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.