Retrotransposons Are the Major Contributors to the Expansion of the \u3ci\u3eDrosophila ananassae\u3c/i\u3e Muller F Element

The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (\u3e18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5′ ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

The 13th Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-IV Survey Mapping Nearby Galaxies at Apache Point Observatory

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) began observations in July 2014. It pursues three core programs: APOGEE-2,MaNGA, and eBOSS. In addition, eBOSS contains two major subprograms: TDSS and SPIDERS. This paper describes the first data release from SDSS-IV, Data Release 13 (DR13), which contains new data, reanalysis of existing data sets and, like all SDSS data releases, is inclusive of previously released data. DR13 makes publicly available 1390 spatially resolved integral field unit observations of nearby galaxies from MaNGA,the first data released from this survey. It includes new observations from eBOSS, completing SEQUELS. In addition to targeting galaxies and quasars, SEQUELS also targeted variability-selected objects from TDSS and X-ray selected objects from SPIDERS. DR13 includes new reductions ofthe SDSS-III BOSS data, improving the spectrophotometric calibration and redshift classification. DR13 releases new reductions of the APOGEE-1data from SDSS-III, with abundances of elements not previously included and improved stellar parameters for dwarf stars and cooler stars. For the SDSS imaging data, DR13 provides new, more robust and precise photometric calibrations. Several value-added catalogs are being released in tandem with DR13, in particular target catalogs relevant for eBOSS, TDSS, and SPIDERS, and an updated red-clump catalog for APOGEE.This paper describes the location and format of the data now publicly available, as well as providing references to the important technical papers that describe the targeting, observing, and data reduction. The SDSS website, http://www.sdss.org, provides links to the data, tutorials and examples of data access, and extensive documentation of the reduction and analysis procedures. DR13 is the first of a scheduled set that will contain new data and analyses from the planned ~6-year operations of SDSS-IV.PostprintPeer reviewe

The fifteenth data release of the Sloan Digital Sky Surveys : first release of MaNGA derived quantities, data visualization tools and stellar library

Twenty years have passed since first light for the Sloan Digital SkySurvey (SDSS). Here, we release data taken by the fourth phase of SDSS(SDSS-IV) across its first three years of operation (July 2014-July2017). This is the third data release for SDSS-IV, and the fifteenth from SDSS (Data Release Fifteen; DR15). New data come from MaNGA - we release 4824 datacubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g. stellar and gas kinematics, emission line, andother maps) from the MaNGA Data Analysis Pipeline (DAP), and a new data visualisation and access tool we call "Marvin". The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials and examples of data use. While SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V(2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.Publisher PDFPeer reviewe

Estimation of the Individual Growth Parameters of the Brown Crab Callinectes Bellicosus (Brachyura, Portunidae) Using a Multi-Model Approach

This study describes the growth parameters of Callinectes bellicosus based on samples from a coastal lagoon in the southern Gulf of California. A multi-model inference (MMI) approach is used for both sexes. The candidate models assessed were the Von Bertalanffy (VBGM), Gompertz, Logistic, and Schnute growth models. The criterion used to select the best models was the Akaike information criterion (AIC). The best models fitted were the Schnute model for males and the VBGM for females. The asymptotic carapace width (CW) in males, averaged according to the MMI principle, was 155.38 mm in males and 125.53 mm in females. This difference resulted from the females’ terminal moult to maturity. In females, no further growth occurs after this moult, whereas males continue to grow. The results of this study show that the use of an MMI approach is important because it can produce an improved description of the growth of crustaceans, such as Callinectes species, that exhibit this particular difference between the sexes.Este estudio describe los parámetros de crecimiento de Callinectes bellicosus basados ​​en muestras de una laguna costera en el sur del Golfo de California. Se utiliza un enfoque de inferencia de múltiples modelos (MMI) para ambos sexos. Los modelos candidatos evaluados fueron los modelos de crecimiento Von Bertalanffy (VBGM), Gompertz, Logistic y Schnute. El criterio utilizado para seleccionar los mejores modelos fue el criterio de información Akaike (AIC). Los modelos más adecuados fueron el modelo Schnute para varones y el VBGM para hembras. El ancho del caparazón asintótico (CW) en los machos, promediado según el principio de MMI, fue de 155,38 mm en los machos y 125,53 mm en las hembras. Esta diferencia resultó de la muda terminal de las hembras hasta su madurez. En las hembras, después de esta muda, no se produce más crecimiento, mientras que los machos continúan creciendo. Los resultados de este estudio muestran que el uso de un enfoque de MMI es importante porque puede producir una descripción mejorada del crecimiento de crustáceos, como las especies de Callinectes, que exhiben esta diferencia particular entre los sexos

Catch—Maximum Sustainable Yield Method Applied to the Crab Fishery (Callinectes spp.) in the Gulf of California

The objective of this study was to determine the maximum sustainable yield (MSY) of the crab fishery in the Gulf of California by applying the catch-MSY method. This fishery occurs in two states—Sonora and Sinaloa, along the mainland coast of the Gulf of California—and involves two species: Callinectes hellicosus and Callinectes arcuatus. The main species supporting the fishery in both states is C. bellicosus, whereas C. arcuatus accounts for 5% of crab catches in Sonora and 20%–30% in Sinaloa. The catch-MSY method uses a set of viable r–k combinations to approximate MSY. The r–k combinations are the carrying capacity k and the maximum rate of population increase r for a given stock in a given ecosystem, which are required in most production models, such as the Schaefer model, to estimate MSY. Prior carrying capacity in this study was set arbitrarily from the maximum catches in a series evaluated to 100 times the maximum catch. This range ensures the real carrying capacity could be determined if catches were at MSY sometime during the period evaluated. Maximum potential could have been realized since 2006 for the Sinaloa stock and since 1996 for the Sonora stock. The evidence for these facts is that the catch per unit of effort decreased, and reductions were observed in the mean size of individuals; these changes occurred in the Sinaloa crab fishery. All methods devoted to management procedures of fisheries stocks entail a number of criticisms, and estimations of carrying capacity and stock biomass are costly; however, because sustainable fisheries are desired and data-poor stocks are common, a simple method like catch-MSY has proved be useful in the management of the crab fishery in the Gulf of California.El objetivo de este estudio fue determinar el rendimiento máximo sostenible (RMS) de la pesquería de centolla en el Golfo de California mediante la aplicación del método de captura-RMS. Esta pesquería se produce en dos estados de Sonora y Sinaloa, a lo largo de la costa continental del Golfo de California, y consiste en dos especies: Callinectes hellicosus y arcuatus Callinectes . Las principales especies que apoyan la pesquería en ambos estados es C. bellicosus , mientras que C. arcuatus representa el 5% de las capturas de cangrejo en Sonora y 20% -30% en Sinaloa. El método de captura-RMS utiliza un conjunto de r-k combinaciones viables para aproximar RMS. Los r-k combinaciones son la capacidad de carga K y la tasa máxima de aumento de la población r para una acción dada en un ecosistema dado, que son necesarios en la mayoría de los modelos de producción, tales como el modelo de Schaefer, para estimar el RMS. Capacidad de carga previa en este estudio se estableció arbitrariamente de las capturas máximas en una serie evaluado a 100 veces la captura máxima. Esta gama garantiza la capacidad de carga real, se pudo determinar si las capturas fueron en RMS en algún momento durante el período evaluado. Máximo potencial podría haberse dado cuenta desde el año 2006 para la población de Sinaloa y desde 1996 para el stock de Sonora. La evidencia de estos hechos es que la captura por unidad de esfuerzo disminuye, y no se observaron reducciones en el tamaño medio de los individuos; estos cambios se produjeron en dicha pesquería Sinaloa. Todos los métodos dedicados a los procedimientos de gestión de las poblaciones de peces conllevan una serie de críticas, y las estimaciones de la capacidad de carga y la biomasa de la población son costosos; sin embargo, porque se desean pesca sostenible y las existencias de escasez de datos son comunes, un método tan simple como ponerse al RMS ha demostrado ser útil en el manejo de la pesquería de cangrejo en el Golfo de California

Modelos múltiples para determinar el crecimiento de organismos juveniles de jaiba azul Callinectes arcuatus en cautiverio

A multi-model approach was used for select the best growth model for juvenile blue crab Callinectes arcuatus under culture conditions. Five variations of Schnute model and the oscillatory model (movb) of Somers were used as candidate models. Despite the oscillatory nature of growth data, the movb was not an adequate support for the data. The best models were case 1 for females, and case 3 for males. Akaike penalizes more severely the movb than other candidate models because it required estimating five parameters instead of four or two parameters for cases 1 and 3. The consequences of selecting a priori the von Bertalanffy model to describe the growth of juvenile C. arcuatus may be an unrealistic estimation of maxim carapace width (ac). However, neither the best fitted models are useful for estimating this parameter because only juveniles were included in the analyses. The best models fitted to data are not useful for estimation of this parameter, because only growth of immature crabs were considered. The best model adjusted to growth data of immature blue crabs are only valid for estimates of growth between sizes from 25 to 80 mm ac.Se utilizó el enfoque multimodelo para seleccionar el que mejor describa el crecimiento de organismos juveniles de la jaiba azul Callinectes arcuatus en cultivo utilizando como candidatos cinco casos del modelo de Schnute y el modelo oscilatorio (movb) de Somers. A pesar de la naturaleza oscilante de los datos de crecimiento en ambos sexos, el movb no tuvo un adecuado soporte en los datos. El mejor modelo en los machos fue el caso 3, mientras que en las hembras fue el caso 1. El índice de Akaike penaliza con mayor severidad el movb porque requiere estimar cinco parámetros, mientras que en los mejores modelos se estimaron cuatro y dos parámetros. Seleccionar a priori el modelo de von Bertalanffy para describir el crecimiento de organismos juveniles de C. arcuatus tendría como consecuencia estimados irreales de ancho de cefalotórax (ac) máximo. Pero tampoco los mejores modelos estimados son útiles para estimar este parámetro porque sólo se incluyen ejemplares juveniles en el análisis. Los resultados acerca del mejor modelo obtenidos en este estudio sólo son aplicables para el intervalo de 25 a 80 mm de ac

Genomics in the Classroom: Unraveling the Dot Chromosome of Drosophila ananassae

Drosophila Genomics is a course that offers a unique opportunity for students to contribute to a real-time research project, through support of the Genomics Education Partnership (GEP). Through instructional tutorials, students use computer programs to identify and assist in the resolution of DNA sequence inconsistencies, a process known as \u27sequence finishing\u27. The current project focuses on finishing the sequence of the unusually large 4th (dot) chromosome of D. ananassae. Once students have completed DNA sequence finishing, each student annotates a large segment of DNA from the D. biarmipes dot chromosome. In the process of annotation, students apply their understanding of gene structure to build models of genes in a specific species, using D. melanogaster as a reference species. Students gain experience accessing internet databases and use of genome analysis tools in identifying genes. Students\u27 finished work is submitted to the GEP for inclusion in future publications