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Figures 37–48 in Lectotype designations in Tetratomidae, Melandryidae, Boridae and Mycteridae, based on material in the Museum of Comparative Zoology, Harvard University (Coleoptera: Tenebrionoidea)

Figures 37–48. Dorsal and lateral habitus of newly designated lectotypes. 37–38. Orchesia gracilis Melsheimer, lectotype. 37) Dorsal habitus. 38) Lateral habitus. Scale lines = 2.0 mm. 39–40. Orchesia ornata Horn, lectotype. 39) Dorsal habitus. 40) Lateral habitus. Scale lines = 1.0 mm. 41–42. Amblyctis praeses LeConte, lectotype. 41) Dorsal habitus. 42) Lateral habitus. Scale lines = 5.0 mm. 43–44. Dircaea sericea Haldeman, female lectotype. 43) Dorsal habitus. 44) Lateral habitus. Scale lines = 2.0 mm. 45–46. Serropalpus obsoletus Haldeman, lectotype. 45) Dorsal habitus. 46) Lateral habitus. Scale lines = 5.0 mm. 47–48. Serropalpus substriatus Haldeman, lectotype. 47) Dorsal habitus. 48) Lateral habitus. Scale lines = 2.0 mm.

Figure 26–36 in Lectotype designations in Tetratomidae, Melandryidae, Boridae and Mycteridae, based on material in the Museum of Comparative Zoology, Harvard University (Coleoptera: Tenebrionoidea)

Figure 26–36. Dorsal and lateral habitus of newly designated lectotypes. 26. Melandrya striata var. bicolor Melsheimer, lectotype, lateral habitus. Scale line = 2.0 mm. 27–28. Melandrya striata var. thoracica Melsheimer, lectotype. 27) Dorsal habitus. 28) Lateral habitus. Scale lines = 5.0 mm. 29–30. Hypulus fulminans LeConte, lectotype. 29) Dorsal habitus. 30) Lateral habitus. Scale lines = 1.0 mm. 31–32. Microscapha arctica Horn, lectotype. 31) Dorsal habitus. 32) Lateral habitus. Scale lines = 0.5 mm. 33–34. Microscapha clavicornis LeConte, lectotype. 33) Dorsal habitus. 34) Lateral habitus. Scale lines = 1.0 mm. 35–36. Orchesia castanea Melsheimer, lectotype. 35) Dorsal habitus. 36) Lateral habitus. Scale lines = 2.0 mm.

Figure 14–25 in Lectotype designations in Tetratomidae, Melandryidae, Boridae and Mycteridae, based on material in the Museum of Comparative Zoology, Harvard University (Coleoptera: Tenebrionoidea)

Figure 14–25. Dorsal and lateral habitus of newly designated lectotypes. 14) Dircaea riversi LeConte, lectotype, lateral habitus. Scale line = 5.0 mm. 15–16. Hypulus trifasciatus Melsheimer, lectotype. 15) Dorsal habitus. 16) Lateral habitus. Scale lines = 2.0 mm. 17–18. Microtonus sericans LeConte, lectotype. 17) Dorsal habitus. 18) Lateral habitus. Scale lines = 1.0 mm. 19–20. Scraptia flavicollis Haldeman, lectotype. 19) Dorsal habitus. Scale line = 2.0 mm. 20) Lateral habitus. Scale line = 1.0 mm. 21–22. Scraptia rugosa Haldeman, lectotype. 21) Dorsal habitus. 22) Lateral habitus. Scale lines = 1.0 mm. 23–24. Melandrya maculata LeConte, male lectotype. 23) Dorsal habitus. 24) Lateral habitus. Scale lines = 2.0 mm. 25) Melandrya striata var. bicolor Melsheimer, lectotype, dorsal habitus.

Figures 49–58 in Lectotype designations in Tetratomidae, Melandryidae, Boridae and Mycteridae, based on material in the Museum of Comparative Zoology, Harvard University (Coleoptera: Tenebrionoidea)

Figures 49–58. Dorsal and lateral habitus of newly designated lectotypes. 49–50. Carebara longula LeConte, lectotype. 49) Dorsal habitus. 50) Lateral habitus. Scale lines = 2.0 mm. 51–52. Hallomenus quadripustulata Melsheimer, lectotype. 51) Dorsal habitus. 52) Lateral habitus. Scale lines = 1.0 mm. 53–54. Mycterus canescens Horn, male lectotype. 53) Dorsal habitus. 54) Lateral habitus. Scale lines = 2.0 mm. 55–56. Mycterus quadricollis Horn, male lectotype. 55) Dorsal habitus. 56) Lateral habitus. Scale lines = 2.0 mm. 57–58. Crymodes discicollis LeConte, lectotype. 57) Dorsal habitus. 58) Lateral habitus. Scale lines = 2.0 mm.

Figures 1–13 in Lectotype designations in Tetratomidae, Melandryidae, Boridae and Mycteridae, based on material in the Museum of Comparative Zoology, Harvard University (Coleoptera: Tenebrionoidea)

Figures 1–13. Dorsal and lateral habitus of newly designated lectotypes. 1–2. Hallomenus scapularis Melsheimer, lectotype. 1) Dorsal habitus. 2) Lateral habitus. Scale lines = 2.0 mm. 3–4. Hallomenus serricornis LeConte, lectotype. 3) Dorsal habitus. 4) Lateral habitus. Scale lines = 2.0 mm. 5–6. Hypulus bicinctus Horn, lectotype. 5) Dorsal habitus. 6) Lateral habitus. Scale lines = 2.0 mm. 7–8. Dircaea liturata LeConte, male lectotype. 7) Dorsal habitus. 8) Lateral habitus. Scale lines = 2.0 mm. 9–10. Dircaea fusca LeConte, female lectotype. 9) Dorsal habitus. 10) Lateral habitus. Scale lines = 2.0 mm. 11–12. Dircaea prona LeConte, male lectotype. 11) Dorsal habitus. 12) Lateral habitus. Scale lines = 5.0 mm. 13). Dircaea riversi LeConte, female lectotype, dorsal habitus. Scale line = 5.0 mm.

opencc-by-4.0Aug 2024View details →

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Data set from the design of experiment assessment rubric, from university students / future teachers

Using an assessment rubric comprising three levels of success, we evaluated six aspects of designing an experiment, which we call dimensions. This way, specific challenges were identified in two of the dimensions: forming a hypothesis and manipulating the experimental variables, where students often failed to succeed and get lower scores. The data presented here were collected from four (4) diagnostic worksheets, which were made available to students at the beginning of the semester, where a theoretical introduction to the course is given, with reference to learning theories and their use in the teaching of Physics. Therefore, data were collected prior to discussions about the inquiry-based approach, experimental investigations, and the scientific content, such as the concepts and phenomena mentioned in the worksheets.  For the present study, we slightly modified and used a rubric that has been proposed to assess the DoE by primary and secondary school students (Lefkos et al., 2011). The modified rubric, has already been tested in a pilot study with fruitful results (Lefkos, 2024). Lefkos, I. (2024). An Assessment Rubric for Future Teachers’ Ability to Design Experiments. In C. Fazio & P. Logman (Eds.), Challenges in Physics Education (pp. 105–117). Springer. https://doi.org/10.1007/978-3-031-48667-8_7 Lefkos, I., Psillos, D., & Hatzikraniotis, E. (2011). Designing experiments on thermal interactions by secondary-school students in a simulated laboratory environment. Research in Science & Technological Education, 29(2), 189–204. https://doi.org/10.1080/02635143.2010.533266

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Supplementary data from: Lacewing-specific universal single-copy orthologs designed towards resolution of backbone phylogeny of Neuropterida

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publicOct 2024View details →

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Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order groups, including the entire angiosperm clade itself.

opencc-zeroDec 2017View details →

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FIGURE 4 in Single syntypes of Somatochlora exuberata Bartenev, 1910 (Odonata: Corduliidae), discovered in both the Milwaukee Public Museum and the University of Michigan Museum of Zoology, U.S.A., with designation of the lectotype

FIGURE 4. Specimen No. 39690 from "Amasia / Asia Minor" received in exchange from Kenneth J. Morton and belonging to the same general series as the type-series of Calopteryx amasina Bartenev, 1912. Scale bar 1 cm.

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FIGURE 3 in Single syntypes of Somatochlora exuberata Bartenev, 1910 (Odonata: Corduliidae), discovered in both the Milwaukee Public Museum and the University of Michigan Museum of Zoology, U.S.A., with designation of the lectotype

FIGURE 3. Syntype of S. exuberata from Gazimurskie Kavykuchi village, Gazimurskiy District, Zabaykal'skaya Oblast', 24 VI 1909 (according to the Julian Calendar), preserved in UMMZ and its labels. This specimen has been designated as the lectotype of Somatochlora exuberata Bartenev, 1910. Scale bar 1 cm.

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FIGURE 2 in Single syntypes of Somatochlora exuberata Bartenev, 1910 (Odonata: Corduliidae), discovered in both the Milwaukee Public Museum and the University of Michigan Museum of Zoology, U.S.A., with designation of the lectotype

FIGURE 2. Syntype of S. exuberata from Gazimurskie Kavykuchi village, Gazimurskiy District, Zabaykal'skaya Oblast', 24 VI 1909 (according to the Julian Calendar), preserved in MPM, and its labels. Scale bar 1 cm.

publicDec 2018View details →

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Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

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Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them

Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.

opencc-zeroDec 2016View details →

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FIGURE 1 in Single syntypes of Somatochlora exuberata Bartenev, 1910 (Odonata: Corduliidae), discovered in both the Milwaukee Public Museum and the University of Michigan Museum of Zoology, U.S.A., with designation of the lectotype

FIGURE 1. Riker mount with Somatochlora specimens by A.N. Bartenev (all but the upper left).