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Teaching UML Models with FLOSS Projects: A study carried out during the period of social isolation imposed by the COVID-19 pandemic
<p>Software Engineering Education must include professional practice experiences so that students are able to specify, design, implement, maintain and evaluate computer systems, using appropriate theories, practices and tools. However, teaching Software Engineering (SE) principles, concepts and practices and relating them to real-world scenarios are challenging tasks. The adoption of Free/Libre/Open-Source Software (FLOSS) projects can assist in facing these challenges. This paper presents an experience report on the pedagogical use of FLOSS projects in a SE course, in the context of social isolation imposed by the COVID-19 pandemic. The course was fully virtualized, with supporting tools such as Google Classroom, Google Meet, Github, Padlet and Trello, and modeled after an instructional design based on Bloom’s taxonomy of cognitive learning objectives. FLOSS projects were used in the context of software modeling activities with UML class, sequence and activity diagrams. An online survey with twenty-six (26) students and an interview with the instructor were conducted to collect their perceptions about such experience. Results showed that most students (i) agreed that the instructional methods addressed the knowledge, comprehension and application levels in a satisfactory way; (ii) were satisfied in working with real software projects developed by others; and (iii) liked the developed activities and the tools used in the classes. The instructor and students (iv) missed face-to-face activities; and (v) agreed that the instructional design could be used in future face-to-face SE classes.</p>
Historical isolation facilitates species radiation by sexual selection: insights from Chorthippus grasshoppers
<p>Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address this question using sympatric grasshopper species of the genus <em>Chorthippus</em>, which have evolved strong behavioral isolation while lacking noticeable eco-morphological divergence. Mitochondrial genomes suggest that the radiation is relatively recent, dating to the mid-Pleistocene, which leads to extensive incomplete lineage sorting throughout the mitochondrial and the nuclear genomes. Nuclear data shows that hybrids are absent in sympatric localities but that all species have experienced gene flow, confirming that reproductive isolation is strong but remains incomplete. Demographic modelling is most consistent with a long period of geographic isolation, followed by secondary contact and extensive introgression. Such initial periods of geographic isolation might facilitate the association between male signaling and female preference, permitting the coexistence of sympatric species that are genetically, morphologically, and ecologically similar, but otherwise behave mostly as good biological species.</p>
The diverse nature of island isolation and its effect on land-bridge insular faunas
<p><span><span><b>Aim</b> Isolation is a key factor in island biology. It is usually defined as the distance to the geographically nearest mainland, but multiple alternatives exist. We explored how testing different isolation indices affects the inference of isolation effects on faunal characteristics. We focused on land-bridge islands and compared the relationships of multiple spatial and temporal (i.e., through time) isolation indices with community-, population-, and individual-level characteristics (species richness, population density, and body size, respectively). </span></span></p> <p><span><span><b>Location </b>Aegean Sea islands, Greece.</span></span></p> <p><span><span><b>Time period: </b>current.</span></span></p> <p><span><span><b>Taxon </b>Multiple animal taxa.</span></span></p> <p><span><span><b>Methods</b> We estimated 21 isolation indices for 205 islands, and recorded species-richness data for 15 taxa (invertebrates and vertebrates). We obtained body size data for seven lizard species and population density data for three. We explored how well indices predict each characteristic, in each taxon, by conducting a series of OLS regressions (controlling for island area when needed), and a meta-analysis.</span></span></p> <p><span><span><b>Results</b> Isolation was significantly (and negatively) associated with species richness in ten of 15 taxa. It was significantly (and positively) associated with body size in only one of seven species, and was not associated with population density. The effect of isolation on species richness was much weaker than island area, regardless of the index tested. Spatial indices generally outperformed temporal indices, and indices directly related to the mainland outperformed those related mainly to neighbouring islands. No index was universally superior to others, including the distance to the geographically nearest mainland. </span></span></p> <p><span><span><b>Main Conclusions </b>The choice of index can alter our perception of the effects of isolation on biological patterns. The nearly automatic, ubiquitous, use of distance to the geographically nearest mainland misrepresents the complexity of isolation effects. We recommend to simultaneously test multiple indices, that represent different aspects of isolation, to produce more constructive and thorough investigations and avoid imprecise inference.</span></span></p>
Asymmetric, but opposing reductions in immigrant viability and fecundity promote reproductive isolation among host-associated populations of an insect herbivore
<p>Immigrant inviability can contribute to reproductive isolation (RI) during ecological speciation by reducing the survival of immigrants in non-native environments. However, studies that assess the fitness consequence of immigrants moving from native to non-native environments typically fail to explore the potential role of concomitant reductions in immigrant fecundity despite recent evidence suggesting its prominent role during local adaptation. Here, we evaluate the directionality and magnitude of both immigrant viability and fecundity to RI in a host specific gall-forming wasp, Belonocnema treatae. Using reciprocal transplant experiments replicated across sites, we measure immigrant viability and fecundity by comparing differences in the incidence of gall formation (viability) and predicted number of eggs per female (fecundity) between residents and immigrants in each of two host-plant environments. Reduced immigrant viability was found in one environment while reduced immigrant fecundity was found in the other. Such habitat-dependent barriers resulted in asymmetric RI between populations. By surveying recent literature on local adaptation, we find that asymmetry in immigrant viability and fecundity are widespread across disparate taxa, which highlights the need to combine estimates of both common and overlooked barriers in cases of potential bi-directional gene flow to create a more comprehensive view of the evolution of RI.</p>
Spin structure relation to phase contrast imaging of isolated magnetic Bloch and Neel skyrmions
<p>Data set associated with publication "Spin structure relation to phase contrast imaging of isolated magnetic Bloch and Neel skyrmions"</p>
Supplementary material 3 from: Palmas P, Gouyet R, Oedin M, Millon A, Cassan J-J, Kowi J, Bonnaud E, Vidal E (2020) Rapid recolonisation of feral cats following intensive culling in a semi-isolated context. NeoBiota 63: 177-200. https://doi.org/10.3897/neobiota.63.58005
Figure S3
Supplementary material 2 from: Palmas P, Gouyet R, Oedin M, Millon A, Cassan J-J, Kowi J, Bonnaud E, Vidal E (2020) Rapid recolonisation of feral cats following intensive culling in a semi-isolated context. NeoBiota 63: 177-200. https://doi.org/10.3897/neobiota.63.58005
Figure S2
Supplementary material 1 from: Palmas P, Gouyet R, Oedin M, Millon A, Cassan J-J, Kowi J, Bonnaud E, Vidal E (2020) Rapid recolonisation of feral cats following intensive culling in a semi-isolated context. NeoBiota 63: 177-200. https://doi.org/10.3897/neobiota.63.58005
Figure S1>
Figure 3 from: Al-Rafyai HM, Alwash MS, Al-Khafaji NS (2021) Quinolone resistance (qnrA) gene in isolates of Escherichia coli collected from the Al-Hillah River in Babylon Province, Iraq. Pharmacia 68(1): 1-7. https://doi.org/10.3897/pharmacia.68.e57819
Figure 3 Distribution of the qnrA gene among quinolone-resistant E. coli isolates in the three sampling sites along the Al-Hillah River.
Figure 2 from: Al-Rafyai HM, Alwash MS, Al-Khafaji NS (2021) Quinolone resistance (qnrA) gene in isolates of Escherichia coli collected from the Al-Hillah River in Babylon Province, Iraq. Pharmacia 68(1): 1-7. https://doi.org/10.3897/pharmacia.68.e57819
Figure 2 Agarose gel electrophoresis of PCR products derived from amplifying the qnrA gene of 61 E. coli isolates (516-bp). Lane M is a 1-kb DNA Ladder, and lanes 1 to 61 are E. coli isolates. Samples were amplified on 1.5% agarose gel, and isolates are labelled at the top of the figure.
Figure 5 from: Al-Rafyai HM, Alwash MS, Al-Khafaji NS (2021) Quinolone resistance (qnrA) gene in isolates of Escherichia coli collected from the Al-Hillah River in Babylon Province, Iraq. Pharmacia 68(1): 1-7. https://doi.org/10.3897/pharmacia.68.e57819
Figure 5 Distribution of the qnrA gene among phylogenetic subgroups of quinolone-resistant E. coli isolates recovered from the three sampling sites.
Figure 4 from: Al-Rafyai HM, Alwash MS, Al-Khafaji NS (2021) Quinolone resistance (qnrA) gene in isolates of Escherichia coli collected from the Al-Hillah River in Babylon Province, Iraq. Pharmacia 68(1): 1-7. https://doi.org/10.3897/pharmacia.68.e57819
Figure 4 Distribution of the qnrA gene among phylogenetic groups of quinolone-resistant E. coli isolates recovered from the three sampling sites.
Context-dependent reproductive isolation: host plant variability drives fitness of hybrid herbivores
<p><span>The role of divergent selection between alternative environments is well-recognized to promote reproductive isolation (RI) between lineages. However, most studies view each divergent environment as homogenous, thereby overlooking the potential role of within environment variation on RI between differentiating lineages. Here we test the importance of microenvironmental variation on RI using individual trees of two host plants each harboring locally adapted populations of the cynipid wasp, <i>Belonocnema treatae</i>. We compared the fitness surrogate (survival) of offspring from hybrid crosses with residents across individuals of each host plant <i>Quercus virginiana</i> and <i>Q. geminata</i>. We found evidence of weak hybrid inviability between host-associated lineages of <i>B. treatae</i> despite strong genomic differentiation. However, averaging across environments, masked great variation in hybrid fitness on individual trees, where hybrids performed worse than, equal to, or better than residents. Considering the environmental context of hybridization is thus critical to improving the predictability of divergence under variable selection.</span></p>
Data from: Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens
Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 hours, with only 8 hours of active hands-on time with minimal modifications.
Data from: Cascading effects of forested area and isolation on seed dispersal effectiveness of rodents on subtropical islands
1. Habitat loss and fragmentation often leads to defaunation of large-bodied mammals, and their loss could trigger release from top-down control or food resource competition for small mammal seed dispersers, which in turn may affect the effectiveness of seed dispersal by altering the number of dispersed seeds or the manner in which they are dispersed. Although rodents are primary seed dispersers in habitat subjected to defaunation, changes in seed dispersal effectiveness of rodents along mammalian defaunation gradients, and empirical support for mechanisms underlying alteration of this ecological process, are unclear. 2. We assessed the direct and indirect effects of forested area and isolation on seed dispersal effectiveness of rodents on 21 study islands with varying levels of defaunation in the Thousand Island Lake, China. We used camera sampling, live traps, and semi-quantitative acorn counts to assess occurrence of large-bodied mammal species, relative abundance of small rodent species, and seed crop size, respectively. Seed dispersal, post-dispersal seed survival, seedling emergence, and seedling survival were estimated by tracking fates of tagged acorns and by planting acorns in exclosures. 3. Forested area had positive indirect effects on seed dispersal effectiveness through defaunation and rodent competition for acorns, whereas isolation had negative direct and weaker positive indirect effects on seed dispersal effectiveness mediated by loss of large-bodied mammals and rodent competition for acorns. Loss of large-bodied mammals negatively affected seed dispersal effectiveness indirectly by virtue of its impact on rodent competition for acorns. Seed dispersal effectiveness exhibited a unimodal relationship with intensity of rodent competition for acorns, peaking at intermediate levels. 4. Synthesis. Indirect effects of island attributes mediated by defaunation of large-bodied mammals on small or isolated islands appear to drive altered competition for food among rodents and decreased seed dispersal effectiveness. Altered interactions between acorns and their rodent consumers/dispersers can substantially affect oak population demography in the Thousand Island Lake system. More broadly our findings highlight the importance to the seed dispersal process of multiple interwoven effects between habitat fragmentation and defaunation of large-bodied mammals.
Data from: Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach
Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White-breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE – disentangled from IBD – in sky island vertebrates and identify potential adaptive genetic variation.
Data from: The magnitude of behavioral isolation is affected by characteristics of the mating community
Gene exchange between species occurs in areas of secondary contact, where two species have the opportunity to hybridize. If heterospecific males are more common than conspecific males, females will experience more encounters with males of other species. These encounters might increase the likelihood of heterospecific matings, and lead to the production of hybrid progeny. I studied the mating behavior of two pairs of sibling species endemic to Africa: Drosophila yakuba/D. santomea and D. simulans/D. sechellia. Drosophila yakuba and D. simulans are cosmopolitan species widely distributed in the African continent, while D. santomea and D. sechellia are island endemics. These pairs of species hybridize in nature and have the potential to exchange genes in natural conditions. I used these two pairs of Drosophila species, and constructed mating communities of different size and different heterospecific:conspecific composition. I found that both the total number of potential mates and the relative frequency of conspecific vs. heterospecific males affect female mating decisions in the cosmopolitan species but not in the island endemics. These results suggest that the population characteristics in which mating occurs may affect the magnitude of premating isolation. Community composition might thus facilitate, or impair, gene flow between species.
Data from: Genetic differentiation among isolates of Teredinibacter turnerae, a widely occurring intracellular endosymbiont of shipworms
Teredinibacter turnerae is a cultivable intracellular endosymbiont of xylotrophic (wood-feeding) bivalves of the Family Teredinidae (shipworms). Although T. turnerae has been isolated from many shipworm taxa collected in many locations, no systematic effort has been made to explore genetic diversity within this symbiont species across the taxonomic and geographical range of its hosts. The mode of symbiont transmission is unknown. Here, we examine sequence diversity in fragments of six genes (16S rRNA, gyrB, sseA, recA, rpoB and celAB) among 25 isolates of T. turnerae cultured from 13 shipworm species collected in 15 locations in the Atlantic, Pacific and Indian Oceans. While 16S rRNA sequences are nearly invariant between all examined isolates (maximum pairwise difference <0.26%), variation between examined protein-coding loci is greater (mean pairwise difference 2.2–5.9%). Phylogenetic analyses based on each protein-coding locus differentiate the 25 isolates into two distinct and well-supported clades. With five exceptions, clade assignments for each isolate were supported by analysis of alleles of each of the five protein-coding loci. These exceptions include (i) putative recombinant alleles of the celAB and gyrB loci in two isolates (PMS-535T.S.1b.3 and T8510), suggesting homologous recombination between members of the two clades; and (ii) evidence for a putative lateral gene transfer event affecting a second locus (recA) in three isolates (T8412, T8503 and T8513). These results demonstrate that T. turnerae isolates do not represent a homogeneous global population. Instead, they indicate the emergence of two lineages that, although distinct, likely experience some level of genetic exchange with each other and with other bacterial species.
Data from: Experimental test of genetic rescue in isolated populations of brook trout
Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.
Data from: The genetic basis of behavioral isolation between Drosophila mauritiana and D. sechellia
Understanding how species form is a fundamental question in evolutionary biology. Identifying the genetic bases of barriers that prevent gene flow between species provides insight into how speciation occurs. Here I analyze a poorly understood reproductive isolating barrier, prezygotic reproductive isolation. I perform a genetic analysis of prezygotic isolation between two closely related species of Drosophila, D. mauritiana and D. sechellia. I first confirm the existence of strong behavioral isolation between D. mauritiana females and D. sechellia males. Next, I examine the genetic basis of behavioral isolation by i) scanning an existing set of introgression lines for chromosomal regions that have a large effect on isolation; and ii) mapping quantitative trait loci (QTL) that underlie behavioral isolation via backcross analysis. In particular, I map QTL that determine whether a hybrid backcross female and a D. sechellia male will mate. I identify a single significant QTL, on the X chromosome, suggesting that few major-effect loci contribute to behavioral isolation between these species. In further work, I refine the map position of the QTL to a small region of the X chromosome.
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