Pond canopy cover: a resource gradient for anuran larvae

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72395/1/j.1365-2427.2005.01497.x.pd

Large and Almost Maximal Neutrino Mixing within the Type II See-Saw Mechanism

Within the type II see-saw mechanism the light neutrino mass matrix is given by a sum of a direct (or triplet) mass term and the conventional (type I) see-saw term. Both versions of the see-saw mechanism explain naturally small neutrino masses, but the type II scenario offers interesting additional possibilities to explain large or almost maximal or vanishing mixings which are discussed in this paper. We first introduce ``type II enhancement'' of neutrino mixing, where moderate cancellations between the two terms can lead to large neutrino mixing even if all individual mass matrices and terms generate small mixing. However, nearly maximal or vanishing mixings are not naturally explained in this way, unless there is a certain initial structure (symmetry) which enforces certain elements of the matrices to be identical or related in a special way. We therefore assume that the leading structure of the neutrino mass matrix is the triplet term and corresponds to zero U_{e3} and maximal theta_{23}. Small but necessary corrections are generated by the conventional see-saw term. Then we assume that one of the two terms corresponds to an extreme mixing scenario, such as bimaximal or tri-bimaximal mixing. Deviations from this scheme are introduced by the second term. One can mimic Quark-Lepton Complementarity in this way. Finally, we note that the neutrino mass matrix for tri-bimaximal mixing can be -- depending on the mass hierarchy -- written as a sum of two terms with simple structure. Their origin could be the two terms of type II see-saw.Comment: 25 pages. Comments and references added, to appear in JHE

Transcript- and annotation-guided genome assembly of the European starling

First published: 28 June 2022The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long- read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short- read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked- reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full- length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 puta-tive nuclear chromosome scaffolds. Species-specific transcript mapping and gene an-notation revealed good gene- level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq tran-script data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.Katarina C. Stuart, Richard J. Edwards, Yuanyuan Cheng, Wesley C. Warren, David W. Burt, William B. Sherwin, Natalie R. Hofmeister, Scott J. Werner, Gregory F. Ball, Melissa Bateson, Matthew C. Brandley, Katherine L. Buchanan, Phillip Cassey, David F. Clayton, Tim De Meyer, Simone L. Meddle, Lee A. Rollin

Data descriptor: a global multiproxy database for temperature reconstructions of the Common Era

Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850-2014. Global temperature composites show a remarkable degree of coherence between high-and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python. (TABLE) Since the pioneering work of D'Arrigo and Jacoby1-3, as well as Mann et al. 4,5, temperature reconstructions of the Common Era have become a key component of climate assessments6-9. Such reconstructions depend strongly on the composition of the underlying network of climate proxies10, and it is therefore critical for the climate community to have access to a community-vetted, quality-controlled database of temperature-sensitive records stored in a self-describing format. The Past Global Changes (PAGES) 2k consortium, a self-organized, international group of experts, recently assembled such a database, and used it to reconstruct surface temperature over continental-scale regions11 (hereafter, ` PAGES2k-2013'). This data descriptor presents version 2.0.0 of the PAGES2k proxy temperature database (Data Citation 1). It augments the PAGES2k-2013 collection of terrestrial records with marine records assembled by the Ocean2k working group at centennial12 and annual13 time scales. In addition to these previously published data compilations, this version includes substantially more records, extensive new metadata, and validation. Furthermore, the selection criteria for records included in this version are applied more uniformly and transparently across regions, resulting in a more cohesive data product. This data descriptor describes the contents of the database, the criteria for inclusion, and quantifies the relation of each record with instrumental temperature. In addition, the paleotemperature time series are summarized as composites to highlight the most salient decadal-to centennial-scale behaviour of the dataset and check mutual consistency between paleoclimate archives. We provide extensive Matlab code to probe the database-processing, filtering and aggregating it in various ways to investigate temperature variability over the Common Era. The unique approach to data stewardship and code-sharing employed here is designed to enable an unprecedented scale of investigation of the temperature history of the Common Era, by the scientific community and citizen-scientists alike

Systematics of the Neotropical Genus Leptodactylus Fitzinger, 1826 (Anura: Leptodactylidae): Phylogeny, the Relevance of Non-molecular Evidence, and Species Accounts

A phylogeny of the species-rich clade of the Neotropical frog genus Leptodactylus sensu stricto is presented on the basis of a total evidence analysis of molecular (mitochondrial and nuclear markers) and non-molecular (adult and larval morphological and behavioral characters) sampled from > 80% of the 75 currently recognized species. Our results support the monophyly of Leptodactylus sensu stricto, with Hydrolaetare placed as its sister group. The reciprocal monophyly of Hydrolaetare and Leptodactylus sensu stricto does not require that we consider Hydrolaetare as either a subgenus or synonym of Leptodactylus sensu lato. We recognize Leptodactylus sensu stricto, Hydrolaetare, Adenomera, and Lithodytes as valid monophyletic genera. Our results generally support the traditionally recognized Leptodactylus species groups, with exceptions involving only a few species that are easily accommodated without proposing new groups or significantly altering contents. The four groups form a pectinate tree, with the Leptodactylus fuscus group diverging first, followed by the L. pentadactylus group, which is sister to the L. latrans and L. melanonotus groups. To evaluate the impact of non-molecular evidence on our results, we compared our total evidence results with results obtained from analyses using only molecular data. Although non-molecular evidence comprised only 3.5% of the total evidence matrix, it had a strong impact on our total evidence results. Only one species group was monophyletic in the molecular-only analysis, and support differed in 86% of the 54 Leptodactylus clades that are shared by the results of the two analyses. Even though no non-molecular evidence was included for Hydrolaetare, exclusion of that data partition resulted in that genus being nested within Leptodactylus, demonstrating that the inclusion of a small amount of non-molecular evidence for a subset of species can alter not only the placement of those species, but also species that were not scored for those data. The evolution of several natural history and reproductive traits is considered in the light of our phylogenic framework. Invasion of rocky outcrops, larval oophagy, and use of underground reproductive chambers are restricted to species of the Leptodactylus fuscus and L. pentadactylus groups. In contrast, larval schooling, larval attendance, and more complex parental care are restricted to the L. latrans and L. melanonotus groups. Construction of foam nests is plesiomorphic in Leptodactylus but their placement varies extensively (e.g., underground chambers, surface of waterbodies, natural or excavated basins). Information on species synonymy, etymology, adult and larval morphology, advertisement call, and geographic distribution is summarized in species accounts for the 30 species of the Leptodactylus fuscus group, 17 species of the L. pentadactylus group, eight species of the L. latrans group, and 17 species of the L. melanonotus group, as well as the three species that are currently unassigned to any species group.Se presenta una filogenia del género Leptodactylus, un ciado neotropical rico en especies, basada en análises combinados de datos moleculares (marcadores nuclear y mitocondriales) y no moleculares (caracteres de la morfología de adultos y larvas así como de comportamiento) se muestrearon > 80% de las 75 especies reconocidas. Los resultados apoyan la monofília de Leptodactylus sensu stricto, con Hydrolaetare como su grupo hermano. La monofília recíproca de Hydrolaetare y Leptodactylus no requiere considerar a Hydrolaetare como un subgénero o sinónimo de Leptodactylus sensu lato. Se reconocen Leptodactylus sensu stricto, Hydrolaetare, Adenomera y Lithodytes como géneros monofiléticos válidos. Los resultados en general resuelven los grupos tradicionalmente reconocidos de Leptodactylus, con excepciones de algunas especies que son reasignadas sin la necesidad de proponer nuevos grupos o alterar significativamente el contenido de los grupos tradicionales. Los cuatro grupos de especies forman una topología pectinada donde el grupo de L. fuscus tiene una posición basal, seguido por el grupo de L. pentadactylus que es el grupo hermano al clado formado por los grupo de L. latrans y L. melanonotus. Se estimó el impacto de los datos no moleculares en los resultados, comparándose los resultados de evidencia total con los de los análises de datos moleculares solamente. Los datos no moleculares representan un 3.5% de la matriz de evidencia total, pero estos datos tuvieron un impacto significativo en los resultados del análisis de evidencia total. En el análisis estrictamente molecular solamente un grupo de especies resultó monofilético, y el apoyo difirió en 86% de los 54 ciados de Leptodactylus compartidos entre los dos análises. A pesar que datos no moleculares no fueron incluidos para Hydrolaetare, la exclusión de evidencia no molecular resultó en el género estar dentro de Leptodactylus, demostrando que la inclusión de evidencia no molecular pequeña para un subgrupo de especies altera no solamente la posición topológica de esas especies, sino tambien de las especies para las cuales dichos datos no fueron codificados. La evolución de patrones de historia natural y reprodución se evalúan en el contexto filogenético. La invasión de afloramientos rocosos y la construción de cámaras de reprodución subterraneas está limitada a los grupos de Leptodactylus fuscus y L. pentadactylus, mientras que la oofagia larval está restringida al grupo de L. pentadactylus. Por otro lado, los cárdumenes larvales, la proteción del cárdumen, y otros comportamientos parentales complejos carecterizan al clado formado por los grupos de especies de L. latrans y L. melanonotus. Los resúmenes de especies incluyen información de sinonimias, etimología, morfología de adultos y larvas, cantos, y distribución geográfica para las 30 especies del grupo de Leptodactylus fuscus, 17 especies del grupo L. pentadactylus, ocho especies del grupo de L. latrans, 17 especies del grupo de L. melanonotus, así como para las tres especies que actualmente no se encuentran asociadas a ninguno de los grupos de especies.Taran Grant was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico Proc. 307001/2011-3 and Fundação de Amparo à Pesquisa do Estado de São Paulo Proc. 2012/10000-5

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Ground motion: frequency of occurrence versus amplitude of disturbing transient events

Successful collider operation requires that ground motion not exceed certain tolerances. In this note it is pointed out that on occasion these tolerances are exceeded. The frequency of such events and their amplitudes, measured as a function of time of day, have been measured. An examination of the data leads one to conclude that most events are of cultural (i.e., man-made) origin. 2 references, 20 figures