Optimal Science Lab Design: Impacts of Various Components of Lab Design on Students’ Attitudes Toward Lab

Variations in science lab design can differentially impact student learning. Quantification of these differential impacts can be used in modeling – an approach we term “optimal lab design.” In this study we estimated relative influences of six characteristics of lab design on students’ attitudes toward science labs in three different first-year college biology lab courses (USA). We used two end-of-semester surveys. The first had students choose their favorite and least favorite lab and answer questions associated with the six characteristics and their choices. The second had students provide an overall rating of each lab and a rating based on their perception of the degree to which the six characteristics impacted the lab. Results of the two assessments were similar and indicated the following: Total Student Attitude = 0.39 Exciting + 0.25 Time Efficient + 0.15 Not Difficult + 0.10 Lecture Help + 0.08 Experimental + 0.03 Open-Ended

Dispersal, Diversity and Divergence: Evolutionary Processes in Prairie Dogs (Genus Cynomys)

Evolutionary biology seeks to understand the processes driving genetic diversity within species and phylogenetic divergence among species. Patterns of diversity may be dictated by both abiotic factors and community interactions. My dissertation research focuses on the processes that influence diversity and divergence in prairie dogs across spatial and temporal scales. At the macroevolutionary scale, habitat constraints influencing metabolism, reproductive period and growth rate may act as selective agents. Gunnison\u27s prairie dogs (Cynomys gunnisoni) have been proposed to exist as two subspecies that occupy distinct habitats and are morphologically distinct in portions of their range. Using complementary approaches of phylogenetic analysis, genetic clustering, and spatial analysis of environment, I examine the contributions of different ecological selection pressures to genetic diversity of Gunnison\u27s prairie dogs throughout their range. I find that elevation and temperature determine the distribution of two unique lineages of Gunnison\u27s prairie dogs, and that plant communities differ between habitats occupied by each subspecies. At the local scale, landscape connectivity may interact with susceptibility to pathogens to influence population structure, particularly in social species such as prairie dogs. Although some land cover types, such as intense urbanization and water bodies, prevent dispersal across them, prairie dogs can travel across multiple land cover types such as grassland, shrubland and agricultural fields. Moreover, although large highways act as dispersal barriers, small roads can actually facilitate prairie dog dispersal, particularly across water bodies. Pathogen susceptibility is likely to influence genetic structure because prairie dogs suffer approximately 99% mortality during plague outbreaks. In Boulder County, re-colonization by black-tailed prairie dogs (C. ludovicianus) occurred 1 - 3 years after extirpation in well-connected colonies. Genetic diversity within the metapopulation was retained. Within some well-connected populations colonized by multiple source populations, genetic variation was maintained or increased, but diversity was lost in some isolated populations. Finally, individuals in recolonized populations had significantly higher heterozygosity than those present before plague. This dissertation will contribute to our understanding of the abiotic and biotic mechanisms of diversification in social species

Evaluating the risk of avian disease in reintroducing the endangered Kiwikiu (Maui Parrotbill: Pseudonestor xanthophrys) to Nakula NAR, Maui, Hawai‘i

Reports were scanned in black and white at a resolution of 600 dots per inch and were converted to text using Adobe Paper Capture Plug-in.Avian malaria and other introduced diseases have had profound negative effects on Hawaiian honeycreepers, contributing to numerous extinctions and severely limiting the ranges of the remaining species. These diseases, concordant with habitat loss, are thought to restrict many species to narrow ranges at high elevations where cooler climates restrict reproduction of both the malaria parasite, Plasmodium relictum, and its mosquito vector, Culex quinquefasciatus. The Kiwikiu (Maui Parrotbill, Pseudonestor xanthophrys) is a critically endangered honeycreeper that formerly existed throughout Maui and Moloka‘i but now occupies roughly 30 km2 above 1400 m above sea level (asl) on the windward slopes of Haleakalā volcano. The species is thought to be highly susceptible to avian malaria based on its limited range and reported mortality in related species. The primary conservation action proposed for Kiwikiu is to expand the species’ range by reintroducing Kiwikiu to high elevation native forests on the south-facing leeward slope of Haleakalā. As part of an assessment of the suitability of the proposed release site, Nakula Natural Area Reserve, we sought to evaluate the risk of avian disease (i.e., avian malaria and pox) to the future Kiwikiu population. To do this, we trapped adult mosquitoes and surveyed for larvae throughout the release area in 2015–2016. We also tested blood samples from common bird species in Nakula using quantitative polymerase chain reaction analyses to estimate disease prevalence within the current bird population at the release site. To compare disease prevalence to habitat currently occupied by Kiwikiu, we also trapped mosquitoes and tested avian blood samples from common species in The Nature Conservancy’s Waikamoi Preserve in 2016. Unexpectedly, we captured adult and larval C. quinquefasciatus at much higher rates in Nakula than those reported from similar locations at comparable elevations (1530-1620 m asl) throughout Hawai‘i but did not capture C. quinquefasciatus in Waikamoi (1675-1700 m asl). Although leeward slopes receive far less rainfall than windward slopes, the drainages in Nakula contain small pools of water that can provide suitable breeding habitat for the mosquitoes. The frequency of high-flow periods in streams in Waikamoi may regularly “flush out” pools, reducing larval habitat. In contrast, the warmer temperatures and long periods between high-flow events may allow mosquitoes to persist year-round in Nakula. In contrast to mosquito capture rates, analysis of blood samples revealed similar or lower rates of avian malaria in two common honeycreeper species in Nakula compared to similar sites. We also found several individuals of two common honeycreeper species (i.e. Hawaiʻi ʻAmakihi [Chlorodrepanis virens] and ʻIʻiwi [Drepanis coccinea]) captured above 1900 m asl in Waikamoi to be positive for avian malaria. These results suggest that 1) although the persistence of mosquitoes represents an increased risk of infection in Nakula, the Plasmodium parasite may still be physiologically limited by environmental conditions at the release site, 2) the management of mosquitoes (e.g. biopesticides) is advisable to reduce infection risk, and 3) Kiwikiu may be at higher risk in its current range than previously considered. While creating a second population of Kiwikiu in Nakula is critical to safeguarding this species from extinction, mitigating the threat of avian malaria on a larger scale will be the only way to achieve island-wide recovery

Data from: Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black-tailed prairie dogs

Introduced diseases can cause dramatic declines in—and even the loss of—natural populations. Extirpations may be followed by low recolonization rates, leading to inbreeding and a loss of genetic variation, with consequences on population viability. Conversely, extirpations may create vacant habitat patches that individuals from multiple source populations can colonize, potentially leading to an influx of variation. We tested these alternative hypotheses by sampling 15 colonies in a prairie dog metapopulation during 7 years that encompassed an outbreak of sylvatic plague, providing the opportunity to monitor genetic diversity before, during and after the outbreak. Analysis of nine microsatellite loci revealed that within the metapopulation, there was no change in diversity. However, within extirpated colonies, patterns varied: In half of the colonies, allelic richness after recovery was less than the preplague conditions, and in the other half, richness was greater than the preplague conditions. Finally, analysis of variation within individuals revealed that prairie dogs present in recolonized colonies had higher heterozygosity than those present before plague. We confirmed plague survivorship in six founders; these individuals had significantly higher heterozygosity than expected by chance. Collectively, our results suggest that high immigration rates can maintain genetic variation at a regional scale despite simultaneous extirpations in spatially proximate populations. Thus, virulent diseases may increase genetic diversity of host populations by creating vacant habitats that allow an influx of genetic diversity. Furthermore, even highly virulent diseases may not eliminate individuals randomly; rather, they may selectively remove the most inbred individuals

genotypes_9loci_forDRYAD

This is a Genepop-formatted file of black-tailed prairie dog genotypes at 9 microsatellite loci. Samples were collected in Boulder, Colorado, genotyped on a Licor 4200 gel sequencer and analyzed in the program GeneImagIR. The top 2 lines are comments, and the next 9 are locus names. Individuals that produced plague antibodies and survived until the next year are denoted with an asterisk

First Genome Sequence of the Gunnison’s Prairie Dog (\u3cem\u3eCynomys gunnisoni\u3c/em\u3e), a Keystone Species and Player in the Transmission of Sylvatic Plague

Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America’s grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison’s prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels

First Genome Sequence of the Gunnison’s Prairie Dog (\u3cem\u3eCynomys gunnisoni\u3c/em\u3e), a Keystone Species and Player in the Transmission of Sylvatic Plague

Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America’s grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison’s prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels

genotypes_9loci_forDRYAD

This is a Genepop-formatted file of black-tailed prairie dog genotypes at 9 microsatellite loci. Samples were collected in Boulder, Colorado, genotyped on a Licor 4200 gel sequencer and analyzed in the program GeneImagIR. The top 2 lines are comments, and the next 9 are locus names. Individuals that produced plague antibodies and survived until the next year are denoted with an asterisk

Data from: Genetic variation and structure in contrasting geographic distributions: widespread vs. restricted black-tailed prairie dogs (subgenus Cynomys)

Species of restricted distribution are considered more vulnerable to extinction because of low levels of genetic variation relative to widespread taxa. Species of the subgenus Cynomys are an excellent system to compare genetic variation and degree of genetic structure in contrasting geographic distributions. We assessed levels of genetic variation, genetic structure, and genetic differentiation in widespread Cynomys ludovicianus and restricted C. mexicanus using 1997bp from the cytochrome b and control region (n = 223 C. ludovicianus; 77 C. mexicanus), and 10 nuclear microsatellite loci (n = 207 and 78, respectively). Genetic variation for both species was high, and genetic structure in the widespread species was higher than in the restricted species. C. mexicanus showed values of genetic variation, genetic structure, and genetic differentiation similar to C. ludovicianus at smaller geographic scales. Results suggest the presence of at least 2 historical refuges for C. ludovicianus and that the Sierra Madre Occidental represents a barrier to gene flow. Chihuahua and New Mexico possess high levels of genetic diversity and should be protected, while Sonora should be treated as an independent management unit. For C. mexicanus, connectivity among colonies is very important and habitat fragmentation and habitat loss should be mitigated to maintain gene flow