Expanding NEON biodiversity surveys with new instrumentation and machine learning approaches

A core goal of the National Ecological Observatory Network (NEON) is to measure changes in biodiversity across the 30-yr horizon of the network. In contrast to NEON’s extensive use of automated instruments to collect environmental data, NEON’s biodiversity surveys are almost entirely conducted using traditional human-centric field methods. We believe that the combination of instrumentation for remote data collection and machine learning models to process such data represents an important opportunity for NEON to expand the scope, scale, and usability of its biodiversity data collection while potentially reducing long-term costs. In this manuscript, we first review the current status of instrument-based biodiversity surveys within the NEON project and previous research at the intersection of biodiversity, instrumentation, and machine learning at NEON sites. We then survey methods that have been developed at other locations but could potentially be employed at NEON sites in future. Finally, we expand on these ideas in five case studies that we believe suggest particularly fruitful future paths for automated biodiversity measurement at NEON sites: acoustic recorders for sound-producing taxa, camera traps for medium and large mammals, hydroacoustic and remote imagery for aquatic diversity, expanded remote and ground-based measurements for plant biodiversity, and laboratory-based imaging for physical specimens and samples in the NEON biorepository. Through its data science-literate staff and user community, NEON has a unique role to play in supporting the growth of such automated biodiversity survey methods, as well as demonstrating their ability to help answer key ecological questions that cannot be answered at the more limited spatiotemporal scales of human-driven surveys

Detection of the PAX3-FKHR fusion gene in paediatric rhabdomyosarcoma: a reproducible predictor of outcome?

Rhabdomyosarcoma has 2 major histological subtypes, embryonal and alveolar. Alveolar histology is associated with the fusion genes PAX3-FKHR and PAX7-FKHR. Definition of alveolar has been complicated by changes in terminology and subjectivity. It is currently unclear whether adverse clinical behaviour is better predicted by the presence of these fusion genes or by alveolar histology. We have determined the presence of the PAX3/7-FKHR fusion genes in 91 primary rhabdomyosarcoma tumours using a combination of classical cytogenetics, FISH and RT-PCR, with a view to determining the clinical characteristics of tumours with and without the characteristic translocations. There were 37 patients with t(2;13)/PAX3-FKHR, 8 with t(1;13) PAX7-FKHR and 46 with neither translocation. One or other of the characteristic translocations was found in 31/38 (82%) of alveolar cases. Univariate survival analysis revealed the presence of the translocation t(2;13)/PAX3-FKHR to be an adverse prognostic factor. With the difficulties in morphological diagnosis of alveolar rhabdomyosarcoma on increasingly used small needle biopsy specimens, these data suggest that molecular analysis for PAX3-FKHR will be a clinically useful tool in treatment stratification in the future. This hypothesis requires testing in a prospective study. Variant t(1;13)/PAX7-FKHR appears biologically different, occurring in younger patients with more localised disease. © 2001 Cancer Research Campaignhttp://www.bjcancer.co

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building

Mistletoe-Vector-Host Interactions: From Within-Host Processes to Population Genetic Structure

The majority of free-living species serve as hosts to multiple parasite and pathogen species, and parasitism is the most frequent interaction type in many food webs. Additionally, diversification rates increase following evolutionary transitions to parasitism. Yet, many aspects of parasite ecology and evolution remain unclear, including how parasites interact within individual hosts, what processes underlie parasite diversification, and how interactions with vectors influence parasite fitness and population dynamics. Parasitic plants provide convenient but underutilized study systems for investigating each of these questions. Entire infections can be characterized and followed in the field over time, and the interactions with vectors can be studied in the framework of pollination and seed dispersal processes. My dissertation concerns host and vector interactions with a geographically widespread, ecologically important parasitic plant, desert mistletoe (Phoradendron californicum), from within host individuals to among host species. I have employed an integrative approach involving experimental (Appendix A) and observational (Appendix B) field ecology, population genetics (Appendix C), and mathematical modeling (Appendix D). At the within-host scale, I show that the size and sex ratio of the infrapopulation (population of one parasite species infecting a single host) independently influence multiple components of parasite fitness through resource competition, within-host mate limitation, and pollen vector attraction (Appendix A). These results, along with genetic structuring at the level of the host individual (Appendix C), indicate that much of mistletoe mating occurs within an infrapopulation. This within-host mating along with differences in flowering phenology and pollinator community composition between mistletoes on velvet mesquite (Prosopis velutina) and other dominant host species (Appendix B) likely contributes to the maintenance of genetically distinct host-associated races that are consistent across space (Appendix C). The genetic and ecological patterns are consistent with the existence of barriers to gene flow between the host races that are asymmetric and stronger at mating (pollination) than at dispersal and establishment (Appendix C). In addition to genetic differences and divergence in many reproductive traits (Appendix B) by host species, the dynamics of parasitic plants may be further complicated by indirect interactions that result from direct interactions between the pollen and seed vectors. Using a simple mathematical model relevant to desert mistletoe and many other mutualistic systems, I find that the persistence and population dynamical outcomes for plants and their partners critically depend on the strength of antagonism between the partners and the degree of specialization of the partners on the mutualistic system (Appendix D). As a whole, this work emphasizes the ecological and evolutionary complexity of parasite-host-vector interactions and the utility of research on parasitic plants for answering fundamental questions in biology

MistRep_Oecologia_Data.xlsx

Data for different aspects of the study are provided on different sheets: Nectar Sugars, Morphology, Pollen Production, Pollinator Visitation, Pollen Deposition, Fruit Success, Parasite Phenology data. Metadata sheet defines the meaning of column names and data values for across all sheets, except "Parasite phenology data" sheet. "Parasite phenology metadata" sheet provides column explanations for that sheet

Data from: Infrapopulation size and mate availability influence reproductive success of a parasitic plant

1. Aggregated distributions of parasite individuals across host individuals are nearly ubiquitous among parasitic taxa. The size and sex ratio of the population of one parasite species infecting a single host (hereafter “infrapopulation”) can influence parasite fitness through intraspecific competition, mate availability, and the ability to attract vectors for transmission of parasite propagules. Competition for both resources and for pollen and seed vector services may limit reproductive success (pollen receipt, fruit production, and seed dispersal) in large infrapopulations of parasitic plants, while mate limitation or reduced ability to attract vectors may limit this success in small infrapopulations. 2. Using a dioecious parasitic plant, desert mistletoe (Phoradendron californicum), we experimentally removed reproductive tissue from male parasites in whole infrapopulations to test for independent effects of infrapopulation size and within-host mate availability on female fitness. As desert mistletoe requires both pollen and seed vectors for successful reproduction, the species provides the opportunity to test how infrapopulation characteristics affect multiple components of parasite fitness. 3. We found that insect-mediated pollen receipt decreased for parasites on treated hosts, consistent with within-host mate limitation. Additionally, the relationship between mate availability and fruit production per flower ranged from neutral to positive depending on year of the experiment. 4. As expected if competition for host resources limits reproductive success more than mate availability in larger infrapopulations, the greater pollen receipt to females in large infrapopulations did not generally translate into increased mistletoe fruit production. Relationships between mistletoe fruit production per flower and infrapopulation size ranged from negative to neutral. 5. Both pollen receipt and pollinator visitation increased with infrapopulation size, indicating that larger populations can be more attractive to pollen vectors independent of mate availability. However, we found no relationship between infrapopulation size and fruit removal by dispersers and, thus, no evidence that attraction of seed dispersal vectors increases with infrapopulation size. 6. Synthesis: These results highlight the interactive roles of within-host processes (resource competition, mate availability, and vector attraction) in determining the fitness of biotically-transmitted parasite individuals

The place of arbitration

All data from the associated manuscript are provided. Natural_infrapopulations sheet provides observational data on infrapopulations assessed in the field. Pollinator_visitation sheet provides data on observation of pollinator visitation to infrapopulations of different characteristics. Pollen_deposition sheet provides data on pollen receipt to flowers of female parasitic plants on control and treated host plants. Fruit_success_removal provides data on fruit set and fruit removal for female parasitic plants on control and treated host plants. Please see the metadata sheet for definitions of all column names provided in the data sheets

Reproductive ecology of a parasitic plant differs by host species: vector interactions and the maintenance of host races

Parasitic plants often attack multiple host species with unique defenses, physiology, and ecology. Reproductive phenology and vectors of parasitic plant genes (pollinators and dispersers) can contribute to or erode reproductive isolation of populations infecting different host species. We asked whether desert mistletoe, Phoradendron californicum (Santalaceae tribe Visceae syn. Viscaceae), differs ecologically across its dominant leguminous hosts in ways affecting reproductive isolation. Parasite flowering phenology on one host species (velvet mesquite, Prosopis velutina) differed significantly from that on four others, and phenology was not predicted by host species phenology or host individual. Comparing mistletoe populations on mesquite and another common host species (catclaw acacia, Senegalia greggii) for which genetically distinct host races are known, we tested for differences in interactions with vectors by quantifying pollinator visitation, reward production, pollen receipt, and fruit consumption. Mistletoes on mesquite produced more pollinator rewards per flower (1.86 times the nectar and 1.92 times the pollen) and received similar to 2 more pollen grains per flower than those on acacia. Mistletoes on the two host species interacted with distinct but overlapping pollinator communities, and pollinator taxa differed in visitation according to host species. Yet, mistletoes of neither host showed uniformly greater reproductive success. Fruit set (0.70) did not differ by host, and the rates of fruit ripening and removal differed in contrasting ways. Altogether, we estimate strong but asymmetric pre-zygotic isolating barriers between mistletoes on the two hosts. These host-associated differences in reproduction have implications for interactions with mutualist vectors and population genetic structure.National Science Foundation (NSF) [DEB-1601370]; Arizona Native Plants Society; University of Arizona; Graduate Research Fellowship [DGE-1143953]12 month embargo; published online: 8 December 2017This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Interactions among interactions: The dynamical consequences of antagonism between mutualists

Species often interact with multiple mutualistic partners that provide functionally different benefits and/or that interact with different life-history stages. These functionally different partners, however, may also interact directly with one another in other ways, indirectly altering net outcomes and persistence of the mutualistic system as a whole. We present a population dynamical model of a three-species system involving antagonism between species sharing a mutualist partner species with two explicit life stages. We find that, regardless of whether the antagonism is predatory or non-consumptive, persistence of the shared mutualist is possible only under a restrictive set of conditions. As the rate of antagonism between the species sharing the mutualist increases, indirect rather than direct interactions increasingly determine species' densities and sometimes result in complex, oscillatory dynamics for all species. Surprisingly, persistence of the mutualistic system is particularly dependent upon the degree to which each of the two mutualistic interactions is specialized. Our work investigates a novel mechanism by which changing ecological conditions can lead to extinction of mutualist partners and provides testable predictions regarding the interactive roles of mutualism and antagonism in net outcomes for species' densities. (C) 2020 Elsevier Ltd. All rights reserved.12 month embargo; available online 31 May 2020This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]