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.
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.
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.
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.
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.
Abstract Phenotypic plasticity allows organisms to cope with variable environmental conditions increasing both performance and fitness. We studied within-generation plasticity and transgenerational effects of thermal conditions on temperature tolerance and demographic parameters in Drosophila melanogaster. We employed a fully factorial design, in which both parental (P) and offspring generations (F1) were reared in a constant or a variable thermal environment. Thermal variability during ontogeny increased heat tolerance in P, but with demographic cost as this treatment resulted in substantially lower survival, fecundity and net reproductive rate. The adverse effects of thermal variability (V) on demographic parameters were less drastic in flies from the F1, which exhibited higher net reproductive rates than their parents. These compensatory responses could not totally overcome the challenges of the thermally variable regime, contrasting with the offspring of flies raised in a constant temperature (C) that showed no reduction in fitness with thermal variation. Thus, the parental thermal environment had effect on thermal tolerance and demographic parameters in fruit-fly. These results demonstrate how transgenerational effects of environmental conditions on heat tolerance, as well as their potential costs on other fitness components, can have a major impact on populations’ resilience to warming temperatures and more frequent thermal extremes.
This paper documents a mass en route mortality event of adult summer chum salmon (Oncorhynchus keta) returning to the Koyukuk River, Alaska in the Yukon River watershed. In response to reports from local communities, researchers (including the author) surveyed ca. 315 km of river on July 26 and 27, 2019 and counted 1,364 dead individuals, but this likely reflects a small fraction of the true number of fish that died. We sampled 73 carcasses to confirm death occurred prematurely prior to complete maturation and spawning, to quantify sex and length. Visual inspection revealed a substantial fraction exhibited patterns of fungal growth consistent with secondary infections of skin lesions caused by the ubiquitous natural bacterial pathogen Flavobacterium columnare. Water temperatures during the survey averaged 17.1°C and the water was approximately 85% saturated with oxygen (ca. 8.5 mg/L), which likely contributed to the stress for upstream migrants. Evidence suggests size-selective en route mortality as female migrants that died were 2% and male migrants 5% shorter than individuals that survived to their spawning grounds on Henshaw Creek. This translates to very strong estimates of natural selection using standardized selection differentials, though randomization tests of size data revealed this observed outcome of selection was expected to occur 25% of the time due to chance alone. It is unclear whether selection acts on body size directly or indirectly through correlated phenotypic traits such as run timing. The mortality event likely underpins the below average returns of summer chum salmon to the Koyukuk in 2019, suggesting an impact on spawner abundance. The future consequences of this, or potentially increasingly frequent, en route mortality events for population productivity and the extent to which genetic adaptation or adaptive phenotypic plasticity of migration behavior may facilitate persistence of these populations is unknown.
We evaluated the richness, diversity and composition of medium and large mammalian community in the Loka Abaya National Park (LANP), southern Ethiopia, and how these parametrs differ among four habitat types: wooded grassland, riverine forest, hilly scrubland and wetland) and between seasons.We recorded total of 2,573 individual animals of 28 medium and large mammal species in the park. This included three globally threatened species: the endangered African wild-dog (Lycaon pictus) and the ‘vulnerable’ Leopard (Penthra pardus) and Hippopotamus (Hippopothamus amphibus). Season had little effect on species richness, diversity and composition both across and within habitat types. However, species richness across season was significantly different among the four habitat types, in declining order of: wooded grassland > riverine forest > hilly scrubland > wetland. The strongest similarity in species composition, both across and within seasons, was found between wooded grassland and riverine forest. In terms of relative abundance, mammalia assemblage of the wooded grassland and wetland habitats had more evenly distributed number of species with different relative abundance categories. Overall, Papio anubis, Chlorocebus aethiops and Tragelephus strepsiceros were the three most abundant species across habitat types. In conclusion, findings of our study reveal that LANP plays an important role in Ethiopia’s mammal conservation. Our findings will serve as a base-line information for managers of the park to make effective conservation decisions and as a baseline for researchers wishing to conduct related ecological studies.
Phenotypic divergence in response to divergent natural selection between environments is a common phenomenon in species of freshwater fishes. Intraspecific differentiation is often pronounced between individual inhabiting lakes versus stream habitats. The different hydrodynamic regimes in the contrasting habitats may promote a variation of body shape, but this could be intertwined with morphological adaptions to a specific foraging mode. Herein, I studied the divergence pattern of the European minnow (Phoxinus phoxinus), a common freshwater fish that has paid little attention despite its large distribution. In many Scandinavian mountain lakes, they are considered as being invasive and were found to pose threats to the native fish populations due to dietary overlap. Minnows were recently found to show phenotypic adaptions in lake versus stream habitats, but the question remained if this divergence pattern is related to trophic niche partitioning. I therefore studied the patterns of minnow divergence in morphology (i.e. using geometric morphometrics) and trophic niches (i.e. using stomach content analyses) in the lake Ånnsjön and its tributaries to link the changes in body morphology to the feeding on specific resources. Lake minnows showed a strong reliance on zooplankton and a more streamlined body shape with an upward facing snout, whereas stream minnows fed on macroinvertebrates (larvae and adults) to a higher degree and had a deeper body with a snout that was pointed down. Correlations showed a significant positive relationship of the proportion of zooplankton in the gut and morphological features present in the lake minnows. The results of this study highlight the habitat-specific divergence pattern in morphology and resource use in this ubiquitous freshwater fish, which may promote contrasting inter-specific interactions in the respective food webs.
1. The role of interspecific interactions in structuring low-diversity helminth communities is a controversial topic in parasite ecology research. Most parasitic communities of fish are species poor; thus, interspecific interactions are believed to be unimportant in structuring these communities. 2. We explored the factors that might contribute to the richness and coexistence of helminth parasites of a poecilid fish in a neotropical river. 3. Repeatability of community structure was examined in parasitic communities among 11 populations of Pseudoxiphophorus bimaculatus in the La Antigua River Basin, Veracruz, Mexico. We examined the species saturation of parasitic communities and explored the patterns of species co-occurrence. We also quantified the associations between parasitic species pairs and analysed the correlations between helminth species abundance to look for repeated patterns among the study populations. 4. Our results suggested that interspecific competition could occur in species-poor communities, aggregation played a role in determining local richness, and intraspecific aggregation allowed the coexistence of species by reducing the overall intensity of interspecific competition.
Aim Kelp forests worldwide are important marine ecosystems that foster high primary to secondary productivity and multiple ecosystem services. These ecosystems are increasingly under threat from extreme storms, changing ocean temperatures, harvesting, and greater herbivore pressure at regional and global scales, necessitating urgent documentation of their historical to present day distributions. Species range shifts to higher latitudes have already been documented in some species that dominate subtidal habitats within Europe. Very little is known about kelp forest ecosystems in Ireland, where rocky coastlines are dominated by Laminaria hyperborea. In order to rectify this substantial knowledge gap, we compiled historical records from an array of sources to present historical distribution, kelp and kelp forest recording effort over time, and present rational for the monitoring of kelp habitats to better understand ecosystem resilience. Location Ireland (Northern Ireland and Éire). Methods Herbaria, literature from the Linnaean society dating back to late 1700s, journal articles, government reports, and online databases were scoured for information on L. hyperborea. Information about kelp ecosystems was solicited from dive clubs and citizen science groups that are active along Ireland’s coastlines. Results Data were used to create distribution maps, analyse methodology and technology used to record L. hyperborea presence and kelp ecosystems within Ireland. We discuss the recent surge in studies on Irish kelp ecosystems and fauna associated with kelp ecosystems that may be used as indicators of ecosystem health and suggest methodologies for continued monitoring. Main Conclusions While there has been a steady increase in recording effort of the dominant subtidal kelp forest species, L. hyperborea, only recently have studies begun to address other important eco-evolutionary processes at work in kelp forests including connectivity among kelp populations in Ireland. Further monitoring, using suggested methodologies, is required to better understand the resilience of kelp ecosystems in Ireland.
Leaf soluble sugars and starch are important components of nonstructural carbohydrates (NSCs), which are crucial for plant growth, development, and reproduction. Although there is a large body of research focusing on the regulation of plant NSC (soluble sugars and starch) concentrations, the response of foliar NSC concentrations to continuous nitrogen (N) and phosphorus (P) addition is still unclear, especially in tropical forests. Here, we used a long-term manipulative field experiment to investigate the response of leaf NSC concentrations to continuous N and P addition (3-, 5-, and 8-year fertilization) in a tropical forest in southern China. We found significant species-specific variation in leaf NSC concentrations in this tropical forest. Phosphorus addition dramatically decreased both leaf soluble sugar and starch concentrations, while N addition had no significant effects on leaf soluble sugar and starch concentrations. These results suggest that, in plants growing in P-limiting tropical soil, leaf NSC concentrations are regulated by soil P availability rather than N availability. Moreover, the negative relationships between NSC concentrations and leaf mass per area (LMA) revealed that NSCs could supply excess carbon (C) for leaf expansion under P addition. This was further supported by the increased structural P fraction after P fertilization in our previous study at the same site. We conclude that soil P availability strongly regulates leaf starch and soluble sugar concentrations in the tropical tree species included in this study. The response of leaf NSC concentrations to long-term N and P addition can reflect the close relationships between plant C dynamics and soil nutrient availability in tropical forests. Maintaining relatively higher leaf NSC concentrations in tropical plants can be a potential mechanism for adapting to P-deficient conditions.
1. Previous macrophysiological studies suggested that temperature-driven colour lightness and body size variations strongly influence biogeographical patterns in ectotherms, but whether these trait-environment relationships scale to local assemblages and the extent to which they can be modified by dispersal remains largely unexplored. We test whether the predictions of the thermal melanism hypothesis and the Bergmann’s rule hold for local assemblages. We also assess whether these trait-environment relationships are more important for species adapted to less stable (lentic) habitats, due to their greater dispersal propensity compared to those adapted to stable (lotic) habitats. 2. We quantified the colour lightness and body volume of 99 European dragon- and damselflies (Odonata) and combined these trait information with survey data for 518 local assemblages across Europe. Based on this continent-wide yet spatially explicit dataset, we tested for effects temperature and precipitation on the colour lightness and body volume of local assemblages and assessed differences in their relative importance and strength between lentic and lotic assemblages, while accounting for spatial and phylogenetic autocorrelation. 3. The colour lightness of assemblages of odonates increased and body size decreased with increasing temperature. Trait-environment relationships in the average and phylogenetic predicted component were equally important for assemblages of both habitat types but were stronger in lentic assemblages when accounting for phylogenetic autocorrelation. 4. Our results show that the mechanism underlying colour lightness and body size variations scale to local assemblages, indicating their general importance. These mechanisms were of equal evolutionary significance for lentic and lotic species, but higher dispersal ability seems to enable lentic species to cope better with historical climatic changes. The documented differences between lentic and lotic assemblages also highlight the importance of integrating interactions of thermal adaptations with proxies of the dispersal ability of species into trait-based models, for improving our understanding of climate-driven biological responses.
Leaf shape is a defining feature of how we recognise and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterised the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing a genome wide association studies (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we performed gene co-expression network analyses from a developmental series, which is publicly available at http://aspleaf.plantgenie.org. We additionally used gene expression measurements across the population to analyse GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.
Predator-prey interactions are critical to understand how communities function. However, we need to describe intraspecific variation in diet to accurately depict those interactions. Harbor seals (Phoca vitulina, Linnaeus 1758) are an abundant marine predator that prey on species of conservation concern. We estimated intrapopulation feeding diversity of harbor seals in the Salish Sea relative to sex, time, and location with a novel approach that combined molecular techniques, repeated cross-sectional sampling of scat, and a specialization metric (within-individual consistency in diet). Based on 1,083 scat samples collected from five haul-out sites during four non-sequential years, we quantified diet using metabarcoding techniques, and determined the sex of the scat depositor using a molecular assay. Results suggest that intrapopulation feeding diversity was pervasive. Specialization was high over short periods (24 - 48 hours,〖PS〗_i = 0.392, 95% CI = 0.013, R = 100,000) and variable in time and space. Females showed more specialization than males, particularly during summer and fall, and demersal and benthic prey species were correlated with more specialized diets. The latter finding suggests that this type of prey likely require specific foraging strategies and that there are trade-offs between pelagic and benthic foraging styles for harbor seals. This differential feeding on prey species, as well as between sexes of harbor seals, indicate that predator-prey interactions in harbor seals are complex and that each sex may have a different impact on species of conservation concern. As such, describing intraspecific variation in diet may unravel hitherto unknown complex predator-prey interactions in the community.
1) The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used, or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. 2) We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25M EDTA, NaCl saturated solution, and 2. ethanol) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. 3) We found that the storage solution has a dramatic effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hours, making samples unsuitable for next-generation-sequencing. 4) We recommend DESS as the most promising solution to improve DNA preservation. These results provide practical and economical advice to improve DNA preservation when sampling for genome-wide applications. Keywords: DMSO, DNA preservation, ethanol, fish, next-generation-sequencing, NGS, snapper
Small mammal abundances are frequently limited by resource availability but predators can exert strong lethal (direct mortality) and non-lethal limitations (e.g. depressed site-level activity). Artificially increasing resource availability for small mammals provides a unique opportunity to examine predator-prey interactions. We monitored the 3-year response of arboreal rodents and their predators at nest platforms (n = 598; 23 young forest sites), using annual inspections and remote cameras (n = 168). One year after adding nest platforms we found a 2.9 to 9.2-fold increase in red tree vole (Arborimus longicaudus) use at the site-level, but little use by potential predators. Predator use of nest platforms began in year two and increased in year three of the study. Most potential nest predators were positively correlated with tree vole presence at nest platforms but effect size and direction varied with temporal grain considered (e.g. hour vs day time-bin widths). Flying squirrels (Glaucomys humboldtensis) were positively correlated with disturbances caused by digging birds. Using a Cormack-Jolly-Seber model and encounter histories produced from visual re-captures of marked tree voles, we estimated apparent annual survival to be 0.099 ± 0.057 (x̄ ± 1 SE) for females and 0.005 ± 0.014 for males. Weasels (Mustela spp.), an active seeking predator, preyed upon tree voles most frequently with 10% of weasel detections resulting in mortality of a tree vole (n = 8) whereas owls, an ambush predator, did not prey upon tree voles at nest platforms even though they were detected at similar frequencies as weasels. Weasels also exerted potential non-lethal effects and we observed a >10-fold reduction in the number of tree vole detections per week after weasel detection. Our evidence indicates that predators exert direct and indirect effects on tree vole populations with active seeking predators being the most important predators at nest sites.
1. Plant leaf stomata are the gatekeepers of the atmosphere-plant interface and are essential building blocks of land surface models as they control transpiration and photosynthesis. Although more stomatal trait data is needed to significantly reduce the error in these model predictions, recording these traits is time-consuming and no standardized protocol is currently available. Some attempts were made to automate stomatal detection from photomicrographs, however, these approaches have the disadvantage of using classic image processing or targeting a narrow taxonomic entity which makes these technologies less robust and generalizable to other plant species. We propose an easy-to-use and adaptable workflow from leaf to label. A methodology for automatic stomata detection was developed using deep neural networks according to the state-of-the-art and its applicability demonstrated across the phylogeny of the angiosperms. 2. We used a patch-based approach for training/tuning three different deep learning architectures. For training, we used 431 micrographs taken from leaf prints made according the nail polish method from herbarium specimens of 19 species. The best performing architecture was tested on 595 images of 16 additional species spread across the angiosperm phylogeny. 3. The nail polish method was successfully applied in 78% of the species sampled here. The VGG19 architecture slightly outperformed the basic shallow and deep architectures, with a confidence threshold equal to 0.7 resulting in an optimal trade-off between precision and recall. Applying this threshold the VGG19 architecture obtained an average F-score of 0.87, 0.89 and 0.67 on the training, validation and unseen test set, respectively. The average accuracy was very high (94%) for computed stomatal counts on unseen images of species used for training. 4. The leaf-to-label pipeline is an easy-to-use workflow for researchers of different areas of expertise interested in detecting stomata more efficiently. The described methodology was based on multiple species and well-established methods so that it can serve as a reference for future work.