Recordings of introductory biology student discussions of clicker questions demonstrate that students use reasoning and questioning in their discussions and that their use of these discussion characteristics is heavily influenced by the cues they hear from learning assistants during discussions.
There is a growing appreciation for the importance of hybrid speciation in angiosperm evolution. Here, we show that Yucca gloriosa (Asparagaceae: Agavoideae) is the product of intersectional hybridization between Y. aloifolia and Y. filamentosa. These species, all named by Carl Linnaeus, exist in sympatry along the southeastern Atlantic coast of the United States. Yucca gloriosa was found to share a chloroplast haplotype with Y. aloifolia in all populations sampled. In contrast, nuclear gene-based microsatellite markers in Y. gloriosa are shared with both parents. The hybrid origin of Y. gloriosa is supported by multilocus analyses of the nuclear microsatellite markers including principal coordinates analysis (PCO), maximum-likelihood hybrid index scoring (HINDEX), and Bayesian cluster analysis (STRUCTURE). The putative parental species share only one allele at a single locus, suggesting there is little to no introgressive gene flow occurring between these species and Y. gloriosa. At the same time, diagnostic markers are segregating in Y. gloriosa populations. Lack of variation in the chloroplast of Y. aloifolia, the putative maternal parent, makes it difficult to rule out multiple hybrid origins of Y. gloriosa, but allelic variation at nuclear loci can be explained by a single hybrid origin of Y. gloriosa. Overall, these data provide strong support for the homoploid hybrid origin of Y. gloriosa.
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
We describe the recursive design process used to generate a nonsurvey introductory biology course built on a framework of evolutionary (social, sexual, natural, and nonadaptive) mechanisms, physicochemical processes and constraints, and systematic behaviors that shape all biological systems. The resulting narrative (based on a free text, Biofundamentals) and associated materials are described, and the ways in which they have been revised on the basis of students’ responses to drawing- and text-based formative assessments, interactive readings, and students’ response to exam questions are elaborated. Strategies to encourage student persistence through assessment strategies (such as “I know it now” tests) are described.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.