The Japanese 'Nominative' Particle: A New Approach

Proceedings of the Twenty-Ninth Annual Meeting of the Berkeley Linguistics Society: General Session and Parasession on Phonetic Sources of Phonological Patterns: Synchronic and Diachronic Explanations (2003

Hybridization between previously isolated ancestors may explain the persistence of exactly two ancient lineages in the genome of the oyster parasite Perkinsus marinus

AbstractTheory predicts that neutral genetic variation accumulates within populations to a level determined by gains through mutation and losses by genetic drift. This balance results in a characteristic distribution of allelic variation with the maximum allelic difference determined by effective population size. Here, we report a striking departure from these expectations in the form of allelic dimorphism, observed at the majority of seven loci examined in Perkinsus marinus, an important oyster parasite that causes Dermo disease. DNA sequences were collected from five loci flanking microsatellite repeats and two loci coding for superoxide dismutase enzymes that may mediate the parasite’s interaction with its host. Based on 474 sequences, sampled across 5000km of the eastern United States coastline, no more than two alleles were observed at each locus (discounting singletons). Depending on the locus, the common allele ranged in overall frequency from 72% to 92%. At each locus the two alleles differed substantially (3.8% sequence difference, on average), and the among-locus variance in divergences was not sufficient to reject a simultaneous origin for all dimorphisms using approximate Bayesian methods. Dimorphic alleles were estimated to have diverged from a common ancestral allele at least 0.9 million years ago. Across these seven loci, only five other alleles were ever observed, always as singletons and differing from the dimorphic alleles by no more than two nucleotides. Free recombination could potentially have shuffled these dimorphisms into as many as 243 multilocus combinations, but the existence of only ten combinations among all samples strongly supports low recombination frequencies and is consistent with the observed absence of intragenic recombination. We consider several demographic and evolutionary hypotheses to explain these patterns. Few can be conclusively rejected with the present data, but we advance a recent hybridization of ancient divergent lineages scenario as the most parsimonious

Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a para- site’s pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases

\u3ci\u3eParelaphostrongylus odocoilei\u3c/i\u3e in Columbia Black-Tailed Deer from Oregon

Documenting the occurrence of Parelaphostrongylus odocoilei has historically relied on the morphological examination of adult worms collected from the skeletal muscle of definitive hosts, including deer. Recent advances in the knowledge of protostrongylid genetic sequences now permit larvae to be identified. Dorsal-spined larvae (DSLs) collected in 2003–2004 from the lung and feces of six Columbian black-tailed deer (Odocoileus hemionus columbianus) from Oregon were characterized genetically. The sequences from unknown DSLs were compared to those from morphologically validated adults and larvae of P. odocoilei at both the second internal transcribed spacer (ITS-2) of ribosomal DNA and the mitochondrial cytochrome oxidase II gene. We provide the first unequivocal identification of P. odocoilei in Columbian black-tailed deer from Oregon. The broader geographic distribution, prevalence, and pathology of P. odocoilei are not known in populations of Oregon deer

Dynamical Packing in the Habitable Zone: The Case of Beta CVn

Uncovering the occurrence rate of terrestrial planets within the habitable zone (HZ) of their host stars has been a particular focus of exoplanetary science in recent years. The statistics of these occurrence rates have largely been derived from transiting planet discoveries, and have uncovered numerous HZ planets in compact systems around M-dwarf host stars. Here we explore the width of the HZ as a function of spectral type, and the dynamical constraints on the number of stable orbits within the HZ for a given star. We show that, although the Hill radius for a given planetary mass increases with larger semimajor axis, the width of the HZ for earlier-type stars allows for more terrestrial planets in the HZ than late-type stars. In general, dynamical constraints allow ~6 HZ Earth-mass planets for stellar masses ≳0.7M⊙, depending on the presence of farther out giant planets. As an example, we consider the case of Beta CVn, a nearby bright solar-type star. We present 20 yr of radial velocities (RV) from the Keck/High Resolution Echelle Spectrometer (HIRES) and Automated Planet Finder (APF) instruments and conduct an injection-recovery analysis of planetary signatures in the data. Our analysis of these RV data rule out planets more massive than Saturn within 10 au of the star. These system properties are used to calculate the potential dynamical packing of terrestrial planets in the HZ and show that such nearby stellar targets could be particularly lucrative for HZ planet detection by direct imaging exoplanet missions

Dynamical Packing in the Habitable Zone: The Case of Beta CVn

Uncovering the occurrence rate of terrestrial planets within the Habitable Zone (HZ) of their host stars has been a particular focus of exoplanetary science in recent years. The statistics of these occurrence rates have largely been derived from transiting planet discoveries, and have uncovered numerous HZ planets in compact systems around M dwarf host stars. Here we explore the width of the HZ as a function of spectral type, and the dynamical constraints on the number of stable orbits within the HZ for a given star. We show that, although the Hill radius for a given planetary mass increases with larger semi-major axis, the width of the HZ for earlier-type stars allows for more terrestrial planets in the HZ than late-type stars. In general, dynamical constraints allow $\sim$6 HZ Earth-mass planets for stellar masses $\gtrsim 0.7 M_\odot$, depending on the presence of farther out giant planets. As an example, we consider the case of Beta CVn, a nearby bright solar-type star. We present 20 years of radial velocities (RV) from the Keck/HIRES and APF instruments and conduct an injection-recovery analysis of planetary signatures in the data. Our analysis of these RV data rule out planets more massive than Saturn within 10~AU of the star. These system properties are used to calculate the potential dynamical packing of terrestrial planets in the HZ and show that such nearby stellar targets could be particularly lucrative for HZ planet detection by direct imaging exoplanet missions.Comment: 10 pages, 6 figures, 2 tables, accepted for publication in the Astronomical Journa

Updated Parameters and a New Transmission Spectrum of HD 97658b

Recent years have seen increasing interest in the characterization of sub-Neptune-sized planets because of their prevalence in the Galaxy, contrasted with their absence in our solar system. HD 97658 is one of the brightest stars hosting a planet of this kind, and we present the transmission spectrum of this planet by combining four Hubble Space Telescope transits, 12 Spitzer/IRAC transits, and eight MOST transits of this system. Our transmission spectrum has a higher signal-to-noise ratio than those from previous works, and the result suggests that the slight increase in transit depth from wavelength 1.1–1.7 μm reported in previous works on the transmission spectrum of this planet is likely systematic. Nonetheless, our atmospheric modeling results are inconclusive, as no model provides an excellent match to our data. Nonetheless, we find that atmospheres with high C/O ratios (C/O ≳ 0.8) and metallicities of ≳100× solar metallicity are favored. We combine the mid-transit times from all of the new Spitzer and MOST observations and obtain an updated orbital period of P = 9.489295 ± 0.000005, with a best-fit transit time center at T₀ = 2456361.80690 ± 0.00038 (BJD). No transit timing variations are found in this system. We also present new measurements of the stellar rotation period (34 ± 2 days) and stellar activity cycle (9.6 yr) of the host star HD 97658. Finally, we calculate and rank the Transmission Spectroscopy Metric of all confirmed planets cooler than 1000 K and with sizes between 1 R⊕ and 4 R⊕. We find that at least a third of small planets cooler than 1000 K can be well characterized using James Webb Space Telescope, and of those, HD 97658b is ranked fifth, meaning that it remains a high-priority target for atmospheric characterization