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The evolutionary histories of many polyploid plant species are difficult to resolve due to a complex interplay of hybridization, incomplete lineage sorting, and missing diploid progenitors. In the case of octoploid strawberry with four subgenomes designated ABCD, the identities of the diploid progenitors for subgenomes C and D have been subject to much debate. By integrating new sequencing data from North American diploids with reticulate phylogeny and admixture analyses, we uncovered introgression from an extinct or unsampled species in the clade ofFragaria viridis,Fragaria nipponica, andFragaria nilgerrensisinto the donor of subgenome A of octoploidFragariaprior to its divergence fromF. vescasubsp. bracteata. We also detected an introgression event fromF. iinumaeinto an ancestor ofF. nipponicaandF. nilgerrensis.Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports ofF. viridisandF. nipponicaas donors of the C and D subgenomes and suggest a greater role than previously thought for homoploid hybridization in the diploid progenitors of octoploid strawberry. The integrated set of approaches used here can help advance polyploid genome analysis in other species where hybridization and incomplete lineage sorting obscure evolutionary relationships. 

Abstract In this work, we develop a differentiable rendering pipeline for visualising plasma emission within tokamaks, and estimating the gradients of the emission and estimating other physical quantities. Unlike prior work, we are able to leverage arbitrary representations of plasma quantities and easily incorporate them into a non-linear optimisation framework. The efficiency of our method enables not only estimation of a physically plausible image of plasma, but also recovery of the neutral Deuterium distribution from imaging and midplane measurements alone. We demonstrate our method with three different levels of complexity showing first that a poloidal neutrals density distribution can be recovered from imaging alone, second that the distributions of neutral Deuterium, electron density and electron temperature can be recovered jointly, and finally, that this can be done in the presence of realistic imaging systems that incorporate sensor cropping and quantisation. 

Polyploidy is a cellular state containing more than two complete chromosome sets. It has largely been studied as a discrete phenomenon in either organismal, tissue, or disease contexts. Increasingly, however, investigation of polyploidy across disciplines is coalescing around common principles. For example, the recent Polyploidy Across the Tree of Life meeting considered the contribution of polyploidy both in organismal evolution over millions of years and in tumorigenesis across much shorter timescales. Here, we build on this newfound integration with a unified discussion of polyploidy in organisms, cells, and disease. We highlight how common polyploidy is at multiple biological scales, thus eliminating the outdated mindset of its specialization. Additionally, we discuss rules that are likely common to all instances of polyploidy. With increasing appreciation that polyploidy is pervasive in nature and displays fascinating commonalities across diverse contexts, inquiry related to this important topic is rapidly becoming unified. 

Providing opportunities for students to talk directly with their peers is a critical dimension to facilitating discussions in mathematics and science, including argumentation‐focused discussions in which students construct arguments and critique others' arguments. Research suggests that supporting student‐to‐student talk and facilitating argumentation discussions are complex and challenging practices for preservice teachers (PSTs). Elementary PSTs from two mathematics and two science methods courses practiced facilitating student‐to‐student talk within the context of an argumentation‐focused discussion. This study's main purpose was to explore the prompts that 29 PSTs used to encourage student‐to‐student talk in a simulated classroom. Findings show the PSTs were able to use direct prompts that encourage student‐to‐student talk but were just as likely to use prompts that may discourage students from talking to each other. Most direct prompts PSTs used to encourage student‐to‐student talk were for the purpose of argumentation construction and/or critique. PSTs were more likely to use indirect prompts, much like Talk Moves, that encourage students to consider others' ideas rather than requesting that students talk with each other. These findings have important implications for future research, as well as for teacher educators and professional learning facilitators who support teachers learning to encourage student‐to‐student talk during argumentation‐focused discussions. 

Abstract Course‐based undergraduate research experiences (CUREs) can be a powerful tool in broadening participation in undergraduate research. In this paper, we review the benefits of and barriers to undergraduate research experiences and explore how CUREs can mitigate some of those issues. As a part of the NSF‐supported Biological Collections in Ecology and Evolution Network (BCEENET) activities, a series of network meetings produced a set of recommendations to increase the accessibility of CUREs for all students at all institution types. We use BCEENET CUREs that focus on digitized natural history collections data to illustrate how leveraging adaptable open educational resources that use freely available data and analysis tools can increase accessibility of undergraduate research. We also discuss how inclusive networks of educators and research collaborators can support broadening CURE implementation. 

Abstract PremiseDigitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs). Methods and ResultsThe gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps. ConclusionsOur pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity‐related concepts into the classroom via the use of herbarium specimens. 

iNaturalist has the potential to be an extremely rich source of organismal occurrence data. Launched in 2008, it now contains over 150 million uploaded observations as of May 2023. Based on the findings of a limited number of past studies assessing the taxonomic accuracy of participatory science-driven sources of occurrence data such as iNaturalist, there has been concern that some portion of these records might be misidentified in certain taxonomic groups. In this case study, we compare Research Grade iNaturalist observations with digitized herbarium specimens, both of which are currently available for combined download from large data aggregators and are therefore the primary sources of occurrence data for large-scale biodiversity/biogeography studies. Our comparisons were confined regionally to the southeastern United States (Florida, Georgia, North Carolina, South Carolina, Texas, Tennessee, Kentucky, and Virginia). Occurrence records from ten plant families (Gentianaceae, Ericaceae, Melanthiaceae, Ulmaceae, Fabaceae, Asteraceae, Fagaceae, Cyperaceae, Juglandaceae, Apocynaceae) were downloaded and scored on taxonomic accuracy. We found a comparable and relatively low rate of misidentification among both digitized herbarium specimens and Research Grade iNaturalist observations within the study area. This finding illustrates the utility and high quality of iNaturalist data for future research in the region, but also points to key differences between data types, giving each a respective advantage, depending on applications of the data.