Education in ecology and evolution often utilizes field instruction to teach key learning outcomes. Remote teaching of learning outcomes that have been traditionally taught in the field, necessitated by the COVID-19 pandemic, presents unique challenges for students, instructors, and institutions. A survey of 117 faculty conducted during spring 2020 revealed substantial reduction of learning outcomes typically taught in the field, and frequent substitutions of less active and more instructor-centered remote activities for field activities. The survey revealed generally negative instructor views on many remote teaching substitutions, yet also showed several approaches that instructors regarded as more effective, despite potential challenges with equitably teaching them. I suggest several models of remote substitutions for traditional field teaching of identification, field techniques, data collection, and study design in the context of the results of this survey.
The coronavirus disease of 2019 (COVID-19) pandemic has impacted educational systems worldwide, in particular primary and secondary schooling. To enable students of the local secondary school in Brisbane, Queensland, to continue with their practical agricultural science learning and facilitate online learning, a small-scale citizen science project was designed and rapidly implemented as a collaboration between the school and a multidisciplinary university research group focused on pollen allergy. Here we reflect on the process of developing and implementing this project from the perspective of the school and the university. A learning package including modules on pollen identification, tracking grass species, measuring field greenness, using a citizen science data entry platform, forensic palynology, as well as video guides, risk assessment and feedback forms were generated. Junior agriculture science students participated in the learning via online lessons and independent data collection in their own local neighborhood and/or school grounds situated within urban environments. The project provided useful data on local distribution and flowering of grass species. The experience allowed two-way knowledge exchange between the secondary and tertiary education sectors. The unique context of restrictions imposed by the social isolation policies as well as Public Health and Department of Education directives, allowed the team to respond by adapting teaching and research activity to develop and trial learning modules and citizen science tools. The project provided a focus to motivate and connect teachers, academic staff, and school students during a difficult circumstance. Extension of this citizen project for the purposes of research and secondary school learning, has the potential to offer ongoing benefits for grassland ecology data acquisition and student exposure to real-world science.
The increasingly wide application of chloroplast(cp) genome super-barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, no complete cp genome for this genus has been reported to date. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and C. tomentellav in Corydalis, conducted a comparative genomics study on them, and a highly variable cp genome structure was found. The cp genomes have a large genome size of 189,029 to 190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955 to 42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola and Papaveraceae species, five NADH dehydrogenase-like genes (ndhF, ndhD, ndhL, ndhG, ndhE) with psaC, rpl32, ccsA and trnL-UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU and trnL-CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.
The current COVID-19 pandemic has forced the global higher education community to rapidly adapt to partially- or fully-online course offerings. For field- or lab-based courses in ecological curricula, this presents unique challenges. Fortunately, a diverse set of active learning techniques exist, and these techniques translate well to online settings. However, limited guidance and resources exist for developing, implementing, and evaluating active learning assignments that fulfil specific objectives of ecology-focused courses. To address these informational gaps, we (1) identify broad learning objectives across a variety of ecology-focused courses, (2) provide examples, based on our collective online teaching experience, of active learning activities that are relevant to the identified ecological learning goals, and (3) provide guidelines for successful implementation of active learning assignments in online courses. Using The Wildlife Society’s list of online higher education ecology-focused courses as a guide, we obtained syllabi from 45 ecology-focused courses, comprising a total of 321 course-specific learning objectives. We classified all course-specific learning objectives into at least one of five categories: (1) Identification, (2) Application of Concepts/Hypotheses/Theories, (3) Management of Natural Resources, (4) Development of Professional Skills, or (5) Evaluation of Concepts/Practices. We then provided two examples of active learning activities for each of the five categories, along with guidance on their implementation in online settings. We suggest that, when based on sound pedagogy, active learning techniques can enhance the online student’s experience by activating ecological knowledge; moreover, active learning techniques should also be incorporated into in-person offerings once the current COVID-19 crisis has abated.
Barriers to fieldwork exist for many reasons such as physical ability, financial cost, and time availability. Unfortunately, these barriers disproportionately affect minority communities and create a disparity in access to fieldwork experience in the natural science community. Travel restrictions and the global lockdown has extended this barrier to fieldwork across the community and led to increased anxiety about gaps in productivity, especially for graduate students and early-career researchers. In this paper, we discuss Agent-Based Modeling as an open-source, accessible, and inclusive resource to substitute for lost fieldwork during COVID-19 and future scenarios of travel restrictions such as climate change. We detail the process of model development with a plethora of examples from the literature on how Agent-Based Models can be applied broadly across life-science research. We aim to amplify awareness and adoption of this technique to broaden the diversity and size of the Agent-Based Modeling community in ecology and evolutionary research. We also describe the benefits of Agent-Based models as a teaching and training resource for students across education levels. Finally, we discuss the current challenges facing Agent-Based Modeling and discuss how the field of quantitative ecology can work in tandem with traditional field ecology to improve both methods.
DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.
Resistance (host capacity to reduce parasite burden) and tolerance (host capacity to reduce impact on its health for a given parasite burden) manifest two different lines of defence. Tolerance can be independent from resistance, traded-off against it, or the two can be positively correlated because of redundancy in underlying (immune) processes. We here tested whether this coupling between tolerance and resistance could differ upon infection with closely related parasite species. We tested this in experimental infections with two parasite species of genus Eimeria. We measured proxies for resistance (the (inverse of) number of parasite transmission stages (oocysts) per gram of feces at the day of maximal shedding) and tolerance (the slope of maximum relative weight loss compared to day of infection on number of oocysts per gram of feces at the day of maximal shedding for each host strain) in four inbred mouse strains and four groups of F1 hybrids belonging to two mouse subspecies, Mus musculus domesticus and M. m. musculus. We found a negative correlation between resistance and tolerance against E. falciformis, while the two are uncoupled against E. ferrisi. We conclude that resistance and tolerance against the first parasite species might be traded off, but evolve more independently in different mouse genotypes against the latter. We argue that evolution of the host immune defences can be studied largely irrespective of parasite isolates if resistance-tolerance coupling is absent or weak (E. ferrisi) but host-parasite coevolution is more likely observable and best studied in a system with negatively correlated tolerance and resistance (E. falciformis).
Scavenging can have important consequences for food web dynamics, for example, it may support additional consumer species and affect predation on live prey. Still, few food web models include scavenging. We develop a dynamic model that includes predators, scavengers, live prey, and a carrion pool to show ramifications of scavenging for predation in simple food webs. We explicitly model carrion biomass and scavenging behavior and investigate the effect of scavenging for predation under different assumptions. Our modeling suggests that the presence of scavengers can both increase and decrease predator kill rates and overall predation in model food webs and the impact varies (in magnitude and direction) with context. In particular, we explore the impact of the amount of dynamics allowed in the predator, scavenger, and prey populations as well as the direction and magnitude of interference competition between predators and scavengers. We provide a road map to the different outcomes and link these theoretical outcomes to evidence from different empirical studies.
Restoring vegetation can effectively reduce soil erosion and significantly improve soil properties and quality. To analyze the response of soil organic carbon components and related enzymes to different vegetation types in the northern Loess Plateau, we collected soil samples of four vegetation types: Xanthoceras sorbifolia (XS), Hippophae rhamnoides (HR), Caragana korshinskii (CK), and Grassland (GL). We used these samples to analyze the organic carbon components (i.e., soil organic carbon (SOC), microbial biomass carbon (MBC), easily oxidized carbon (EOC), particulate organic carbon (POC) )and enzyme activities (i.e., amylase, catalase, urease and sucrase). We found that the content of the soil organic carbon fractions and the enzyme activities was greater in the upper layer than in the lower layer for each vegetation type except for MBC and catalase activity, where we observed no significant difference between soil layers. The EOC and amylase of GL vegetation were significantly higher than in other vegetation types. POC, SOC, urease and sucrase were considerably higher in SX vegetation than in other vegetation types. The maximum soil MBC content was found in HR vegetation, and among the four vegetation types, MBC content varied significantly differences in the lower layer, but no significant difference was observed in the surface soil. Correlation analysis demonstrated that the MBC content significantly influenced urease and sucrase activities, and that SOC significantly influenced urease and sucrase activities. These results emphasize the importance of the organic components of soil and the activities of soil enzymes in different kinds of vegetation in the Loess Plateau, providing a basis for improving the sustainable restoration of vegetative ecosystems.
Nutritional geometry has advanced our understanding of how macronutrients (e.g., proteins and carbohydrates) influence the expression of life history traits and their corresponding trade-offs. For example, recent work has revealed that reproduction and immune function in male decorated crickets are optimized at very different protein:carbohydrate (P:C) dietary ratios. However, it is unclear how an individual’s macronutrient intake interacts with its perceived infection status to determine investment in reproduction or other key life history traits. Here, we employed a fully factorial design in which calling effort and immune function were quantified for male crickets fed either diets previously demonstrated to maximize calling effort (P:C = 1:8) or immune function (P:C = 5:1), and then administered a treatment from a spectrum of increasing infection cue intensity using heat-killed bacteria. Both diet and a simulated infection threat independently influenced the survival, immunity, and reproductive effort of males. If they called, males increased calling effort at the low infection cue dose, consistent with the terminal investment hypothesis, but interpretation of responses at the higher threat levels was hampered by the differential mortality of males across infection cue and diet treatments. A high protein, low carbohydrate diet severely reduced the health, survival, and overall fitness of male crickets. There was, however, no evidence of an interaction between diet and infection cue dose on calling effort, suggesting that the threshold for terminal investment was not contingent on diet as investigated here.
Phenotypic variation among individuals and species is a fundamental principle of natural selection. In this review, we focus on numerous experiments involving the model species Daphnia (Crustacea) and categorize the factors, especially secondary ones, affecting intraspecific variations in inducible defense. Primary factors, such as predator type and density, determine the degree to which inducible defense expresses and increases or decreases. Secondary factors, on the other hand, act together with primary factors to inducible defense, or without primary factors on inducible defense. The secondary factors increase intra-species variation in inducible defense, and thus the level of adaptation of organisms varies within species. Future research will explore the potential for new secondary factors, as well as the relative importance between factors needs to be clarified.
The use of biota to analyze the spatial range and distribution of biogeographic regions is essential to gain a better understanding of the ecological processes that cause biotic differentiation and biodiversity at multiple spatiotemporal scales. Recently, the collection of high-resolution biological distribution data (e.g., specimens) and advances in analytical theory have led to their quantitative analysis and more refined spatial delineation. This study was conducted to redefine floristic zones in the southern part of the Korean Peninsula and to better understand the eco-evolutionary significance of the spatial distribution patterns. Based on the distribution data of 309,333 vascular plant species in the Korean Peninsula, we derived floristic zones using self-organizing maps. We compared the characteristics of the derived regions with those of historical floristic zones and ecologically important environmental factors (climate, geology, and geography). In a clustering analysis of the floristic assemblages, four distinct regions were identified, namely, the cold floristic zone (Zone I) in high-altitude regions at the center of the Korean Peninsula, cool floristic zone (Zone II) in high-altitude regions in the south of the Korean Peninsula, warm floristic zone (Zone III) in low-altitude regions in the central and southern parts of the Korean Peninsula, and maritime warm floristic zone (Zone IV) including the volcanic islands of Jejudo and Ulleungdo. A total of 1,099 taxa were common to the four floristic zones. Zone IV had the highest abundance of specific plants (those found in only one zone), with 404 taxa. This study improves floristic zone definitions using high-resolution regional biological distribution data. It will help better understand and re-establish regional species diversity. In addition, our study provides key data for hotspot analysis techniques required for the conservation of plant diversity.
As college courses transition to online instruction in response to COVID-19 incorporating inquiry-based learning is all the more essential for student engagement. However, implementation can prove challenging for instructors. I describe a strategy for inquiry-based learning that is straightforward to apply in a variety of course modalities, including asynchronous and synchronous online courses. I describe an assignment where students explore the developmental basis of morphological evolution. Flowers offer an excellent example to address this concept and are easy for students to access and describe. Students were asked to conduct research on local flowering plants by collecting and dissecting flower specimens to determine their whorl patterns and then generate hypotheses to explain the developmental genetic basis of the patterns identified. This task allowed students to apply their scientific thinking skills, explore nature, and connect their understanding of the developmental basis of evolutionary change to everyday life. I designed this assignment to be completed asynchronously, and it can be easily modified for synchronous online and traditional face-to-face meetings. Incorporating inquiry using readily available, tangible, tractable real-world examples is a pragmatic and effective approach during and beyond COVID-19.
As microbiome research moves away from model organisms to wildlife, new challenges for microbiome high throughput sequencing arise caused by the variety of wildlife diets. High levels of contamination are commonly observed emanating from the host (mitochondria) or diet (chloroplast). Such high contamination levels affect the overall sequencing depth of wildlife samples thus decreasing statistical power and leading to poor performance in downstream analysis. We developed an amplification protocol utilizing PNA-DNA clamps to maximize the use of resources and to increase the sampling depth of true microbiome sequences in samples with high levels of plastid contamination. We chose two study organisms, a bat (Leptonyteris yerbabuenae) and a bird (Mimus parvulus), both relying on heavy plant-based diets that sometimes lead to traces of plant-based faecal material producing high contamination signals from chloroplasts and mitochondria. On average, our protocol yielded a 13-fold increase in bacterial sequence amplification compared with the standard protocol (Earth Microbiome Protocol) used in wildlife research. For both focal species, we were able significantly to increase the percentage of sequences available for downstream analyses after the filtering of plastids and mitochondria. Our study presents the first results obtained by using PNA-DNA clamps to block the PCR amplification of chloroplast and mitochondrial DNA from the diet in the gut microbiome of wildlife. The method involves a cost-effective molecular technique instead of the filtering out of unwanted sequencing reads. As 33% and 26% of birds and bats, respectively, have a plant-based diet, the tool that we present here will optimize the sequencing and analysis of wild microbiomes.
As science and student populations continue to diversify, it is important for ecologists, evolutionary scientists, and educators to foster inclusive environments in their research and teaching. Academics are often poorly trained in diversity, equity, and inclusion best practices and may not know where to start to make scientific environments more welcoming and inclusive. We propose that by approaching research and teaching with empathy, flexibility, and a growth mindset, scientists can be more supportive and inclusive of their colleagues and students. This paper provides guidance, explores strategies, and directs scientists to resources to better cultivate an inclusive environment in three common settings: the classroom, the research lab, and the field. As ecologists and evolutionary scientists, we have an opportunity to adapt our teaching and research practices in order to foster an inclusive educational ecosystem for students and colleagues alike.
Bird feathers serve multiple functions through their physical structure and coloration, but the evolution of functional novelty in bird feathers remains poorly understood. We investigated how selective pressures gave rise to seasonal coloration change in the feathers of the New World Warblers (Aves: Parulidae), a family with a remarkable diversity of plumage, molt, and life history strategies. Seasonal color changes in the plumages of migratory warblers are hypothesized to reflect a tradeoff between natural and sexual selection on the breeding and non-breeding distributions. We used comparative methods including phylogenetic path analysis to examine nested hypotheses relating to the evolution of seasonal dichromatism (i.e. breeding and nonbreeding plumages) and the molts that produce these plumages. We found that biannual molts likely evolved in response to increased feather wear and that changes in feather coloration evolved after the biannual molt itself. These results demonstrate that structural needs, not seasonal selection on coloration, drive the evolution of molt strategies in Parulidae. Importantly, once a biannual molt evolves, it served as a preadaptation for seasonal changes in plumage color. These results reveal how life history strategies act upon multiple and separate feather functions to drive the evolution of feather replacement patterns and bird coloration.
The level of the genetic contribution to phenotypic variation (namely the heritability) determines the response to selection. In honeybee, the haplodiploid sex determination does not allow the straightforward use of classical quantitative genetics methods to estimate heritability and genetic correlation. Nevertheless, specific methods have been developed for about 40 years. In particular, sib-analyses are frequently used with three main methods: an historical model using the average colony relatedness, a half-sibs/full-sibs model and the more recent animal model. We compared those three methods using experimental and simulated datasets to see which performs the best. Our experimental dataset is composed of 10 colonies with 853 workers in total. All individuals were genotyped to reconstitute the pedigree, and phenotypic traits were measured: the proboscis- and wing-associated lengths. We also simulated phenotypic datasets with varying levels of heritability, common environmental effect and genetic correlation between traits. The simulation approach showed that the average colony relatedness was highly biased in presence of common environmental effect whereas the half-sibs/full-sibs and the animal model gave reliable estimates of heritability. The animal model provided the greatest precision in genetic correlations. Using this latter method, we found that wing-related traits had high heritabilities, allowing the use of those morphometric characters to discriminate between populations. On the contrary, the palpus length (associated to proboscis) was more sensitive to environmental factors. Finally, significant genetic correlations among measured traits indicate that they do not evolve independently.
Every host is colonized by a variety of microbes, some of which can protect their hosts from pathogen infection. However, pathogen presence naturally varies over time in nature, such as in the case of seasonal epidemics. We experimentally coevolved populations of Caenorhabditis elegans worm hosts with bacteria possessing protective traits (Enterococcus faecalis), in treatments varying the infection frequency with pathogenic Staphylococcus aureus every host generation, alternating host generations, every fifth host generation or never. We additionally investigated the effect of initial pathogen presence at the formation of the defensive symbiosis. Our results show that enhanced microbe-mediated protection evolved during host-protective microbe coevolution when faced with rare infections by a pathogen. Initial pathogen presence had no effect on the evolutionary outcome of microbe-mediated protection. We also found that protection was only effective at preventing mortality during the time of pathogen infection. Overall, our results suggest that resident microbes can be a form of transgenerational immunity against rare pathogen infection.