The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

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Citation: Beck, C. W., and L. S. Blumer. 2012. Inquiry-based ecology laboratory courses improve student confidence and scientific reasoning skills. Ecosphere 3(12):112. http://dx.doi.org/10.1890/ES12-00280.1Abstract. Recently, the AAAS Vision and Change report renewed the push to incorporate inquiry throughout the biology curriculum. Even prior to the report, many ecology faculty have used inquirybased approaches in their laboratory and field courses. However, the efficacy of these approaches has been assessed only to a limited degree and often at a single institution. Therefore, whether one may generalize the results of previous studies of inquiry-based teaching in laboratory courses is unclear. We examined the change in student confidence and scientific reasoning skills using published, validated instruments in inquiry-based ecology laboratory courses at two different institutions (a historically black, all-male, liberal arts college and a private research university) across multiple semesters. Students exhibited a significant increase in overall confidence and scientific reasoning skills with students in the lowest quartile at the beginning of the semester for each construct exhibiting a significantly greater gain in comparison to students in the highest quartile for the same construct. Institution had no effect on learning gains, indicating that the positive impact of inquiry-based learning is general, at least for students at our two institutions. Although weaker students exhibited greater learning gains, significant differences in confidence and scientific reasoning skills between the lowest and highest quartile persisted at the end of the semester; thus, a single, inquiry-based laboratory course is not sufficient to overcome initial differences among students. Interestingly, gains in confidence were not significantly correlated with gains in scientific reasoning with some weaker students increasing in confidence while their scientific reasoning skills decreased, which suggests that our inquiry-based laboratories did not help these students develop important metacognitive skills. Overall, our results indicate that inquiry-based laboratory courses in ecology can lead to significant learning gains, but that performance gaps among students might only be bridged by students taking multiple inquiry-based courses.

We conducted two experiments with the southern toad (Bufo terrestris) to examine whether individual variation in (i) metamorph body size and metabolic rate and (ii) age and size at metamorphosis were related to differences in survivorship or growth rate of postmetamorphic individuals. Results from the first experiment indicated that neither initial body size nor metabolic rate was related to survivorship or growth. Results from the second experiment showed that (i) size at metamorphosis was positively correlated with survivorship to first census (after 2 weeks), (ii) age and size at metamorphosis had no significant effect on survivorship from first to second census (after 2 months), (iii) size at metamorphosis had a marginally significant positive effect on survivorship from metamorphosis to second census, and (iv) age and size at metamorphosis were not significantly correlated with total growth. Our results suggest that in the southern toad, size at metamorphosis may lead to early differences in survival, size, and growth that later disappear. Furthermore, early differences in growth and survival attributable to size at metamorphosis are not due to size-related differences in metabolic rate. Therefore, although age and size at metamorphosis affect metabolic rate, they may not be related to fitness via effects on postmetamorphic survival and growth.

Numerous national reports have called for reforming laboratory courses so that all students experience the research process. In response, many course-based research experiences (CREs) have been developed and implemented. Research on the impact of these CREs suggests that student benefits can be similar to those of traditional apprentice-model research experiences. However, most assessments of CREs have been in individual courses at individual institutions or across institutions using the same CRE model. Furthermore, which structures and components of CREs result in the greatest student gains is unknown. We explored the impact of different CRE models in different contexts on student self-reported gains in understanding, skills, and professional development using the Classroom Undergraduate Research Experience (CURE) survey. Our analysis included 49 courses developed and taught at seven diverse institutions. Overall, students reported greater gains for all benefits when compared with the reported national means for the Survey of Undergraduate Research Experiences (SURE). Two aspects of these CREs were associated with greater student gains: 1) CREs that were the focus of the entire course or that more fully integrated modules within a traditional laboratory and 2) CREs that had a higher degree of student input and results that were unknown to both students and faculty.

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