Phylogeny of the nematode genus Pristionchus and implications for biodiversity, biogeography and the evolution of hermaphroditism

<p>Abstract</p> <p>Background</p> <p>The nematode <it>Pristionchus pacificus </it>has originally been developed as a satellite organism for comparison to <it>Caenorhabditis elegans</it>. A 10X coverage of the whole genome of <it>P. pacificus </it>is available, making <it>P. pacificus </it>the first non-<it>Caenorhabditis </it>nematode with a fully sequenced genome. The macroevolutionary comparison between <it>P. pacificus </it>and <it>C. elegans </it>has been complemented by microevolutionary studies of closely related strains and species within the genus <it>Pristionchus</it>. In addition, new understanding of the biology of <it>Pristionchus </it>from field studies, demonstrating a close association with various scarab beetles and the Colorado potato beetle, supports consideration of this nematode in studies of ecosystems. In the course of field studies on four continents more than 1,200 isolates were established from 15,000 beetle specimens representing 18 <it>Pristionchus </it>species. Two remarkable features of the <it>Pristionchus </it>– beetle association are the high species specificity of the interaction and the interception of the beetle's sex communication system for host recognition by the nematodes, as suggested by chemotaxis studies. Evolutionary interpretations of differences in developmental, behavioral and ecological patterns require a phylogenetic framework of the genus <it>Pristionchus</it>.</p> <p>Results</p> <p>Here, we provide a robust phylogeny of all 18 available <it>Pristionchus </it>species based on a set of 27 ribosomal protein genes encompassing a total of 10,971 bp. The phylogenetic tree provides evidence for North American and European clades, which are embedded in a deeper clade that includes Asian species. It also indicates putative invasion events. Of the 18 <it>Pristionchus </it>species, 13 are gonochoristic and five are hermaphroditic. The phylogeny indicates that all hermaphroditic species have arisen independently within the genus <it>Pristionchus</it>.</p> <p>Conclusion</p> <p>Combined ribosomal protein cDNA data can provide the basis for reconstruction of a robust phylogenetic framework for microevolutionary and biogeographic analyses. An additional major implication of our studies is the use of <it>Pristionchus </it>for nematode biodiversity assessments. While some species are represented by more than 100 isolates, others were found less than four times. Such patterns were observed on all continents and in all phylogenetic clades indicating that species asymmetry is a widespread phenomenon, which can now be further investigated by molecular tools.</p

Sex, bugs and Haldane's rule: the nematode genus Pristionchus in the United States

BACKGROUND: The nematode Pristionchus pacificus has been developed as a satellite organism in evolutionary developmental biology for comparison to Caenorhabditis elegans. Comparative studies have revealed major differences in the regulation of developmental processes between P. pacificus and C. elegans. To place evolutionary developmental biology and the observed developmental differences between species in a comprehensive evolutionary context, such studies have to be complemented with ecological aspects. Knowledge about the ecology of the organism in question might indicate specific environmental conditions that can result in developmental adaptations and could account for species differences in development. To this end, we have started to investigate the ecology of Pristionchus nematodes. In recent field studies in Western Europe we found six Pristionchus species that are closely associated with scarab beetles and the Colorado potato beetle. This Pristionchus – beetle association provides the unique opportunity to combine research in evolutionary developmental biology with ecology. However, it remains unknown how general these findings from Europe are on a global scale. RESULTS: Here, we describe the Pristionchus species associated with scarab and Colorado potato beetles in the Eastern United States and show striking transatlantic differences and unexpected evolutionary and ecological patterns. Twohundredeighty of 285 (98%) isolates from American scarab beetles belong to five Pristionchus species, all of which are different from the European species. We describe four of them as novel Pristionchus species. The five American Pristionchus species fall into a single phylogenetic clade and have a male-female (gonochoristic) mode of reproduction, whereas the majority of European isolates are hermaphroditic. Crosses between the two most closely related species, P. aerivorus and P. pseudaerivorus n. sp., follow Haldane's rule in that heterogametic F1 males are inviable. We observed P. aerivorus and P. pseudaerivorus n. sp. coexisting on the same scarab beetle and obtained two cases of F1 hybrids from wild beetles. Finally, the Colorado potato beetle is associated with the same nematode, P. uniformis in the United States and Europe. Given the introduction of the Colorado potato beetle to Europe in 1877, our results suggest that P. uniformis was introduced together with its beetle vector. CONCLUSION: Taken together, the Pristionchus – beetle association provides a powerful tool for studying biodiversity, biogeography, speciation and species invasion on a global scale

Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution

<p>Abstract</p> <p>Background</p> <p>Nematodes are putatively the most species-rich animal phylum. They have various life styles and occur in a variety of habitats, ranging from free-living nematodes in aquatic or terrestrial environments to parasites of animals and plants. The rhabditid nematode <it>Caenorhabditis elegans </it>is one of the most important model organisms in modern biology. <it>Pristionchus pacificus </it>of the family of the Diplogastridae has been developed as a satellite model for comparison to <it>C. elegans</it>. The Diplogastridae, a monophyletic clade within the rhabditid nematodes, are frequently associated with beetles. How this beetle-association evolved and whether beetle-nematode coevolution occurred is still elusive. As a prerequisite to answering this question a robust phylogeny of beetle-associated Diplogastridae is needed.</p> <p>Results</p> <p>Sequences for the nuclear small subunit ribosomal RNA and for 12 ribosomal protein encoding nucleotide sequences were collected for 14 diplogastrid taxa yielding a dataset of 5996 bp of concatenated aligned sequences. A molecular phylogeny of beetle-associated diplogastrid nematodes was established by various algorithms. Robust subclades could be demonstrated embedded in a phylogenetic tree topology with short internal branches, indicating rapid ancestral divergences. Comparison of the diplogastrid phylogeny to a comprehensive beetle phylogeny revealed no major congruence and thus no evidence for a long-term coevolution.</p> <p>Conclusion</p> <p>Reconstruction of the phylogenetic history of beetle-associated Diplogastridae yields four distinct subclades, whose deep phylogenetic divergence, as indicated by short internal branch lengths, shows evidence for evolution by successions of ancient rapid radiation events. The stem species of the Diplogastridae existed at the same time period when the major radiations of the beetles occurred. Comparison of nematode and beetle phylogenies provides, however, no evidence for long-term coevolution of diplogastrid nematodes and their beetle hosts. Instead, frequent host switching is observed. The molecular phylogeny of the Diplogastridae provides a framework for further examinations of the evolution of these associations, for the study of interactions within the ecosystems, and for investigations of diplogastrid genome evolution.</p

Inactivation of Eα and Eβ expression in inbred and wild mice by multiple distinct mutations, some of which predate speciation within Mus species

The H-2 MHC of mice encodes two functional class II heterodimeric proteins: AαAβ (A) and EαEβ (E). While failure to express the A protein has not been reported, a significant proportion of of H-2 haplotypes In both Inbred and wild mice do not express E proteins. We and others have previously characterized the molecular basis for defective E expression in haplotypes from Mus domestlcus (b, f, q, s, from inbred strains) and Af. castaneus (w17, wild-derived) species, identifying six distinct defects in the genes for Eα or Eβ. In this report we have extended these studies to other E- haplotypes, Including several from f-haplotype-bearlng M. domesticus mice (w29, w57, w302) and one derived from the Asian species M. bactrianus (w301). Analyses at the protein, RNA and DNA levels were employed to Identify the defects in the genes for Ea and Eb. At least one new defect was identified that prevents Eβ expression in a t-associated H-2 haplotypes (w57), bringing the number of distinct mutations causing the Eβ phenotype to seven. Another t-associated haplotype, w302, was found to share the same Eβ defect with mice of the inbred q haplotype and of the w17 haplotype from Af. castaneus, while its Ea gene contains the deletion carried also by the Inbred b and s haplotypes and by a number of wild haplotypes. The mutations in the Ea and Eb genes of the w301 haplotype from M. bactrianus were found to be Identical to those of the Inbred f haplotype. This indicates that the origin of the mutations in the Eb genes of the q, w17 and w302 haplotypes and in the Ea and Eb genes of the f and w301 haplotypes, predated speciation within Mus, thought to have occurred ∼0.35-1 million years ago. Their maintenance in mouse populations suggests that in certain conditions the failure to express EαEβ proteins may be advantageous and selected fo

Analyzing the actions of the Administration of Novy Vasyugan rural settlement

The paper analyzes the actions of the Administration of Novy Vasyugan rural settlement. Novy Vasyugan is a village in Tomsk oblast and an administrative center of rural settlement. The Administration is a key element of a democratic society. Every citizen deals with an administration. Nowadays it is developing and legislative branch does not work in a perfect way as its financial and economic resources are limited. The paper describes the structure of rural administration: the duties of municipal bodies, its rights. The goals and results of Novy Vasyugan municipal programs are described: socio-economic growth plan, fire safety municipal target program, energy efficiency municipal target program and antiextremism complex municipal program

Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana

Scaffold/matrix attachment regions (S/MARs) are essential for structural organization of the chromatin within the nucleus and serve as anchors of chromatin loop domains. A significant fraction of genes in Arabidopsis thaliana contains intragenic S/MAR elements and a significant correlation of S/MAR presence and overall expression strength has been demonstrated. In this study, we undertook a genome scale analysis of expression level and spatiotemporal expression differences in correlation with the presence or absence of genic S/MAR elements. We demonstrate that genes containing intragenic S/MARs are prone to pronounced spatiotemporal expression regulation. This characteristic is found to be even more pronounced for transcription factor genes. Our observations illustrate the importance of S/MARs in transcriptional regulation and the role of chromatin structural characteristics for gene regulation. Our findings open new perspectives for the understanding of tissue- and organ-specific regulation of gene expression

Source Dimensions in Ultrarelativistic Heavy Ion Collisions

Recent experiments on pion correlations, interpreted as interferometric measurements of the collision zone, are compared with models that distinguish a prehadronic phase and a hadronic phase. The models include prehadronic longitudinal expansion, conversion to hadrons in local kinetic equilibrium, and rescattering of the produced hadrons. We find that the longitudinal and outward radii are surprisingly sensitive to the algorithm used for two-body collisions. The longitudinal radius measured in collisions of 200 GeV/u sulfur nuclei on a heavy target requires the existence of a prehadronic phase which converts to the hadronic phase at densities around 0.8-1.0 GeV/fm$^3$. The transverse radii cannot be reproduced without introducing more complex dynamics into the transverse expansion.Comment: RevTeX 3.0, 28 pages, 6 figures, not included, revised version, major change is an additional discussion of the classical two-body collision algorithm, a (compressed) postscript file of the complete paper including figures can be obtained from Authors or via anonymous ftp at ftp://ftp_int.phys.washington.edu/pub/herrmann/pisource.ps.