The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism—both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community.
A critical analysis of plant science literature reveals ongoing inequities
The field of plant science has grown dramatically in the past two decades, but global disparities and systemic inequalities persist. Here, we analyzed ~300,000 papers published over the past two decades to quantify disparities across nations, genders, and taxonomy in the plant science literature. Our analyses reveal striking geographical biases—affluent nations dominate the publishing landscape and vast areas of the globe have virtually no footprint in the literature. Authors in Northern America are cited nearly twice as many times as authors based in Sub-Saharan Africa and Latin America, despite publishing in journals with similar impact factors. Gender imbalances are similarly stark and show remarkably little improvement over time. Some of the most affluent nations have extremely male biased publication records, despite supposed improvements in gender equality. In addition, we find that most studies focus on economically important crop and model species, and a wealth of biodiversity is underrepresented in the literature. Taken together, our analyses reveal a problematic system of publication, with persistent imbalances that poorly capture the global wealth of scientific knowledge and biological diversity. We conclude by highlighting disparities that can be addressed immediately and offer suggestions for long-term solutions to improve equity in the plant sciences.
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- NSF-PAR ID:
- 10417457
- Date Published:
- Journal Name:
- Proceedings of the National Academy of Sciences
- Volume:
- 120
- Issue:
- 10
- ISSN:
- 0027-8424
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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null (Ed.)Computing education (CEd), or computer science education (CSEd), research has the potential to affect not only what and how we teach, but also who is taught and where. While CEd has grown as a discipline over the past two decades, many institutions still lack formal departments or programs. Given that it is a specialized and interdisciplinary area of research, we wanted to assess the values of collaboration and access. To develop a better understanding of the researchers and institutions working in CEd, we manually collected publication data from the Innovation and Technology in Computer Science Education (ITiCSE) and the ACM International Computing Education Research (ICER) conferences, and the ACM Transactions on Computing Education journal, between 2015 and 2020. Using a collective total of 1099 publications, we analyzed affiliation information about the authors and their institutions. Although we hoped to uncover a global presence and collaborative relationships demonstrating a “CSEd for all” mindset, instead we found that North America and Europe were over-represented relative to other continents. Additionally, collaborations remained a national or regional affair, for the most part. While many factors may contribute, from language barriers to financial obstacles, communication across country lines needs to improve to truly develop a more equitable international presence in the field. Through this research, we hope to raise awareness of where CEd research is being conducted and what level of collaboration occurs between institutions and countries. Moreover, we want to encourage researchers to seek alternative perspectives and to expand their collaborations to ensure CEd work truly encompasses a broader worldview.more » « less
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Abstract Background . Though many studies have long considered the broad social implications of climate change, researchers have only recently started to consider the gendered unevenness of the global landscape of vulnerability, exposure, and adaptive capacity to environmental stressors and shocks. Historically, policies and interventions addressing natural resource-based livelihoods have rarely considered underlying gender dynamics despite the global pervasiveness of gendered disparities in both economic opportunities and welfare outcomes.Methods/Design . Using two electronic databases, Web of Science and Scopus, we conducted a systematic review of peer-reviewed academic literature describing livelihoods policies or interventions that included documentation of gendered impacts. We focused on natural resource-based livelihoods most likely to be affected by climate change, centering on interventions targeting agriculture, fisheries and aquaculture, and forestry.Review Results/Synthesis . We identified 131 relevant articles, most of which focus on adoption or participation in interventions rather than outcomes. In general, women are less likely than men to engage with sustainable livelihoods interventions. When women do engage, some researchers have documented income and food security gains as well as improvements in environmental indicators in the short-term. However, these initiatives have also been found to increase women’s labor burden without corresponding gains in income. Few studies measure longer-term effects of women’s engagement on welfare and environmental outcomes, a key gap in the literature. Additionally, relatively few studies explore the intersectional impacts of initiatives, such as the added burdens of ethnicity, class, education, or other differences that modify gender disparities.Discussion . Climate change has gendered impacts on natural resource-based livelihoods. In general, existing initiatives designed to increase livelihood resilience fail to reduce gender disparities and improve women’s livelihoods. Greater attention should be paid to gender when designing sustainable livelihoods policies and interventions in order to increase adoption and participation, negotiate trade-offs, improve environmental conditions, and promote broadly beneficial welfare outcomes. -
It takes great effort to manually or semi-automatically convert free-text phenotype narratives (e.g., morphological descriptions in taxonomic works) to a computable format before they can be used in large-scale analyses. We argue that neither a manual curation approach nor an information extraction approach based on machine learning is a sustainable solution to produce computable phenotypic data that are FAIR (Findable, Accessible, Interoperable, Reusable) (Wilkinson et al. 2016). This is because these approaches do not scale to all biodiversity, and they do not stop the publication of free-text phenotypes that would need post-publication curation. In addition, both manual and machine learning approaches face great challenges: the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other) in manual curation, and keywords to ontology concept translation in automated information extraction, make it difficult for either approach to produce data that are truly FAIR. Our empirical studies show that inter-curator variation in translating phenotype characters to Entity-Quality statements (Mabee et al. 2007) is as high as 40% even within a single project. With this level of variation, curated data integrated from multiple curation projects may still not be FAIR. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardized vocabularies (ontologies). We argue that the authors describing characters are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project's semantics and ontology. This will speed up ontology development and improve the semantic clarity of the descriptions from the moment of publication. In this presentation, we will introduce the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists, which consists of three components: a web-based, ontology-aware software application called 'Character Recorder,' which features a spreadsheet as the data entry platform and provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens (this application also facilitates semantic clarity and consistency across species descriptions); a set of services that produce RDF graph data, collects terms added by authors, detects potential conflicts between terms, dispatches conflicts to the third component and updates the ontology with resolutions; and an Android mobile application, 'Conflict Resolver,' which displays ontological conflicts and accepts solutions proposed by multiple experts. a web-based, ontology-aware software application called 'Character Recorder,' which features a spreadsheet as the data entry platform and provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens (this application also facilitates semantic clarity and consistency across species descriptions); a set of services that produce RDF graph data, collects terms added by authors, detects potential conflicts between terms, dispatches conflicts to the third component and updates the ontology with resolutions; and an Android mobile application, 'Conflict Resolver,' which displays ontological conflicts and accepts solutions proposed by multiple experts. Fig. 1 shows the system diagram of the platform. The presentation will consist of: a report on the findings from a recent survey of 90+ participants on the need for a tool like Character Recorder; a methods section that describes how we provide semantics to an existing vocabulary of quantitative characters through a set of properties that explain where and how a measurement (e.g., length of perigynium beak) is taken. We also report on how a custom color palette of RGB values obtained from real specimens or high-quality specimen images, can be used to help authors choose standardized color descriptions for plant specimens; and a software demonstration, where we show how Character Recorder and Conflict Resolver can work together to construct both human-readable descriptions and RDF graphs using morphological data derived from species in the plant genus Carex (sedges). The key difference of this system from other ontology-aware systems is that authors can directly add needed terms to the ontology as they wish and can update their data according to ontology updates. a report on the findings from a recent survey of 90+ participants on the need for a tool like Character Recorder; a methods section that describes how we provide semantics to an existing vocabulary of quantitative characters through a set of properties that explain where and how a measurement (e.g., length of perigynium beak) is taken. We also report on how a custom color palette of RGB values obtained from real specimens or high-quality specimen images, can be used to help authors choose standardized color descriptions for plant specimens; and a software demonstration, where we show how Character Recorder and Conflict Resolver can work together to construct both human-readable descriptions and RDF graphs using morphological data derived from species in the plant genus Carex (sedges). The key difference of this system from other ontology-aware systems is that authors can directly add needed terms to the ontology as they wish and can update their data according to ontology updates. The software modules currently incorporated in Character Recorder and Conflict Resolver have undergone formal usability studies. We are actively recruiting Carex experts to participate in a 3-day usability study of the entire system of the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists. Participants will use the platform to record 100 characters about one Carex species. In addition to usability data, we will collect the terms that participants submit to the underlying ontology and the data related to conflict resolution. Such data allow us to examine the types and the quantities of logical conflicts that may result from the terms added by the users and to use Discrete Event Simulation models to understand if and how term additions and conflict resolutions converge. We look forward to a discussion on how the tools (Character Recorder is online at http://shark.sbs.arizona.edu/chrecorder/public) described in our presentation can contribute to producing and publishing FAIR data in taxonomic studies.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1073/pnas.2217564120
