These sequences are identical to GenBank JBDLLE000000000 (Punto Rojo) and JBDLLD000000000 (Cherry Pie). The sequences are named to comply with the PanSN-spec, i.e., PR:1:chr1 and so on. We use : in place of # to facilitate parsing the GFFs in certain software. The annotation sets include those transferred from cs10 with Liftoff (-liftoff-wg), predicted resistance genes (-nlr), predicted terpene synthases (-tps), LTRs as deduced by EDTA (-repeats), regions of suspicious coverage as called by Flagger (-flagger), and high-error regions as estimated by YAK (-yak-her).Questions are best directed towards the GitHub repository, where one may also find the codebase: https://github.com/COMInterop/PRCP

These are the scripts and files used in the wheat spatial transcriptomic and single-cell sequencing study.This update added scripts and data for smFISH gene imputation, cellular trajectories using Monocle 3, and gene network analysis. We also added the source file for the visualization website for displaying smFISH original and imputed genes.We also corrected the smFISH stage W3.25 to W3.5.

Supplementary data from simulations for the paper "Network Formation and Dynamics among Multi-LLMs".

Supplementary data from simulations for the paper "Network Formation and Dynamics among Multi-LLMs".

Abiotic constraints, such as drought and heat driven by climate change, negatively impact the production of the common bean (Phaseolus vulgaris L.), an essential grain legume worldwide. The ability to tolerate drought and heat stress in common bean can be improved by introducing genetic variation from related species, such as tepary bean (Phaseolus acutifolius A. Gray), which has recently gained attention because of its adaptation to drought and heat stresses and potential use as a genetic resource and alternative crop. To better understand the phenotypic response of tepary bean to drought and heat stress in multiple environments and trials and to select highly adapted tepary beans, we conducted two field experiments. In Experiment 1, we compared the adaptation to drought stress of tepary bean (n = 10), common bean (n = 10), and Lima bean (Phaseolus lunatus L.; n = 9) by assessing the reduction in grain yield under terminal drought compared to well-irrigated conditions in two California locations with arid summer conditions. Of the three species, tepary bean showed the statistically strongest adaptation to terminal drought, followed by Lima bean and common bean. In Experiment 2, we evaluated a set of 22 tepary beans from contrasting origins for drought and heat stresses across multi-environment trials (METs), in California, Nebraska, and Colombia, with common bean as a control. We found a considerable variation in the tepary bean phenotypic response to these MET conditions, as a result of a strong genotype x environment (G x E) interaction. Also, we identified tepary bean accessions adapted to drought, heat, and well-irrigated conditions across multiple climate zones. Understanding the performance of tepary bean across multiple environments and identifying tepary beans with broad and target-specific adaptation will maximize the potential use of the species.

Across much of the semiarid conifer forests of western North America (“dry conifer forests”), the dominant tree species are non-serotinous, lack soil seedbanks, and rarely disperse seeds much farther than 100 m, so tree regeneration in large, high-severity burned patches is expected to be highly seed-limited. Conifer seedlings do, however, sometimes establish at high densities deep within high-severity patches in these forests, implying that seeds can sometimes survive intense wildfire even when all overstory trees die. Does seed survival in the canopies of non-serotinous trees provide an unexpected source of forest resilience? To answer this question, we surveyed tree survival, fire severity, and seedling abundance across two very large wildfires in the first year after fire. Several of the study species had a good seed cone production year at the time of the fires. We stratified many of our plots deep within high-severity patches far from surviving trees, where existing models predict regeneration failure due to a lack of viable seeds. Contrary to such expectations, we found that conifer seedling densities in these areas were generally far greater than needed to replace fire-killed trees and sometimes approached seedling densities observed near surviving trees. Seedling densities in high-severity areas far from surviving trees correlated negatively with local burn intensity (canopy foliage consumption), supporting the local origin of the seeds and highlighting a critical driver of post-fire recovery that is easily missed by traditional surveys conducted > 2 years following fire. Seedling density was also strongly associated with burn date, suggesting that persistence of viable canopy seeds depends on synchrony between wildfire and cone ripening dates. Together, our results demonstrate that under the right conditions, canopy seed survival can lead to dense seedling establishment across large, severely burned areas and may substantially support the resilience of dry conifer forests to the uncharacteristically severe fires that are becoming increasingly prevalent in this system.

El lote de datos incluye la identificación de helmintos a partir de disecciones gastrointestinales de 11 especies de NHP en libertad (N = 190 individuos) donadas por cazadores indígenas de subsistencia en dos áreas, una bien conservada y otra contaminada con petróleo, en la región de Loreto en el noreste de la Amazonía peruana. La información recolectada incluye datos de lo primates e información de los helmintos encontrados en su interior, incluyendo taxonomía del helminto y carga parasitaria (número de helmintos encontrados para cada taxon). Cada registro contiene la ubicación geográfica. Este estudio contribuye a nuestra comprensión de la salud de los primates y la ecología de los parásitos en una región de alta biodiversidad, y proporciona información valiosa para comprender las posibles consecuencias del calentamiento global en la transmisión de infecciones parasitarias.

Climate change-induced alterations to human-wildlife interactions are recognized to pose a fundamental challenge for global conservation initiatives. However, the extent to which specific climatic disturbances influence the dynamics of human-wildlife conflict across different taxonomic groups remains poorly understood. Here, we leverage an extensive dataset of community-derived human-wildlife conflict incidents to examine the influence of drought, represented by the variation in summed precipitation over the prior 12 months, on conflict reporting. We show that prolonged decreases in precipitation are associated with increased overall conflict occurrences across taxa and are significantly associated with increased conflict with carnivore species in particular. A future with increasingly severe and frequent droughts could lead to resource scarcity that not only causes conflict between humans but also between humans and the natural world around them.

Multi-species sensory networks, where different species prioritize different sensory modalities and then use heterospecific information in a likely non-cooperative fashion, may allow animals to improve foraging over large areas for cryptic prey. We test this hypothesis in procellariiform seabirds that forage in mixed flocks, where both prey odors and visual cues provided by other foraging hetero- and con-specifics might improve success rates. Using agent-based models, we explored the impact of social strategies on olfactory foraging for Antarctic krill (Euphausia superba). Our results suggest that social foraging enables species with different sensory adaptations to achieve similar success rates. Additionally, our results indicate that foraging is more successful in mixed-species rather than single-species flocks, where individuals can monitor the activity of other birds that are using different sensory foraging strategies than themselves to find prey. These results suggest that sensory-based foraging networks may be more critical to their survival than previously assumed. Finally, we show that success rates decrease at low population densities. As seabird populations continue to decline, understanding and preserving these social foraging networks may be essential for their conservation and ecological success. Overall, our study provides insights into the critical role of multi-species sensory networks for foraging success, wherein different species have different sensory adaptations for locating prey. While we used empirical anatomical and behavioral data specific to procellariiforms to inform our models, our approach and results may have broader implications for other species as well.

"Thecodont" refers to teeth implanted in sockets within the jaw, a condition traditionally associated with living mammals and crocodylians, which also coincidentally have teeth attached by ligaments to the socket walls (gomphosis). For over a century, the bony periodontium of many other amniotes has been described as a single tissue, "bone of attachment”, causing confusion over dental tissue homology. Conventional definitions of “thecodonty” exclude species with fused teeth (“ankylothecodonts”), implying a fundamental difference between mammals, crocodylians, and most other vertebrates. However, the stereotypically “thecodont” attachment tissues have been discovered in all major amniote clades, showing that gomphosis and ankylosis likely stem from heterochronic changes in the timing and extent of cementum and alveolar bone mineralization. This challenges (1) previous hypotheses regarding the evolution of the amniote periodontium, (2) the “bone of attachment” paradigm, and (3) the significance of “thecodonty”. We suggest a new nomenclatural approach that incorporates recent histological and evolutionary research and divides thecodonty into anatomical categories to clarify their origin and evolution. We propose the terms anisothecodont and isothecodont to denote, respectively, asymmetric and symmetric implantation of teeth in their sockets. Regardless of the geometry of the connection, we propose using ankylosis and gomphosis to denote the mode of tooth attachment.