A CR1 element is embedded in a novel tandem repeat (HinfI repeat) within the chicken genome.

Highly repetitive DNA sequences constitute a significant portion of most eukaryotic genomes, raising questions about their evolutionary origins and amplification dynamics. In this study, a novel chicken repetitive DNA family, the HinfI repeat, was characterized. The basic repeating unit of this family displays a uniform length of 770 bp, which was defined by the recognition site of HinfI. The HinfI repeat was specifically localized in the pericentric region of chromosome 4 by fluorescence in situ hybridization and constitutes 0.51% of the chicken genome. Interestingly, a chicken repeat 1 (CR1) element has been identified within this basic repeating unit. Like other CR1 elements, this CR1 element also displays typical retrotransposition characteristics, including a highly conserved 3' region and a badly truncated 5' end. This direct evidence from sequence analysis, together with our Southern blot results, suggests that the HinfI repeat may originate from a unique region containing a retrotransposed CR1 element.     

Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data

Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto . The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.     

Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza

Inter simple sequence repeat (ISSR) polymorphism was used to determine genetic diversity and phylogenetic relationships in Oryza. Forty two genotypes including 17 wild species, representing AA,BB,CC,EE,FF,GG,BBCC,CCDD, and HHJJgenomes, two cultivated species, Oryza sativa (AA) and Oryza glaberrima (AA), and three related genera, Porteresia coarctata, Leersia and Rhynchoryza subulata, were used in ISSR analysis. A total of 30 ISSR primers were screened representing di-, tri-, tetra- and penta-nucleotide repeats, of which 11 polymorphic and informative patterns were selected to determine the genetic diversity. The consensus tree constructed using binary data from banding patterns generated by ISSR-PCR clustered 42 genotypes according to their respective genomes. ISSR analysis suggests that the genus Oryza may have evolved following a polyphyletic pathway; Oryza brachyantha (FF genome) is the most divergent species in Oryza and Oryza australiensis (EE genome) does not fall under the Officinalis complex. DNA profiles based on ISSR markers have revealed potential diagnostic fingerprints for various species and genomes, and also for individual accessions/cultivars. Additionally ISSR revealed 87 putative genome/species-specific molecular markers for eight of the nine genomes of Oryza. The ISSR markers are thus useful in the fingerprinting of cultivated and wild species germplasm, and in understanding the evolutionary relationships of Oryza. Received: 23 August 1999 / Accepted: 10 November 1999     

Phylogeographic carrion, hooded and jungle crows (Aves, Corvidae) from data on partial sequencing of the mitochondrial DNA cytochrome B gene

Distribution of mitochondrial DNA cytochrome b gene haplotypes in two crow species was examined by means of sequencing of the 336-bp gene fragment. The topology of the NJ and UPGMA trees showed that the carrion crow range was split into two parts due to the presence of significantly diverged ancestral lineage localized in the southeastern part of the range. The carrion crow populations, inhabiting a territory ranging from France to northern Sakhalin, along with interspersed hooded crow populations and hybrid Siberian populations, shared a common haplotype. The border between two carrion crow lineages revealed is located in central Sakhalin. The subdivision of two weakly differentiated lineages within the jungle crown range, also observed within this territory, coincided with the subspecies division of this species. The estimated genetic distances indicate the isolation of the subgenus Coloeus. These data also suggest the convergent similarity between the chough Pyrrhocorax pyrrhocorax and the Corvus genus, as well as the conspecificity of Corvus corone corone and C. c. cornix.     

The fruit and tribal affinity of genus cionomene (Menispermaceae)

Fruits of Cionomene Krukoff, a monotypic genus known hitherto only from staminate plants, have the vermiform embryo embedded in laminate endosperm that characterizes tribe Anomospermeae. The genus is related, not to Curarea Barneby & Krukoff, as surmised by the describer, but to Anomospermum Miers and Caryomene Barneby & Krukoff.     

Genetic diversity and phylogenetic relationships of the genus Lycopersicon (Tourn.) Mill. as revealed by inter-simple sequence repeat (ISSR) analysis

Inter-simple sequence repeat (ISSR) analysis was for the first time used to study the genetic diversity and phylogenetic relationships in 54 wild accessions and cultivars of the genus Lycopersicon. Analysis involved 14 ISSR primers homologous to microsatellite repeats and containing additional selective anchor nucleotides. In total, 318 ISSR fragments were amplified for the wild and cultivated tomato genomes. The interspecific polymorphism revealed with the ISSR primers was 95.6%. Species-specific ISSR fragments were detected for each tomato species. The highest number (more than 20) of species-specific fragments were obtained for L. esculentum sensu lato, although the intraspecific variation of ISSR patterns was low. UPGMA cluster analysis was used to construct a dendrogram and to estimate the genetic distances between the species of the genus Lycopersicon; between populations of L. peruvianum, L. pimpinellifolium, and L. esculentum; and between tomato cultivars. The ISSR-based phylogeny was generally consistent with Lycopersicon taxonomy based on morphological and molecular evidence, suggesting the applicability of ISSR analysis for genotyping and phylogenetic studies in tomato.     

srRNA evolution and phylogenetic relationships of the genus Naegleria (Protista: Rhizopoda)

A rapid RNA sequencing technique was used to partially sequence the small-subunit ribosomal RNA (srRNA) of four species of the amoeboid genus Naegleria. The extent of nucleotide sequence divergence between the two most divergent species was roughly similar to that found between mammals and frogs. However, the pattern of variation among the Naegleria species was quite different from that found for those species of tetrapods characterized to date. A phylogenetic analysis of the consensus Naegleria sequence showed that Naegleria was not monophyletic with either Acanthamoeba castellanii or Dictyostelium discoideum, two other amoebas for which sequences were available. It was shown that the semiconserved regions of the srRNA molecule evolve in a clocklike fashion and that the clock is time dependent rather than generation dependent.     

Analysis of fractalkine receptor CX(3)CR1 function by targeted deletion and green fluorescent protein reporter gene insertion

The seven-transmembrane receptor CX(3)CR1 is a specific receptor for the novel CX(3)C chemokine fractalkine (FKN) (neurotactin). In vitro data suggest that membrane anchoring of FKN, and the existence of a shed, soluble FKN isoform allow for both adhesive and chemoattractive properties. Expression on activated endothelium and neurons defines FKN as a potential target for therapeutic intervention in inflammatory conditions, particularly central nervous system diseases. To investigate the physiological function of CX(3)CR1-FKN interactions, we generated a mouse strain in which the CX(3)CR1 gene was replaced by a green fluorescent protein (GFP) reporter gene. In addition to the creation of a mutant CX(3)CR1 locus, this approach enabled us to assign murine CX(3)CR1 expression to monocytes, subsets of NK and dendritic cells, and the brain microglia. Analysis of CX(3)CR1-deficient mice indicates that CX(3)CR1 is the only murine FKN receptor. Yet, defying anticipated FKN functions, absence of CX(3)CR1 interferes neither with monocyte extravasation in a peritonitis model nor with DC migration and differentiation in response to microbial antigens or contact sensitizers. Furthermore, a prominent response of CX(3)CR1-deficient microglia to peripheral nerve injury indicates unimpaired neuronal-glial cross talk in the absence of CX(3)CR1.     

Re-visiting phylogenetic and taxonomic relationships in the genus saga (insecta: orthoptera)

Twelve of the 13 bushcricket species of the Saga genus are bisexuals and diploids, except the parthenogenetic and tetraploid bush cricket, Saga pedo. Despite a continuous research effort stretching through the 1900s, the taxonomic relationships of the Saga species are still disputed. In this study, our primary aim was to reveal natural relationships of the European Saga species and three of their Asian relatives, with special attention to the problematic taxonomy of two subspecies: S. campbelli campbelli and S. c. gracilis. Following a phylogenetic analysis of eight species, a comprehensive study was carried out on the above three taxa by using acoustic and morphometric approaches in parallel. Our phylogenetic data showed that European Saga species evolved from a monophyletic lineage. The geographical transitional species S. cappadocica was positioned between European and Asian lineages supporting the idea that the European Saga lineage originated phylogeographically from the Asian clade. The above results showed better agreement with the morphological data than with earlier ones based either on karyology or acoustic information only. After reviewing our data, we concluded that Saga pedo has most likely evolved from S. c. gracilis and not from S. rammei or S. ephippigera, as proposed by earlier studies. S. c. gracilis shares the same ITS2 haplotype with S. pedo, indicating that the latter could have evolved from populations of the former, probably through whole genome duplication. Based on acoustic and morphometric differences, we propose to elevate the two subspecies, S. campbelli campbelli and S. c. gracilis, to species level status, as Saga gracilis Kis 1962, and Saga campbelli Uvarov 1921. The present work sets the stage for future genetic and experimental investigations of Saginae and highlights the need for additional comprehensive analysis involving more Asian Saga species.     

Multiple origins of XY female mice (genus Akodon): phylogenetic and chromosomal evidence

Despite the diversity in sex determination across organisms, theory predicts that the evolution of XY females is rare in mammals due to fitness consequences associated with infertility or the loss of YY zygotes. We investigated this hypothesis from a phylogenetic perspective by examining the inter- and intraspecific distribution of Y chromosomes in males and females (XY females) in South American field mice (Akodon). We found that XY females occurred at appreciable frequencies (10-66%) in at least eight Akodon species, raising the possibility that this system of sex determination has arisen multiple times independently. To determine the number of origins of XY females in Akodon, we constructed a molecular phylogeny of 16 species of Akodon based on mitochondrial DNA control region sequences. Both parsimony and maximum-likelihood reconstruction of ancestral states suggest that multiple steps (gains or losses of XY females) best explain the evolution of XY females, but do not clearly differentiate between single and multiple origins. We then directly compared functional and non-functional Y chromosomes in six species by Southern blot analysis. We found that male and female Y chromosome restriction fragment length polymorphism patterns were identical within species, but always differed between species, providing evidence that XY females arose at least six times within the Akodon lineage. To our knowledge, this pattern in Akodon is the first documentation of a novel sex-determining system arising multiple times within a tight clade of mammals. In addition, this system provides a clear test of the accuracy of phylogenetic methods to reconstruct ancestral states.     

Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus Desulfonema)

Microscopy of organic-rich, sulfidic sediment samples of marine and freshwater origin revealed filamentous, multicellular microorganisms with gliding motility. Many of these neither contained sulfur droplets such as the Beggiatoa species nor exhibited the autofluorescence of the chlorophyll-containing cyanobacteria. A frequently observed morphological type of filamentous microorganism was enriched under anoxic conditions in the dark with isobutyrate plus sulfate. Two strains of filamentous, gliding sulfate-reducing bacteria, Tokyo 01 and Jade 02, were isolated in pure cultures. Both isolates oxidized acetate and other aliphatic acids. Enzyme assays indicated that the terminal oxidation occurs via the anaerobic C₁ pathway (carbon monoxide dehydrogenase pathway). The 16S rRNA genes of the new isolates and of the two formerly described filamentous species of sulfate-reducing bacteria, Desulfonema limicola and Desulfonema magnum, were analyzed. All four strains were closely related to each other and affiliated with the δ-subclass of Proteobacteria. Another close relative was the unicellular Desulfococcus multivorans. Based on phylogenetic relationships and physiological properties, Strains Tokyo 01 and Jade 02 are assigned to a new species, Desulfonema ishimotoi. A new, fluorescently labeled oligonucleotide probe targeted against 16S rRNA was designed so that that it hybridized specifically with whole cells of Desulfonema species. Filamentous bacteria that hybridized with the same probe were detected in sediment samples and in association with the filamentous sulfur-oxidizing bacterium Thioploca in its natural habitat. We conclude that Desulfonema species constitute an ecologically significant fraction of the sulfate-reducing bacteria in organic-rich sediments and microbial mats. Received: 30 December 1998 / Accepted: 19 July 1999     

L1 (LINE-1) retrotransposon evolution and amplification in recent human history

L1 (LINE-1) elements constitute a large family of mammalian retrotransposons that have been replicating and evolving in mammals for more than 100 Myr and now compose 20% or more of the DNA of some mammals. Here, we investigated the evolutionary dynamics of the active human Ta L1 family and found that it arose approximately 4 MYA and subsequently differentiated into two major subfamilies, Ta-0 and Ta-1, each of which contain additional subsets. Ta-1, which has not heretofore been described, is younger than Ta-0 and now accounts for at least 50% of the Ta family. Although Ta-0 contains some active elements, the Ta-1 subfamily has replaced it as the replicatively dominant subfamily in humans; 69% of the loci that contain Ta-1 inserts are polymorphic for the presence or absence of the insert in human populations, as compared with 29% of the loci that contain Ta-0 inserts. This value is 90% for loci that contain Ta-1d inserts, which are the youngest subset of Ta-1 and now account for about two thirds of the Ta-1 subfamily. The successive emergence and amplification of distinct Ta L1 subfamilies shows that L1 evolution has been as active in recent human history as it has been found to be for rodent L1 families. In addition, Ta-1 elements have been accumulating in humans at about the same rate per generation as recently evolved active rodent L1 subfamilies.