Geographical and climatic limits of needle types of one- and two-needled pinyon pines

Aim The geographical extent and climatic tolerances of one- and two-needled pinyon pines (Pinus subsect. Cembroides) are the focus of questions in taxonomy, palaeoclimatology and modelling of future distributions. The identification of these pines, traditionally classified by one- versus two-needled fascicles, is complicated by populations with both one- and two-needled fascicles on the same tree, and the description of two more recently described one-needled varieties: the fallax-type and californiarum-type. Because previous studies have suggested correlations between needle anatomy and climate, including anatomical plasticity reflecting annual precipitation, we approached this study at the level of the anatomy of individual pine needles rather than species. Location Western North America. Methods We synthesized available and new data from field and herbarium collections of needles to compile maps of their current distributions across western North America. Annual frequencies of needle types were compared with local precipitation histories for some stands. Historical North American climates were modeled on a c. 1-km grid using monthly temperature and precipitation values. A geospatial model (ClimLim), which analyses the effect of climate modulated physiological and ecosystem processes, was used to rank the importance of seasonal climate variables in limiting the distributions of anatomical needle types. Results The pinyon needles were classified into four distinct types based upon the number of needles per fascicle, needle thickness and the number of stomatal rows and resin canals. The individual needles fit well into four categories of needle types, whereas some trees exhibit a mixture of two needle types. Trees from central Arizona containing a mixture of Pinus edulis and fallax-type needles increased their percentage of fallax-type needles following dry years. All four needle types occupy broader geographical regions with distinctive precipitation regimes. Pinus monophylla and californiarum-type needles occur in regions with high winter precipitation. Pinus edulis and fallax-type needles are found in regions with high monsoon precipitation. Areas supporting californiarum-type and fallax-type needle distributions are additionally characterized by a more extreme May–June drought. Main conclusions These pinyon needle types seem to reflect the amount and seasonality of precipitation. The single needle fascicle characterizing the fallax type may be an adaptation to early summer or periodic drought, while the single needle of Pinus monophylla may be an adaptation to summer–autumn drought. Although the needles fit into four distinct categories, the parent trees are sometimes less easily classified, especially near their ancestral Pleistocene ranges in the Mojave and northern Sonoran deserts. The abundance of trees with both one- and two-needled fascicles in the zones between P. monophylla, P. edulis and fallax-type populations suggest that needle fascicle number is an unreliable characteristic for species classification. Disregarding needle fascicle number, the fallax-type needles are nearly identical to P. edulis, supporting Little’s (1968) initial classification of these trees as P. edulis var. fallax, while the californiarum-type needles have a distinctive morphology supporting Bailey’s (1987) classification of this tree as Pinus californiarum

Low-power multi-chip module and board-level links for data transfer

Advanced device technologies such as Vertical Cavity Surface-Emitting Lasers (VCSELs) and diffractive micro lenses can be obtained with novel packaging techniques to allow low-power interconnection of parallel optical signals. These interconnections can be realized directly on circuit boards, in a multi-chip module format, or in packages that emulate electrical connectors. For applications such as stacking of Multi-Chip Module (MCM) layers, the links may be realized in bi-directional form using integrated diffractive microlenses. In the stacked MCM design, consumed electrical power is minimized by use of a relatively high laser output from high efficiency VCSELs, and a receiver design that is optimized for low power, at the expense of dynamic range. Within certain constraints, the design may be extended to other forms such as board-level interconnects

Using GIS-linked Bayesian Belief Networks as a tool for modelling urban biodiversity

The ability to predict spatial variation in biodiversity is a long-standing but elusive objective of landscape ecology. It depends on a detailed understanding of relationships between landscape and patch structure and taxonomic richness, and accurate spatial modelling. Complex heterogeneous environments such as cities pose particular challenges, as well as heightened relevance, given the increasing rate of urbanisation globally. Here we use a GIS-linked Bayesian Belief Network approach to test whether landscape and patch structural characteristics (including vegetation height, green-space patch size and their connectivity) drive measured taxonomic richness of numerous invertebrate, plant, and avian groups. We find that modelled richness is typically higher in larger and better-connected green-spaces with taller vegetation, indicative of more complex vegetation structure and consistent with the principle of ‘bigger, better, and more joined up’. Assessing the relative importance of these variables indicates that vegetation height is the most influential in determining richness for a majority of taxa. There is variation, however, between taxonomic groups in the relationships between richness and landscape structural characteristics, and the sensitivity of these relationships to particular predictors. Consequently, despite some broad commonalities, there will be trade-offs between different taxonomic groups when designing urban landscapes to maximise biodiversity. This research demonstrates the feasibility of using a GIS-coupled Bayesian Belief Network approach to model biodiversity at fine spatial scales in complex landscapes where current data and appropriate modelling approaches are lacking, and our findings have important implications for ecologists, conservationists and planners

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

Consensus guidelines for the definition, detection and interpretation of immunogenic cell death.

Cells succumbing to stress via regulated cell death (RCD) can initiate an adaptive immune response associated with immunological memory, provided they display sufficient antigenicity and adjuvanticity. Moreover, multiple intracellular and microenvironmental features determine the propensity of RCD to drive adaptive immunity. Here, we provide an updated operational definition of immunogenic cell death (ICD), discuss the key factors that dictate the ability of dying cells to drive an adaptive immune response, summarize experimental assays that are currently available for the assessment of ICD in vitro and in vivo, and formulate guidelines for their interpretation

The Magnitude of Global Marine Species Diversity

Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century

Solar parameters for modeling interplanetary background

The goal of the Fully Online Datacenter of Ultraviolet Emissions (FONDUE) Working Team of the International Space Science Institute in Bern, Switzerland, was to establish a common calibration of various UV and EUV heliospheric observations, both spectroscopic and photometric. Realization of this goal required an up-to-date model of spatial distribution of neutral interstellar hydrogen in the heliosphere, and to that end, a credible model of the radiation pressure and ionization processes was needed. This chapter describes the solar factors shaping the distribution of neutral interstellar H in the heliosphere. Presented are the solar Lyman-alpha flux and the solar Lyman-alpha resonant radiation pressure force acting on neutral H atoms in the heliosphere, solar EUV radiation and the photoionization of heliospheric hydrogen, and their evolution in time and the still hypothetical variation with heliolatitude. Further, solar wind and its evolution with solar activity is presented in the context of the charge exchange ionization of heliospheric hydrogen, and in the context of dynamic pressure variations. Also the electron ionization and its variation with time, heliolatitude, and solar distance is presented. After a review of all of those topics, we present an interim model of solar wind and the other solar factors based on up-to-date in situ and remote sensing observations of solar wind. Results of this effort will further be utilised to improve on the model of solar wind evolution, which will be an invaluable asset in all heliospheric measurements, including, among others, the observations of Energetic Neutral Atoms by the Interstellar Boundary Explorer (IBEX).Comment: Chapter 2 in the planned "Cross-Calibration of Past and Present Far UV Spectra of Solar System Objects and the Heliosphere", ISSI Scientific Report No 12, ed. R.M. Bonnet, E. Quemerais, M. Snow, Springe

The Theory of Brown Dwarfs and Extrasolar Giant Planets

Straddling the traditional realms of the planets and the stars, objects below the edge of the main sequence have such unique properties, and are being discovered in such quantities, that one can rightly claim that a new field at the interface of planetary science and and astronomy is being born. In this review, we explore the essential elements of the theory of brown dwarfs and giant planets, as well as of the new spectroscopic classes L and T. To this end, we describe their evolution, spectra, atmospheric compositions, chemistry, physics, and nuclear phases and explain the basic systematics of substellar-mass objects across three orders of magnitude in both mass and age and a factor of 30 in effective temperature. Moreover, we discuss the distinctive features of those extrasolar giant planets that are irradiated by a central primary, in particular their reflection spectra, albedos, and transits. Aspects of the latest theory of Jupiter and Saturn are also presented. Throughout, we highlight the effects of condensates, clouds, molecular abundances, and molecular/atomic opacities in brown dwarf and giant planet atmospheres and summarize the resulting spectral diagnostics. Where possible, the theory is put in its current observational context.Comment: 67 pages (including 36 figures), RMP RevTeX LaTeX, accepted for publication in the Reviews of Modern Physics. 30 figures are color. Most of the figures are in GIF format to reduce the overall size. The full version with figures can also be found at: http://jupiter.as.arizona.edu/~burrows/papers/rm

Meta-analysis of type 2 Diabetes in African Americans Consortium

Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15 × 10(-94)<P<5 × 10(-8), odds ratio (OR)  = 1.09 to 1.36). Fine-mapping revealed that 88 of 158 previously identified T2D or glucose homeostasis loci demonstrated nominal to highly significant association (2.2 × 10(-23) < locus-wide P<0.05). These novel and previously identified loci yielded a sibling relative risk of 1.19, explaining 17.5% of the phenotypic variance of T2D on the liability scale in African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies.Peer reviewe