineages (RL1 and RL2) were detected whose sequences differ by 31%, each of which is found in both human and nonhuman hosts.     

The ecology, genetic diversity, and phylogeny of Huaiyangshan virus in China

Surveys were carried out to better understand the tick vector ecology and genetic diversity of Huaiyangshan virus (HYSV) in both regions of endemicity and regions of nonendemicity. Haemaphysalis longicornis ticks were dominant in regions of endemicity, while Rhipicephalus microplus is more abundant in regions of nonendemicity. HYSV RNA was found in human and both tick species, with greater prevalence in H. longicornis and lesser prevalence in R. microplus. Phylogenetic analyses indicate that HYSV is a novel species of the genus Phlebovirus.     

Prevalence of infection with hantavirus in rodent populations of central Argentina

We studied hantavirus seroprevalence and virus variability in rodent populations in Diego Gaynor, northwest of Buenos Aires province, Argentina. Rodent samplings were conducted in railroads and cropfield borders in March and July 1999, September and December 2000, and March 2001. Antibody detection was performed by an enzyme link immunosorbent assay (ELISA), using the recombinant nucleoprotein of Andes (AND) virus as antigen. Tissue samples were taken from positive antibody individuals in order to confirm the presence of hantavirus genomic material and to identify virus genotypes. Akodon azarae was the most abundant species, followed by Oligoryzomys flavescens, while Calomys laucha and C. musculinus were rarely caught. We found a rate of seroprevalence of 9.3% for a total sample of 291 A. azarae and 13.5% for 37 O. flavescens. After molecular analyses of hantavirus, we confirmed the presence of hantavirus genomic material in 16 individuals with ELISA (+) results and two individuals with ELISA (-). Four amplimers for each species were sequenced and compared to the corresponding sequences of representative hantaviruses. We identified the AND Cent Lec from three O. flavescens, and the Pergamino virus from four A. azarae and from one O. flavescens. A. azarae males had higher seroprevalence than females, and heavier individuals showed higher seroprevalence than lighter ones. We did not find seroprevalence differences according to sex in O. flavescens, although this result may have been produced by the low sample size. The lowest seroprevalence was found in a period of high rodent density, when juveniles prevailed in the population. We found higher seroprevalences than those detected in previous studies for other localities of central Argentina where cases of hantavirus pulmonary syndrome (HPS) have been reported. The presence of AND Cent Lec virus in rodent populations of the study area, which is responsible of HPS cases in central Argentina, suggests that human populations are at risk of HPS disease, although there were not reported cases of this disease until today.     

Microsatellite variation in maize landraces from Northwestern Argentina: genetic diversity,population structure and racial affiliations

The highland region or Northwestern Argentina (NWA) is one of the southernmost areas of native maize cultivation and constitutes an expansion of the peruvian Andes sphere of influence. To examine the genetic diversity and racial affiliations of the landraces cultivated in this area, 18 microsatellite markers were used to characterize 147 individuals from 6 maize races representative of traditional materials. For the whole data set, a total of 184 alleles were found, with an average of 10.2 alleles per locus. The average gene diversity was 0.571. The observed patterns of genetic differentiation suggest that historical association is probably the main factor in shaping population structure for the landraces studied here. In agreement with morphological and cytogenetic data, Bayesian analysis of NWA landraces revealed the occurrence of three main gene pools. Assessment of racial affiliations using a combined dataset including previous data on American landraces showed a clear relationship between one of these gene pools and typical Andean races, whereas the remaining two gene pools exhibited a closer association to Caribbean accessions and native germplasm from the United States, respectively. These results highlight the importance of integrating regional genetic studies if a deeper understanding of maize diversification and dispersal is to be achieved.     

Molecular phylogeny and genetic diversity of Tunisian Quercus species using chloroplast DNA CAPS markers

Chloroplast DNA variation was studied in five evergreen Quercus species from the Western part of Tunisia using Cleaved Amplified Polymorphic Sequence (CAPS) technique. Five primer pair/endonuclease combinations have been used. Chlorotypes of Quercus species have been identified. The enzyme HinfI was more efficient in detecting polymorphism in oak species than TaqI. The phenogram showed five groups defining the five studied oak species: suber group, afares group, coccifera group, canariensis group and ilex group. The topology of phenogram showed that the classification depends only on species and independently of their geographic origin. The principal component analysis (ACP) corroborated the results of the tree branching and confirmed the existence of five species groups. Our results showed a genetic proximity between Quercus afares and Quercus coccifera species that may be due to temperature tolerance or the demographic history of these species. Nevertheless, a high value of G_ST calculated (G_ST = 1), suggesting that the maximum of variation is maintained among oak species. This result was confirmed by the low value of the genetic diversity within species (h_S = 0), the value obtained of the total genetic diversity (h_T = 0.378) and the absence of gene flow between species (N_m = 0). A high genetic proximity has been registered between Q. afares, Quercus suber and Quercus canariensis. Moreover, Q. afares shared the chlorotype of Q. suber and Q. canariensis which suggests its hybrid origin.     

Fish microsporidia: fine structural diversity and phylogeny

Structural diversity of fish microsporidian life cycle stages and of the host-parasite interface is reviewed. In the infected cell of the fish host, microsporidia may either cause serious degradation of the cytoplasm and demise of the cell, or they may elicit host cell hypertrophy, producing a parasite-hypertrophic host cell complex, the xenoma. The structure of the xenoma and of its cell wall may differ according to the genus of the parasite, and seems to express properties of the parasite rather than those of the host. In merogony, the parasite cell surface interacts with the host cell in diverse ways, the most conspicuous being the production of thick envelopes of different types. Sporogony stages reveal different types of walls or membranes encasing the sporoblasts and later the spores and these envelopes may be of host or parasite origin. Nucleospora differs from all other fish microsporidia by its unique process of sporogony. Except for the formation of conspicuous xenomas, there are no essentially different structures in fish-infecting microsporidia compared with microsporidia from other hosts. Although the structures associated with the development of fish microsporidia cannot be attributed importance in tracing the phylogeny, they are relevant for practical determination and assessing the relation to the host. The possibility of the existence of an intermediate host is discussed. Higher-level classification of Microsporidia is briefly discussed and structure and evolutionary rates in microsporidian rDNA are reviewed. Discussion of rDNA molecular phylogeny of fish-infecting microsporidia is followed by classification of these parasites. Most form a rather cohesive clade. Outside this clade is the genus Nucleospora, separated at least at the level of Order. Within the main clade, however, there are six species infecting hosts other than fish. Based on data available for analysis, a tentative classification of fish-infecting microsporidia into five groups is proposed. Morphologically defined groups represent families, others are referred to as clades. Group 1, represented by family Pleistophoridae, includes Pleistophora, Ovipleistophora and Heterosporis; Vavraia and Trachipleistophora infect non-fish hosts. Group 2, represented by family Glugeidae, is restricted to genus Glugea and Tuzetia weidneri from crustaceans. Group 3 comprises three clades: Loma and a hyperparasitic microsporidian from a myxosporean; Ichthyosporidium and Pseudoloma clade and the Loma acerinae clade. For the latter species a new genus has to be established. Group 4 contains two families, Spragueidae with the genus Spraguea and Tetramicridae with genera Microgemma and Tetramicra, and the Kabatana and Microsporidium seriolae clade. Group 5 is represented by the family Enterocytozoonidae with the genus Nucleospora and mammal-infecting genus Enterocytozoon.     

Spatial patterns of dicot diversity in Argentina

In this paper, we analyzed the taxonomic diversity of the Argentine dicots to evaluate their relationships with area, latitude, and longitude. We also evaluated species diversity and higher taxa diversity relationships. The families, genera and species diversity in Argentine dicots was not explained by the area of each province but it varied through latitudinal and longitudinal gradients. The taxonomic diversity of these plants increased from high to low latitudes and west–east longitudes. These patterns would explain why the main diversity centers are located in the North region of this country. As we expected the species diversity and higher taxa diversity showed a positive relationship. At this scale, higher taxa diversity could be use as surrogate for species diversity.     

Ecology: linking species diversity and genetic diversity

Although there is a great deal of interest in the biological diversity of species and of genes, it is only recently that researchers have begun to investigate the processes that exert parallel influences on these different levels of diversity.     

Analysis of genetic diversity in earthworms using DNA markers

Earthworms are one of the most important and beneficial macrofauna, and are used extensively in organic farming. Earthworms mediate soil biological regulation systems, and produce biogenic structures. They help to maintain soil structure, water infiltration, and regulate the availability of nutrients assimilated by plants. The objectives of this study were to perform morphological and molecular characterizations of 24 earthworm individuals collected from geographically diverse locations to assess the level of genetic variation. For molecular analysis, the effectiveness of RAPD, ISSR, and Universal rice primers (URPs) markers was investigated to identify polymorphism among 24 isolates of earthworms. A total of 62 molecular markers were used for amplification of genomic DNA of earthworms. Of these, 10 RAPD, 10 ISSR, and 10 URPs markers were used for characterization, which showed 95.7%, 96.7% and 98.3% polymorphism, respectively. The dendrogram, generated from the DNA markers by the unweighted pair group method using arithmetic averages, grouped all the isolates into two main clusters. All Eisenia fetida isolates were clustered in group A, whereas group B included three isolates belonging to Eudrilus eugeniae. Molecular markers allowed a rapid assessment of genetic variation among these closely related isolates of earthworms. These results suggest that molecular markers are a good choice for diversity analysis of earthworm individuals.     

Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species

A combined phylogenetic and multilocus DNA sequence analysis of 26 Pseudomonas stutzeri strains distributed within the 9 genomovars of the species has been performed. Type strains of the two most closely related species (P. balearica, former genomovar 6, and P. mendocina), together with P. aeruginosa, as the type species of the genus, have been included in the study. The extremely high genetic diversity and the clonal structure of the species were confirmed by the sequence analysis. Clustering of strains in the consensus phylogeny inferred from the analysis of seven nucleotide sequences (16S ribosomal DNA, internally transcribed spacer region 1, gyrB, rpoD, nosZ, catA, and nahH) confirmed the monophyletic origin of the genomovars within the Pseudomonas branch and is in good agreement with earlier DNA-DNA similarity analysis, indicating that the selected genes are representative of the whole genome in members of the species.     

Ichthyosauria: their diversity, distribution, and phylogeny

The Ichthyosauria is the group of Mesozoic marine reptiles that was most highly adapted to the aquatic environment. The first ichthyosaurs from the upper Lower Triassic (Spathian) already show a suite of unique characters (very large eyes, elongate snout, deeply amphicoelous vertebrae, limb modified to fins) correlated with a fully aquatic existence and probably were unable to leave the water. The key evolutionary innovation was vivipary, giving birth to live young, which is documented by the fossil record since the end of the Anisian. Major evolutionary trends in the locomotor apparatus are the increasing modification of the fin skeleton to a mosaic of bones and the change from anguiliform swimming in the earliest forms to thunniform swimming in the Jurassic and later forms, as evidenced by the shortening of the body and the evolution of a semilunate tail fin. Almost from the beginning, ichthyosaurs had a cosmopolitan distribution which was retained until their extinction in the Cenomanian. Ichthyosaurian diversity is greatest in the Middle Triassic with piscivorous, heterodont, and durophagous forms. Jurassic diversity is greatest in the Liassic, declining to one genus (Platypterygius) in the Cretaceous. Although skull characters indicate that ichthyosaurs were diapsids, their exact position within Diapsida is unclear. A cladistic analysis of the well known genera clarifies relationships within the Ichthyosauria. Most basal areGrippia andUtatsusaurus, followed by the Mixosauridae (Mixosaurus andPhalarodon). The Shastasauridae (Cymbospondylus, Shonisaurus, Besanosaurus) are the most advanced Triassic forms and represent the sistergroup of all post-Triassic ichthyosaurs. These are clearly monophyletic and are termed here the Neoichthyosauria.     

Assessment of genetic diversity of accessions in Brassicaceae genetic resources by frequency distribution analysis of S haplotypes

Plant genetic resources are important sources of genetic variation for improving crop varieties as breeding materials. Conservation of such resources of allogamous species requires maintenance of the genetic diversity within each accession to avoid inbreeding depression and loss of rare alleles. For assessment of genetic diversity in the self-incompatibility locus (S locus), which is critically involved in the chance of mating, we developed a dot-blot genotyping method for self-incompatibility (S) haplotypes and applied it to indigenous, miscellaneous landraces of Brassica rapa, provided by the IPK Gene Bank (Gatersleben, Germany) and the Tohoku University Brassica Seed Bank (Sendai, Japan), in which landraces are maintained using different population sizes. This method effectively determined S genotypes of more than 500 individuals from the focal landraces. Although our results suggest that these landraces might possess sufficient numbers of S haplotypes, the strong reduction of frequencies of recessive S haplotypes occurred, probably owing to genetic drift. Based on these results, we herein discuss an appropriate way to conserve genetic diversity of allogamous plant resources in a gene bank.     

Analysis of genomic diversity among photosynthetic stem-nodulating rhizobial strains from northeast Argentina

The genomic diversity among photosynthetic rhizobia from northeast Argentina was assessed. Forty six isolates obtained from naturally occurring stem and root nodules of Aeschynomene rudis plants were analyzed by three molecular typing methods with different levels of taxonomic resolution: repetitive sequence-based PCR (rep-PCR) genomic fingerprinting with BOX and REP primers, amplified 16S rDNA restriction analysis (ARDRA), and 16S-23S rDNA intergenic spacer-restriction fragment length polymorphism (IGS-RFLP) analysis. The in vivo absorption spectra of membranes of strains were similar in the near infrared region with peaks at 870 and 800 nm revealing the presence of light harvesting complex I, bacteriochlorophyll-binding polypeptides (LHI-Bchl complex). After extraction with acetone-methanol the spectra differed in the visible part displaying peaks belonging to canthaxanthin or spirilloxanthin as the main carotenoid complement. The genotypic characterization by rep-PCR revealed a high level of genomic diversity among the isolates and almost all the photosynthetic ones have identical ARDRA patterns and fell into one cluster different from Bradyrhizobium japonicum and Bradyrhizobium elkanii. In the combined analysis of ARDRA and rep-PCR fingerprints, 7 clusters were found including most of the isolates. Five of those contained only photosynthetic isolates; all canthaxanthin-containing strains grouped in one cluster, most of the other photosynthetic isolates were grouped in a second large cluster, while the remaining three clusters contained a few strains. The other two clusters comprising reference strains of B. japonicum and B. elkanii, respectively. The IGS-RFLP analysis produced similar clustering for almost all the strains. The 16S rRNA gene sequence of one representative isolate was determined and the DNA sequence analysis confirmed the position of photosynthetic rhizobia in a distinct phylogenetic group within the Bradyrhizobium rDNA cluster.     

Analysis of genetic diversity of Lactarius hatsudake in south China

Lactarius hatsudake is a type of ectomycorrhizal fungus that significantly influences the growth of pine trees. It is widely prevalent in Asian countries and has a high economic value. Artificial cultivation of this fungus has not been achieved as yet; therefore, excessive manual harvesting may cause serious damages to the site of its production. In this study, we analyzed 41 samples of L. hatsudake from south China using internal transcribed spacer (ITS) sequences. By comparing the differences among ITS sequences to identify the haplotype diversity within each population, the relationships among local populations, the relationship between the level of genetic differentiation and geographical separation, and the contributions of local and regional geographical separations to the overall ITS haplotype variation were analyzed. Genetic analysis indicates that ITS sequences obtained from these 41 L.?hatsudake samples could be identified as 18 haplotypes, of which 13 haplotypes were contained in only a single sample, whereas the remaining sequence types all were contained in two or more samples. The most common sequence type, haplotype 6, was found in 16 samples and was distributed across nearly every region. The Mantel test demonstrated that there is no significant linear relationship between geographical distance and the F(ST) value of genetic difference. Results of this research illustrates that there exists a certain degree of genetic intermixing among natural populations of L. hatsudake. From the group genetic analysis, it appears that there exists genetic differentiation of lower frequencies in natural populations of L. hatsudake; however, the linear relationship between the degree of genetic differentiation and geographical distance is not distinctly apparent.     

Freshwater selenium-methylating bacterial thiopurine methyltransferases: diversity and molecular phylogeny

The diversity of bacterial thiopurine methyltransferases (bTPMT) among five natural Se-methylating freshwaters was investigated by polymerase chain reaction (PCR) screenings and sequencings. DNA sequence analyses confirmed the cloned products' identity and revealed a broad diversity of freshwater TPMTs. Neighbour-joining (NJ) phylogenetic analyses combining these sequences, all GenBank entries closely related to these sequences and deduced TPMTs obtained in this work from selected gamma-proteobacteria showed TPMTs to form a distinct radiation, closely related to UbiG methyltransferases. Inside the TPMT phylogenetic cluster, eukaryote sequences diverged early from the bacterial ones, and all the bacterial database entries belonged to a subgroup of gamma-proteobacteria, with an apparent lateral transfer of a particular allele to beta-proteobacteria of Bordetella. The NJ phylogenetic tree revealed 22 bTPMT lineages, 10 of which harboured freshwater sequences. All lineages showed deep and long branches indicative of major genetic drifts outside regions encoding highly conserved domains. Selected residues among these highly variable domains could reflect adaptations for particular ecological niches. PCR lineage-specific primers differentiated Se-methylating freshwaters according to their 'tpm lineage' signatures. Most freshwater tpm alleles were found to be distinct from those available in the databases, but a group of tpm was found encoding TPMTs identical to an Aeromonas veronii TPMT characterized in this work.     

Glossogeny and phylogeny: cultural evolution meets genetic evolution

Evolutionary theorists since Darwin have been interested in the parallels and interactions between biological and cultural evolution. Recent applications of empirical techniques originally developed to analyze molecular genetic data to linguistic data offer new insights into the historical evolution of language, revealing fascinating parallels between language change and biological evolution. This work offers considerable potential toward unified theories of genetic and cultural change.     

Distribution and abundance of sigmodontine rodents in relation to hantavirus in Neuquén, Argentina.

In order to estimate spatial distribution, temporal variation, and prevalence of Andes hantavirus antibody in the rodent community, and especially in Oligoryzomys longicaudatus populations, four different ecosystems were trapped seasonally between spring 2001 and winter 2002 in Neuquen, northwestern Argentinean Patagonia. Five peridomestic settings were sampled within the same period. The rodent O. longicaudatus had the widest distribution in Neuquen, as it was the only species captured at every sample site except for the High Andean steppe, and it was also the most common species captured. Rodents of 13 species were tested for hantavirus antibody prevalence, but O. longicaudatus and Abrothrix longipilis were the only seropositive species. Seropositive individuals were captured during spring and summer in the Subantarctic forest and in winter 2001 in a peridomestic setting in the Patagonian steppe. The dominant presence of O. longicaudatus throughout Neuquen must be incorporated into strategies to prevent human exposure to hantavirus.     

Analysis of genetic diversity and relationships in East African banana germplasm

The genetic diversity and phylogenetic relationships of 29 East African highland banana (Musa spp.) cultivars and two outgroup taxa, M. acuminata Calcutta 4 and Agbagba were surveyed by RAPD analysis. A genetic similarity matrix was established based on the presence or absence of polymorphic amplified fragments. Phylogenetic relationships were determined by UPGMA cluster analysis. RAPDs showed that the highland bananas are closely related with a narrow genetic base. Nevertheless, there were sufficient RAPD polymorphisms that were collectively useful in distinguishing the cultivars. The dendrogram was divisible into a major cluster composed of all the AAA highland banana cultivars and Agbagba (AAB) and a minor cluster consisting of Kisubi (AB), Kamaramasenge (AB) and Calcutta 4 (AA). Several subgroups are recognized within the major cluster. RAPD data did not separate beer and cooking banana cultivars. Our study showed that RAPD markers can readily dissect genetic differences between the closely related highland bananas and provide a basis for the selection of parents for improvement of this germplasm. Received: 28 June 2000 / Accepted: 1 August 2000