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116 records · Page 7

Breeding latitude is associated with the timing of nesting and migration around the annual calendar among Purple Martin (Progne subis) populations

Timing is critical for species that migrate seasonally, as timing mismatches can lead to reduced reproductive success and population declines. We investigated the effect of breeding latitude on the migration timing of a long-distance migratory songbird (Purple Martin, Progne subis subis) by using light-level geolocators deployed across breeding sites between 26° and 53° latitude (n = 329). We used nesting data (1st egg dates; n=28,165) to explore latitudinal patterns in the timing of breeding. Using generalized linear mixed models (GLMMs) we found that breeding latitude was highly associated with timing around the calendar, explaining population-level timing across both spring and fall migration. Populations breeding at more northern latitudes migrated later in fall (mean days/degree latitude =2), in spring (mean days/degree latitude =3), and nested later (days/degree latitude = 3) than populations breeding at more southern latitudes. Generalized additive mixed models (GAMMs) revealed significant non-linearity between breeding latitude and spring and fall migration timing, and the timing of nesting. In spring, the most northern breeders (> 40 degrees N) were more synchronous in their timing, departing their nonbreeding sites and arriving earlier at their breeding sites relative to their breeding latitude. These most northern breeders also had similar nest timing and fall migration departure timing. Breeding latitude was also associated with seasonal partitioning of migratory and sedentary periods. The most northern breeders spent 10% more time on fall migration, 2% more at wintering grounds, 1% more on spring migration, and 13% less time at their breeding sites. Our results support the notion that selection for timing at breeding latitudes can have year-round effects on the timing of seasonal events in long-distance migratory songbirds. Future studies should examine whether these timing patterns associated with latitude limit phenotypic responses to climate change.

54 ENVIRONMENTAL SCIENCES↗

Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp.

ABSTRACT The impacts of microsporidia on host individuals are frequently subtle and can be context dependent. A key example of the latter comes from a recently discovered microsporidian symbiont of Daphnia , the net impact of which was found to shift from negative to positive based on environmental context. Given this, we hypothesized low baseline virulence of the microsporidian; here, we investigated the impact of infection on hosts in controlled conditions and the absence of other stressors. We also investigated its phylogenetic position, ecology, and host range. The genetic data indicate that the symbiont is Ordospora pajunii , a newly described microsporidian parasite of Daphnia . We show that O. pajunii infection damages the gut, causing infected epithelial cells to lose microvilli and then rupture. The prevalence of this microsporidian could be high (up to 100% in the lab and 77% of adults in the field). Its overall virulence was low in most cases, but some genotypes suffered reduced survival and/or reproduction. Susceptibility and virulence were strongly host-genotype dependent. We found that North American O. pajunii were able to infect multiple Daphnia species, including the European species Daphnia longispina , as well as Ceriodaphnia spp. Given the low, often undetectable virulence of this microsporidian and potentially far-reaching consequences of infections for the host when interacting with other pathogens or food, this Daphnia–O. pajunii symbiosis emerges as a valuable system for studying the mechanisms of context-dependent shifts between mutualism and parasitism, as well as for understanding how symbionts might alter host interactions with resources. IMPORTANCE The net outcome of symbiosis depends on the costs and benefits to each partner. Those can be context dependent, driving the potential for an interaction to change between parasitism and mutualism. Understanding the baseline fitness impact in an interaction can help us understand those shifts; for an organism that is generally parasitic, it should be easier for it to become a mutualist if its baseline virulence is relatively low. Recently, a microsporidian was found to become beneficial to its Daphnia hosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidium Ordospora pajunii . Despite the parasitic nature of microsporidia, we found O. pajunii to be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establish O. pajunii is a valuable model for investigating shifts along the mutualism-parasitism continuum.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution of a σ–(c-di-GMP)–anti-σ switch

Filamentous actinobacteria of the genus Streptomyces have a complex lifecycle involving the differentiation of reproductive aerial hyphae into spores. We recently showed c-di-GMP controls this transition by arming a unique anti-σ, RsiG, to bind the sporulation-specific σ, WhiG. The Streptomyces venezuelae RsiG–(c-di-GMP) 2 –WhiG structure revealed that a monomeric RsiG binds c-di-GMP via two E(X) 3 S(X) 2 R(X) 3 Q(X) 3 D repeat motifs, one on each helix of an antiparallel coiled-coil. Here we show that RsiG homologs are found scattered throughout the Actinobacteria. Strikingly, RsiGs from unicellular bacteria descending from the most basal branch of the Actinobacteria are small proteins containing only one c-di-GMP binding motif, yet still bind their WhiG partners. Our structure of a Rubrobacter radiotolerans (RsiG) 2 –(c-di-GMP) 2 –WhiG complex revealed that these single-motif RsiGs are able to form an antiparallel coiled-coil through homodimerization, thereby allowing them to bind c-di-GMP similar to the monomeric twin-motif RsiGs. Further data show that in the unicellular actinobacterium R. radiotolerans , the (RsiG) 2 –(c-di-GMP) 2 –WhiG regulatory switch controls type IV pilus expression. Phylogenetic analysis indicates the single-motif RsiGs likely represent the ancestral state and an internal gene-duplication event gave rise to the twin-motif RsiGs inherited elsewhere in the Actinobacteria. Thus, these studies show how the anti-σ RsiG has evolved through an intragenic duplication event from a small protein carrying a single c-di-GMP binding motif, which functions as a homodimer, to a larger protein carrying two c-di-GMP binding motifs, which functions as a monomer. Consistent with this, our structures reveal potential selective advantages of the monomeric twin-motif anti-σ factors.

59 BASIC BIOLOGICAL SCIENCES↗

The effects of environmental conditions on eggshell thickness of two North American secondary cavity-nesting birds

Egg hatchability in birds is a critical component of individual reproductive success and is associated with eggshell integrity. Contaminants, such as DDT, can influence eggshell thickness and are known to cause population declines. Moisture content and temperature can also impact eggshell thickness, but the influence of environmental conditions on the natural variation in eggshell thickness in wild populations is not well understood. Our goal was to investigate the relationship between environmental conditions and eggshell thickness of Western Bluebird (Sialia mexicana) and Ash-throated Flycatcher (Myiarchus cinerascens) eggs from 1997 to 2013 on the Pajarito Plateau in northern New Mexico. We tested whether nesting elevation, temperature, precipitation, and drought conditions influenced eggshell thickness in these two secondary cavity-nesting species, while also looking at eggshell thickness over time. Over the 16 years, nonviable or abandoned eggs were collected, and the analyzed dataset included 330 bluebird eggs and 113 flycatcher eggs. There was a significant increase in eggshell thickness over time for both species. Flycatcher eggshells were correlated with higher temperatures, whereas bluebird eggshells were influenced by an interaction between temperature and drought severity. In drought conditions, bluebird eggshell thickness was positively correlated with temperature, whereas in wet conditions, eggshell thickness was negatively correlated with temperature. Thicker eggshells in drought conditions may be a way of reducing water loss from eggs, which occurs faster at higher temperatures. In the southwestern United States, frequent and severe drought, higher temperatures, and decreases in precipitation are all expected to continue. In conclusion, the structure of eggs will be important to consider regarding how species may or may not adapt to novel conditions or persist in new environments.

59 BASIC BIOLOGICAL SCIENCES↗

AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae

Introduction: Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience. Methods: The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species. Results: The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers. Discussion: This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.

09 BIOMASS FUELS↗

Advancing Enhanced Raman Spectroscopy to Detect and Measure NOW Pheromones (CPRB 2022 proposal)

Insect sex pheromones are chemical compounds that insects release to attract their partners over distances of hundreds of meters or even kilometers, in complete darkness and without any audible signals. Use of synthetic forms of key compounds have in some cases become an essential component of monitoring and/or managing key pests of agricultural crops, including navel orangeworm (Amyelois transitella) (NOW) in California tree nuts. These pheromone-based strategies can include monitoring, mating disruption, mass trapping, attract-and-kill and push-pull. There are currently multiple commercially available mating disruption products available for NOW and recent studies have demonstrated that they can be effectively used to reduce crop damage by this pest. Just how mating disruption works is not fully established and likely varies across products and target species. For instance, the extent to which synthetic pheromones compete with natural pheromone is not well understood, or in the case of monitoring, how efficaciously the insect follows the diffusing plumes, especially across large blocks and at plot borders. Furthermore, there may be specific conditions under which poor or impeded diffusion of synthetic pheromone diminishes the disruption effect, which could result in some males effectively locating females for reproduction. At the same time, many commercially available synthetic lures are also available, and growers have been effectively using them to track population development – although the attractive range of these lures remains unclear. That is, while pheromone lures can attract many moths, the relationship between trap capture and local populations, much less crop damage, remains unclear. Regardless of the emission source (aerosol puffers, meso emitters, lures etc.), we currently lack the ability to fully understand how these synthetic pheromone compounds diffuse away from their point-source of emission – and subsequently how this might affect the efficacy of mating disruption and/or the accuracy of monitoring efforts. Raman spectroscopy (RS) may offer a means to detect synthetic pheromone because of its analytical properties and recent technological advancements. In combination with nanostructured probes, RS has a demonstrated capability to detect volatiles at extremely low concentrations. While other methods for detecting pheromones have proven to be successful, such analytical methods like mass spectrometry (MS) gas chromatography (GC) require sampling in the fields and are not real-time. Other methods such as EAG/ EAD are also invasive (use antennas) but are of course valuable. Opto-electronic, micro and nano sensors just recently enticed interest. We fall in this latter category, proposing the use of optical spectroscopy (Raman) in a fiber aided by nanostructures to provide a chemical fingerprint without transductions and in real-time (i.e. no sampling). To date, we have been able to generate Raman signatures for the main chemicals in synthetic pheromones (a first for science, to the best of our knowledge), observe their trends at different concentrations, and also provide a clear distinction of such signatures in mixed samples via Principal Component Analysis (PCA) – all of which strengthens our conclusions on the ability of RS to detect emissions in more realistic conditions. We also established processes to enhance the detection sensitivity via preconcentration with Solid Phase Micro Extraction (SPME) fibers and Surface Enhanced Raman Spectroscopy (SERS) to increase the overall optical signals. Furthermore, we explored limitations and requirements for detecting from dispensers, lures, or live moths, including Dept. of Energy and CA State regulatory approvals. Finally, we setup some of our first “orchard in a box” experiments to measure pheromone diffusion along with developing appropriate models.

42 ENGINEERING↗

Apomixis in Farmers’ Fields: Overview, Case Studies from Forage Grasses and Considerations for Future Apomictic Crops

Apomixis occurs naturally in several commercially important species from diverse plant families. While in some of these species apomixis is yet to be exploited in breeding schemes aimed at fixing heterosis, genetic progress and cultivar development, in other species apomixis has been integrated at different stages of breeding. Some of the most relevant examples come from the subfamily Panicoideae, the second largest subfamily of the Poaceae, and are the main focus of this review. The subfamily encompasses many tropical and sub-tropical grasses and grains of worldwide economic importance. Apomictic tropical forages are prime examples of how apomixis can be used and exploited in the development of marketable cultivars, which are essential to the meat and milk production industries globally. The main commercial forages used as grass pastures covering millions of hectares in tropical and sub-tropical regions are polyploids exhibiting gametophytic apomixis that belong to the genus Urochloa spp. (brachiariagrasses) and to the species Megathyrsus maximus (guineagrass). Buffel grass (Cenchrus ciliaris) and Paspalum spp. are other important apomictic forages bred and used in these regions. Breeding involves large germplasm collections from the centers of origin of the species, and for most of them, sexually reproducing diploid plants have been found. Chromosomically duplicated plants that maintain sexual reproduction are used in crosses with apomictic genotypes for the development and selection of cultivars to be marketed or used as progenitors in subsequent breeding cycles. The peculiarities of each genus/species breeding programs, the cultivars obtained from these programs, and the impact of use of marker assisted selection in cultivar development are presented. In addition, the test or implementation of new technologies such as high throughput phenotyping, and the use of machine learning methods for trait prediction and genomic selection are positively impacting the selection and speed of development of new polyploid apomictic cultivars. Furthermore, genetic transformation techniques, including genome editing, provide an additional layer for design of tailor-made, customer-oriented cultivars.

Cenchrus↗

Challenges of COVID-19 Case Forecasting in the US, 2020–2021

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub ( https://covid19forecasthub.org ). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1–4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.

59 BASIC BIOLOGICAL SCIENCES↗