Evolutionary history of a Scottish harbour seal population

ACKNOWLEDGEMENTS The authors wish to thank Shaneve Tripp (NYU School of Law) and Wendy West (DAFF) for their english corrections. Ludovic Hoarau (IFREMER) for his help on ArcGis. Katia Feve (INRAE) for her help with the DNA extraction protocol. DNA samples were extracted at INRAE and genotyped at the Toulouse Genopole Platform (http://www.genotoul.fr/). Anonymous reviewers provided many helpful comments on an earlier version of the manuscript. Funding This work was supported by INRAE (FRANCE), Genotoul platform (FRANCE), and University of Aberdeen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data Availability The following information was supplied regarding data availability: Data is available at INRAE: Nikolic, Natacha; Thompson, Paul; De Bruyn, Mark; Macé, Matthias; Chevalet, Claude, 2020, ‘‘Microsatellite data from: Evolutionary history of a Scottish harbour seal population’’, https://doi.org/10.15454/AOZ7JI, Portail Data INRAE, V2.Peer reviewedPublisher PD

Publisher correction: Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

Correction to: Scientific Reports https://doi.org/10.1038/s41598-019-47899-7, published online 09 August 201

Animals, protists and bacteria share marine biogeographic patterns

Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Este artículo contiene 10 páginas, 3 figuras.The use of molecular tools to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species’ range shifts. This is important when managing range shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here, we investigated the ascidian NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NNS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the biodiversity survey and the COI datasets, but failed to capture the complete incidence of all NNS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing both thriving NNS and threatened species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.L.E.H. was supported by the Natural Environmental Research Council (grant no. NE/L002531/1) and research in South Africa was supported by the Newton Fund (grant no. ES/N013913/1).Peer reviewe

Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks

Current approaches to ecological assessment are limited by the traditional morpho-taxonomic methods presently employed and the inability to meet increasing demands for rapid assessments. Advancements in high throughput sequencing now enable rapid high-resolution ecological assessment using environmental DNA (eDNA). Here we test the ability of using eDNA-based ecological assessment methods against traditional assessment of two key indicator groups (diatoms and macroinvertebrates) and show how eDNA across multiple gene regions (COI, rbcL, 12S and 18S) can be used to infer interactive networks that link to ecological assessment criteria. We compared results between taxonomic and eDNA based assessments and found significant positive associations between macroinvertebrate (p < 0.001 R2 = 0.645) and diatom (p = 0.015, R2 = 0.222) assessment metrics. We further assessed the ability of eDNA based assessment to identify environmentally sensitive genera and found an order of magnitude greater potential for 18S, versus COI or rbcL, to determine environmental filtering of ecologically assessed communities. Lastly, we compared the ability of traditional metrics against co-occurrence network properties of our combined 18S, COI and rbcL indicator genera to infer habitat quality measures currently used by managers. We found that transitivity (network connectivity), linkage density and cohesion were significantly associated with habitat modification scores (HMS), whereas network properties were inconsistent with linking to the habitat quality score (HQS) metric. The incorporation of multi-marker eDNA network assessment opens up a means for finer scale ecological assessment, currently limited using traditional methods. While utilization of eDNA-based assessment is recommended, direct comparisons with traditional approaches are difficult as the methods are intrinsically different and should be treated as such with regards to future research. Overall, our findings show that eDNA can be used for effective ecological assessment while offering a wider range of scope and application compared to traditional assessment methods

The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species

The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution – from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species’ potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus’ early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet’s closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species

Two-stage Examinations in STEM: A Narrative Literature Review

  Written, invigilated examinations are valued for their reliability, economy and academic integrity. Nevertheless, examinations are problematic. Final, summative examinations can disadvantage students who experience assessment anxiety, and students may not receive useable feedback. An alternative is the two-stage examination, where a traditional examination is followed by a group examination with similar questions. Students gain peer feedback on their examination performance, and can meaningfully apply this feedback. Use of this format in tertiary STEM education in universities has indicated that students prefer the format, although it has been little studied in Australia. Furthermore, its effects on reducing stress and fostering deeper learning are not well understood. The COVID-19 pandemic and switch to online learning has provided us with an opportunity to review our assessment practices and has led to a new willingness to test different examination formats. Here we provide a narrative review of the results of previous studies on two-stage examinations and, based on this and our experience teaching in large-cohort introductory biology courses at an Australian university, we propose a formula for employing them in this context

Two-staging a comeback: A review of two-stage exams from 1996 to 2022

BACKGROUND Two-stage examinations are an alternative to a traditional examination, where an individual examination is followed by a group examination, often on the same questions. With pandemic remote learning leading to a re-assessment of examination formats, we investigated previous research on two-stage exams to understand how these assessments have been delivered and received by students, and we make suggestions based on this research and our own experience for how to deliver these exams in a large-cohort introductory biology unit. This research was published in the International Journal of Innovation in Science and Mathematics Educations (IJISME; Lee et al., 2022). AIMS We aimed to investigate trends in how two-stage exams were set, their discipline context, student performance and the student experience in studies published in the last ~25 years. DESIGN AND METHODS We performed a narrative literature review of research papers involving the use of two-stage examinations in STEM, from 1996 to 2022. We extracted from the 39 included studies data about the discipline, the weighting and timing of the group component, the type of questions asked, how groups were formed and the cohort size. We also extracted data on the student’s response: whether scores were higher in the group component, whether the exam improved understanding or retention, whether students favoured the format and whether stress was alleviated. RESULTS Trends were identified, with most surveyed exams using multiple-choice questions that were the same in the individual and the group component. Student feedback was very positive, and group component marks were almost always higher than individual component marks. However, results varied on improved understanding and reduction in stress, and few studies tested these factors. CONCLUSIONS Two-stage exams are well received by students, and group exams increase performance relative to individual exams. Further research is needed into measurable beneficial effects from the format. We provide our suggestions for implementing these examinations in a large introductory biology unit. REFERENCE Lee, T. R. C., Pye, M., Lilje, O., Nguyen, H. D., Hockey, S., de Bruyn, M. and can den Berg, F. T. (2022) Two-stage examinations in STEM: A narrative literature review. International Journal of Innovation in Science and Mathematics Education, 30(5), 73-90