Highly accurate long-read HiFi sequencing data for five complex genomes.

The PacBio HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes.

Climate-associated drivers of plasma cytokines and contaminant concentrations in Beaufort Sea polar bears (Ursus maritimus).

Assessing polar bear (Ursus maritimus) immune function in relation to environmental stressors, including habitat change, nutritional stress, pathogen prevalence, and pollution, has been identified as critical for improved understanding of the species' health. The objectives of this study were two-fold: 1) to assess the role of climate-associated factors (habitat use, body condition) in explaining the plasma concentrations of contaminants in southern Beaufort Sea (SB) polar bears, and 2) to investigate how climate-associated factors, contaminant concentrations, and pathogen sero-prevalence influence the plasma concentrations of immune-signaling proteins called cytokines. A commercially available multiplex canine cytokine panel was validated for the quantification of five pro- and anti-inflammatory cytokines in polar bear plasma: tumor necrosis factor alpha (TNF-α), interleukin 6 (IL-6), IL-8, IL-10, and interferon gamma-induced protein 10 (IP-10).

Rewilding in the face of climate change.

Expansion of the global protected-area network has been proposed as a strategy to address threats from accelerating climate change and species extinction. A key step in increasing the effectiveness of such expansion is understanding how novel threats to biodiversity from climate change alter concepts such as rewilding, which have underpinned many proposals for large interconnected reserves. We reviewed potential challenges that climate change poses to rewilding and found that the conservation value of large protected areas persists under climate change.

Effects of artificial light at night on the foraging behavior of an endangered nocturnal mammal.

Modification of nighttime light levels by artificial illumination (artificial light at night; ALAN) is a rapidly increasing form of human disturbance that affects natural environments worldwide. Light in natural environments influences a variety of physiological and ecological processes directly and indirectly and, as a result, the effects of light pollution on species, communities and ecosystems are emerging as significant. Small prey species may be particularly susceptible to ALAN as it makes them more conspicuous and thus more vulnerable to predation by visually oriented predators.

Human land uses reduce climate connectivity across North America.

Climate connectivity, the ability of a landscape to promote or hinder the movement of organisms in response to a changing climate, is contingent on multiple factors including the distance organisms need to move to track suitable climate over time (i.e. climate velocity) and the resistance they experience along such routes.

Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon.

Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection.

Seed freeze sensitivity and ex situ longevity of 295 species in the native Hawaiian flora.

Premise: Ex situ seed banking is critical for plant conservation globally, especially for threatened floras in tropical ecosystems like Hawai'i. Seed bank managers must maximize longevity, and species managers must plan restoration before seeds lose viability. Previous observations suggested some native Hawaiian seeds lost viability in frozen storage (-18°C).

Biological and Sociopolitical Sources of Uncertainty in Population Viability Analysis for Endangered Species Recovery Planning.

Although population viability analysis (PVA) can be an important tool for strengthening endangered species recovery efforts, the extent to which such analyses remain embedded in the social process of recovery planning is often unrecognized. We analyzed two recovery plans for the Mexican wolf that were developed using similar data and methods but arrived at contrasting conclusions as to appropriate recovery goals or criteria. We found that approximately half of the contrast arose from uncertainty regarding biological data, with the remainder divided between policy-related decisions and mixed biological-policy factors.

Non-native insects dominate daytime pollination in a high-elevation Hawaiian dryland ecosystem.

Premise Of The Study: Over one-third of the native flowering plant species in the Hawaiian Islands are listed as federally threatened or endangered. Lack of sufficient pollination could contribute to reductions in populations, reproduction, and genetic diversity among these species but has been little studied.

Methods: We used systematic observations and manual flower treatments to quantify flower visitation and outcrossing dependency of eight native (including four endangered) plant species in a dryland ecosystem in Hawaii: Argemone glauca, Bidens menziesii, Dubautia linearis, Haplostachys haplostachya, Sida fallax, Silene lanceolata, Stenogyne angustifolia, and Tetramolopium arenarium.

Climatic, topographic, and anthropogenic factors determine connectivity between current and future climate analogs in North America.

As climatic conditions shift in coming decades, persistence of many populations will depend on their ability to colonize habitat newly suitable for their climatic requirements. Opportunities for such range shifts may be limited unless areas that facilitate dispersal under climate change are identified and protected from land uses that impede movement. While many climate adaptation strategies focus on identifying refugia, this study is the first to characterize areas which merit protection for their role in promoting climate connectivity at a continental extent.

Assessing agreement among alternative climate change projections to inform conservation recommendations in the contiguous United States.

Addressing uncertainties in climate vulnerability remains a challenge for conservation planning. We evaluate how confidence in conservation recommendations may change with agreement among alternative climate projections and metrics of climate exposure. We assessed agreement among three multivariate estimates of climate exposure (forward velocity, backward velocity, and climate dissimilarity) using 18 alternative climate projections for the contiguous United States.

Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation.

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution.

Distribution and protection of climatic refugia in North America.

As evidenced by past climatic refugia, locations projected to harbor remnants of present-day climates may serve as critical refugia for current biodiversity in the face of modern climate change. We mapped potential climatic refugia in the future across North America, defined as locations with increasingly rare climatic conditions. We identified these locations by tracking projected changes in the size and distribution of climate analogs over time.

Environmental conditions and herbivore biomass determine coral reef benthic community composition: implications for quantitative baselines.

Our ability to understand natural constraints on coral reef benthic communities requires quantitative assessment of the relative strengths of abiotic and biotic processes across large spatial scales. Here, we combine underwater images, visual censuses and remote sensing data for 1566 sites across 34 islands spanning the central-western Pacific Ocean, to empirically assess the relative roles of abiotic and grazing processes in determining the prevalence of calcifying organisms and fleshy algae on coral reefs. We used regression trees to identify the major predictors of benthic composition and to test whether anthropogenic stress at inhabited islands decouples natural relationships.

Defending the scientific integrity of conservation-policy processes.

Government agencies faced with politically controversial decisions often discount or ignore scientific information, whether from agency staff or nongovernmental scientists. Recent developments in scientific integrity (the ability to perform, use, communicate, and publish science free from censorship or political interference) in Canada, Australia, and the United States demonstrate a similar trajectory. A perceived increase in scientific-integrity abuses provokes concerted pressure by the scientific community, leading to efforts to improve scientific-integrity protections under a new administration.

Not just browsing: an animal that grazes phyllosphere microbes facilitates community heterogeneity.

Although grazers have long been recognized as top-down architects of plant communities, animal roles in determining microbial community composition have seldom been examined, particularly in aboveground systems. To determine the extent to which an animal can shape microbial communities, we conducted a controlled mesocosm study in situ to see if introducing mycophageous tree snails changed phyllosphere fungal community composition relative to matched control mesocosms. Fungal community composition and change was determined by Illumina sequencing of DNA collected from leaf surfaces before snails were introduced, daily for 3 days and weekly for 6 weeks thereafter.

Connecting today's climates to future climate analogs to facilitate movement of species under climate change.

Increasing connectivity is an important strategy for facilitating species range shifts and maintaining biodiversity in the face of climate change. To date, however, few researchers have included future climate projections in efforts to prioritize areas for increasing connectivity. We identified key areas likely to facilitate climate-induced species' movement across western North America.

Scale-dependent complementarity of climatic velocity and environmental diversity for identifying priority areas for conservation under climate change.

As most regions of the earth transition to altered climatic conditions, new methods are needed to identify refugia and other areas whose conservation would facilitate persistence of biodiversity under climate change. We compared several common approaches to conservation planning focused on climate resilience over a broad range of ecological settings across North America and evaluated how commonalities in the priority areas identified by different methods varied with regional context and spatial scale. Our results indicate that priority areas based on different environmental diversity metrics differed substantially from each other and from priorities based on spatiotemporal metrics such as climatic velocity.

Locally Downscaled and Spatially Customizable Climate Data for Historical and Future Periods for North America.

Large volumes of gridded climate data have become available in recent years including interpolated historical data from weather stations and future predictions from general circulation models. These datasets, however, are at various spatial resolutions that need to be converted to scales meaningful for applications such as climate change risk and impact assessments or sample-based ecological research. Extracting climate data for specific locations from large datasets is not a trivial task and typically requires advanced GIS and data management skills.

Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub.

Flavobacterium spp. have been cultivated from diverse aquatic and terrestrial habitats. F.

Biotic and Climatic Velocity Identify Contrasting Areas of Vulnerability to Climate Change.

Metrics that synthesize the complex effects of climate change are essential tools for mapping future threats to biodiversity and predicting which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extirpation. The most commonly used of such metrics is the velocity of climate change, which estimates the speed at which species must migrate over the earth's surface to maintain constant climatic conditions. However, "analog-based" velocities, which represent the actual distance to where analogous climates will be found in the future, may provide contrasting results to the more common form of velocity based on local climate gradients.

Semen decontamination for the elimination of seminal HIV-1.

The risk of human immunodeficiency virus (HIV) transmission to the female partner, or potential offspring of an HIV-1 infected man can be reduced using semen decontamination procedures before assisted reproductive treatment (ART). The objective of this study was to determine the efficiency of decontaminating semen samples (n = 186) from 95 HIV-1 sero-positive patients. Aliquots of neat semen were submitted for viral validation by qualitative and quantitative polymerase chain reaction.

Metagenomic shotgun sequencing of a Bunyavirus in wild-caught Aedes aegypti from Thailand informs the evolutionary and genomic history of the Phleboviruses.

Arthropod-borne viruses significantly impact human health. They span multiple families, all of which include viruses not known to cause disease. Characterizing these representatives could provide insights into the origins of their disease-causing counterparts.