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.
1.) Understanding how abiotic conditions influence dispersal patterns of organisms is important for understanding the degree to which species can track and persist in the face of changing climate. 2.) The goal of this study was to understand how weather conditions influence the dispersal pattern of multiple non-migratory grasshopper species from lower elevation grassland habitats in which they ¬¬complete their life-cycles to higher elevations that extend beyond their range limits. 3.) Using over a decade of weekly spring to late-summer field survey data along an elevational gradient, we explored how abundance and richness of dispersing grasshoppers were influenced by temperature, precipitation, and wind speed and direction. We also examined how changes in population sizes at lower elevations might influence these patterns. 4.) We observed that the abundance of displaced grasshoppers along the gradient declined 4-fold from the foothills to the subalpine and increased with warmer conditions and when wind flow patterns were mild or in the downslope direction. Thirty-eight unique grasshopper species from lowland sites were detected as dispersers across the survey years, and warmer years and weak upslope wind conditions also increased the richness of these displaced grasshoppers. The pattern of grasshoppers along the gradient was not sex biased. The positive effect of temperature on dispersal rates was likely explained by an increase in dispersal propensity rather than by an increase in the density of grasshoppers at low elevation sites. 5.) The results of this study support the hypothesis that the dispersal patterns of organisms are influenced by changing climatic conditions themselves and as such, that this context-dependent dispersal response should be considered when modeling and forecasting the ability of species to respond to climate change.
The COVID-19 pandemic has forced the transition of many traditional face-to-face classes into an online format with little time to prepare best practice guidelines. In this article we share ways to adapt a group field activity into an individual lab assignment that can be completed during shelter-in-place restrictions. We address the tactics, difficulties, successes, and ideas for future applications while staying mindful of the ways in which this pandemic has highlighted the inequities of the classroom.
Online educational videos have the potential to enhance undergraduate biology learning, for example by showcasing contemporary scientific research and providing content coverage. Here, we describe the integration of nine videos into a large-enrollment introductory evolution and ecology course via weekly homework assignments. We predicted that videos that feature research stories from contemporary scientists could reinforce topics introduced in lecture and provide students with novel insights into the nature of scientific research. Using qualitative analysis of open-ended written feedback from the students on each video assigned throughout the term (n=133-229 responses per video), we identified ten common themes in student perspectives. On the whole, the video homework assignments received more positive than negative comments and all videos received comments suggesting that they were engaging and contributed to learning goals. We discuss opportunities and challenges for the use of online educational videos in teaching ecology and evolution, and we provide guidelines instructors can use to integrate them into their courses.
1. Urban areas are often considered to be a hostile environment for wildlife as they are highly fragmented and frequently disturbed. However, these same habitats can contain abundant resources, while lacking many common competitors and predators. The urban environment can have a direct impact on the species living there, but can also have indirect effects on their parasites and pathogens. To date, relatively few studies have measured how fine-scale spatial heterogeneity within urban landscapes can affect parasite transmission and persistence. 2. Here we surveyed 237 greenspaces across the urban environment of Edinburgh (UK) to investigate how fine-scale variation in socio-economic and ecological variables can affect red fox (Vulpes vulpes) marking behaviour, gastrointestinal (GI) parasite prevalence and parasite community diversity, 3. We found that the presence and abundance of red fox faecal markings was non-uniformly distributed across greenspaces, and instead was dependent on the ecological characteristics of a site. Specifically, common foraging areas were left largely unmarked, which indicates that suitable resting and denning sites may be limiting factor in urban environments. In addition, the amount of greenspace around each site was positively correlated with overall GI parasite prevalence, species richness and diversity, highlighting the importance of greenspace (a commonly used measure of landscape connectivity) in determining the composition of the parasite community in urban areas. 4. Our results suggest that fine scale variation within urban environments can be important for understanding the ecology of infectious diseases in urban wildlife and could have wider implication for the management of urban carnivores.
1. Organisms may internally or behaviourally regulate their body temperatures or conform to the ambient air temperatures. Previous studies are inconclusive on whether pigmentation influences thermoregulation in various odonates. 2. We investigated the thermal response of sympatric North American Calopteryx aequabilis and Calopteryx maculata with a thermal imaging study across a 25 °C ambient temperature range. 3. We found that regressions of thorax temperature on ambient temperature had similar slopes for male and female C. maculata, but females were consistently 1.5 °C warmer than males. 4. In contrast, the sexes of C. aequabilis differed in slope, with C. aequabilis females having a slope less than 1.0 and males having a slope greater than 1.0. 5. Given that C. aequabilis is strongly sexually dimorphic in pigment, but C. maculata is not, our findings suggest that pigmentation does influence thermal response rate in sympatric populations of both species.
Herbivores can exert major controls over biogeochemical cycling. As invertebrates are highly sensitive to their environment (ectothermal), the abundances of insects in high-latitude systems, where climate warming is rapid, is expected to increase. In subarctic mountain birch forests research has focussed on geometrid moth outbreaks, while the contribution of background insect herbivory (BIH) to elemental cycling is poorly constrained. In northern Sweden, we estimated BIH along 9 elevational gradients distributed across a gradient in regional elevation, temperature and precipitation to allow evaluation of consistency in local vs. regional variation. We converted foliar loss via BIH to fluxes of C, nitrogen (N), and phosphorus (P) from the birch canopy to the soil to compare with other relevant soil inputs of the same elements, and assessed different abiotic and biotic drivers of the observed variability. We found that leaf area loss due to BIH was ~1.6% on average. This is comparable to estimates from tundra, but considerably lower than ecosystems at lower latitudes. The C, N and P fluxes from canopy to soil associated with BIH were 1-2 orders of magnitude lower than the soil input from senesced litter and external nutrient sources such as biological N fixation, atmospheric deposition of N and P weathering estimated from the literature. Hence, despite the minor contribution to overall elemental cycling in subarctic birch forests, the higher quality and earlier timing of the input of herbivore deposits to soils compared to senesced litter may make this contribution disproportionally important for various ecosystem functions. BIH increased significantly with leaf N-content as well as local elevation along each transect, yet showed no significant relationship with temperature or humidity, nor the commonly used temperature proxy, absolute elevation. The lacking consistency between the local and regional elevational trends calls for caution when using elevation gradients as climate proxies.
Diversification rates and evolutionary trajectories are known to be influenced by phenotypic traits and the geographic history of the landscapes that organisms inhabit. One of the most conspicuous traits in butterflies is their wing color pattern, which has been shown to be important in speciation. The evolution of many taxa in the Neotropics has also been influenced by the closure of the Panama Isthmus and the dynamic uplift of the Andes. Using a dated, species-level molecular phylogenetic hypothesis for Preponini, a colorful Neotropical butterfly tribe, we evaluated if diversification rates were constant or varied through time, and if they were dependent on color patterns or biogeographic events. We also estimated the rate of forewing color evolution and ancestral geographic ranges. We found that Preponini originated approximately 28 million years ago and that diversification has increased through time dependent on Andean uplift. Even though some clades show evolutionarily rapid transitions in coloration, these traits seem decoupled from diversification regimes. Preponini apparently originated within South America and range evolution has since been dynamic, congruent with Andean geologic activity, closure of the Panama Isthmus and Miocene climate variability. The potential involvement in mimicry rings with other butterfly groups might explain rapid changes in dorsal color patterns in this tribe.
1. Some small mammals exhibit Dehnel’s phenomenon, a drastic decline in body mass, braincase and brain size from summer to winter, followed by a regrowth in spring. This is accompanied by a reorganization of the brain and changes in other organs. The evolutionary link between these changes and seasonality remains unclear, although the magnitude of change varies between locations as the phenomenon is thought to lead to energy savings during winter. 2. Here we explored geographic variation of the intensity of Dehnel’s phenomenon in Sorex araneus. We compiled the literature on seasonal changes in braincase size, brain and body mass, supplemented by our own data from Poland, Germany and Czech Republic. 3. We analysed the effect of geographic and climate variables on the magnitude of change and patterns of brain reorganization. 4. From summer to winter the braincase height decreased by 13%, followed by 10% regrowth in spring. For body mass the changes were -21%/+82%, respectively. Changes increased along the north-east axis. Several climate variables were correlated with these transformations, confirming a link of the magnitude of the changes with environmental conditions. This relationship differed for the brain mass decline vs. regrowth, suggesting that they may have evolved under different selective pressures. 5. We found no geographic trends explaining variability in the brain mass changes although they were similar (-21%/+10%) to those of the braincase size. Underlying patterns of change in brain organisation in North-Eastern Poland were almost identical to the pattern observed in Southern Germany. This indicates that local habitat characteristics may play a more important role in determining brain structure than broad scale geographic conditions. 6. We discuss the techniques and criteria used for studying this phenomenon, as well as its potential presence in other taxa and the importance of distinguishing it from other kinds of seasonal variation.
ABSTRACT Aim Invasive species are one of the main causes of biodiversity loss world-wide. As introduced populations increase in abundance and geographical range, so does the potential for negative impacts on native communities. As such, there is a need to better understand the processes driving range expansion as species become established in recipient landscapes. We investigated the potential for population growth and range expansion of introduced populations of a non-native lizard (Podarcis muralis), considering multi-scale factors influencing growth and spatial spread. Location England, UK Methods We collated records of P. muralis presence through field surveys and a citizen science campaign. We used presence-only models to predict climate suitability at a national scale (5km resolution), and fine-scale habitat suitability at the local scale (2m resolution). We then integrated local models into an individual-based modelling platform to simulate population dynamics and forecast range expansion for 10 populations in heterogeneous landscapes. Results National-scale models indicated climate suitability restricted to the southern parts of the UK, limited by a latitudinal cline in overwintering conditions. Patterns of population growth and range expansion were related to differences in local landscape configuration and heterogeneity. Growth curves suggest populations could be in the early stages of exponential growth. However, annual rates of range expansion are predicted to be low (5-16 m). Conclusions We conclude that extensive nationwide range expansion through secondary introduction is likely to be restricted by currently unsuitable climate beyond southern regions of the UK. However, exponential growth of local populations in habitats providing transport pathways is likely to increase opportunities for regional expansion. The broad habitat niche of P. muralis, coupled with configuration of habitat patches in the landscape, allows populations to increase locally with minimal dispersal.
1. Fire and frost represent two major hurdles for the persistence of trees in open grassy biomes and have both been proposed as drivers of grassland-forest boundaries in Africa. 2. We assess the response of young tree seedlings, which represent a vulnerable stage in tree recruitment, to traumatic fire and frost disturbances. 3. In a greenhouse experiment, we investigated how seedling traits predicted survival and resprouting ability in response to fire vs frost; we characterised survival strategies of seedlings in response to the two disturbances, and we documented how the architecture of surviving seedlings is affected by fire vs frost injury. 4. Survival rates were similar under both treatments. However, different species displayed different levels of sensitivity to fire and frost. Seedling survival was higher for older seedlings and seedlings with more basal leaves. Survivors of a fire event lost more biomass than the survivors of a frost event. However, the architecture of recovered fire and frost treated seedlings were mostly similar. Seedlings that recovered from fire and frost treatments were often shorter than those that had not been exposed to any disturbance, with multiple thin branches, which may increase vulnerability to the next frost or fire event. 5. Synthesis. Fire caused more severe aboveground damage compared to frost, suggesting that trees in these open grassland systems may be subjected to a seedling release bottleneck maintained by fire. However, the woody species composition will almost certainly be influenced by phenomena that affect the timing and frequency of seedling exposure to damage, as mortality was found to be dependent on seedling age. Therefore, changes in fire regime and climate (esp. changes that bring about less frost and reduced fire intensity and frequency) are likely to result in changes in the composition and the structure of the woody components of these systems.
Population genomics is a useful tool in the integrated pest management toolbox for elucidating population dynamics, demography, and histories of invasion. However, next-generation sequencing approaches can be hampered by low DNA input from small organisms, such as insect pests. Here, we use a restriction-site associated DNA sequencing approach combined with whole-genome amplification to assess genomic population structure of a newly described pest of canola, the diminutive canola flower midge, Contarinia brassicola. We find that whole-genome amplification prior to library preparation caused a reduction in the overall number of loci sequenced and an increase in overall sequencing depth but had no discernable impact on genotyping consistency for population genetic analysis. Clustering analyses recovered little geographic structure across the main canola production region, but differentiated several geographically disparate populations at edges of the agricultural zone. Given a lack of alternative hypotheses for this pattern, we suggest these data support alternative hosts for this species and thus our canola-centric view of this midge as a pest has limited our understanding of its biology. These results speak to the need for increased surveying effort across multiple habitats and other potential hosts within Brassicaceae, to elucidate both our ecological and evolutionary knowledge of this species as well as potential management implications.
Most herbivorous insects are diet specialists in spite of the apparent advantages of being a generalist. This conundrum might be explained by fitness trade-offs on alternative host plants, yet evidence of such trade-offs has been elusive. Another hypothesis is that specialization is non-adaptive, evolving through neutral population genetic processes and within the bounds of historical constraints. Here we report on a striking lack of evidence for the adaptiveness of specificity in tropical canopy communities of armored scale insects. We show that specialists abound and that host-use is phylogenetically conservative, but in comparison to generalists, specialists occur on fewer of their potential hosts, and are no more abundant where they do occur. Of course local communities might not reflect regional diversity patterns. But based on our samples, comprising hundreds of species of hosts and armored scale insects at two widely separated sites, host-use specialists do not appear to outperform generalists.
1. Deep roots have long been thought to allow trees to coexist with shallow-rooted grasses. Due to the difficulties of working belowground, data demonstrating water uptake and niche partitioning are uncommon. 2. We describe tree and grass root distributions using a depth-specific tracer experiment in a subtropical savanna, Kruger National Park, South Africa. The depth-specific tracer experiment was conducted three times during each of two growing seasons. These point-in-time measurements (i.e., tracer-defined root distributions) were then used in a soil water flow model to estimate continuous water uptake by depth and plant growth form (trees and grasses) across the two growing seasons. 3. Most active tree and grass roots were in shallow soils: the mean depth of water uptake was 22 cm for trees and 17 cm for grasses. However, slightly deeper rooting distributions provided trees with 5% more soil water than the grasses in a drier precipitation year, but 13% less water in a wet year. Small differences in rooting distributions also provided both trees and grasses with depths and times at which each rooting distributions (tree or grass) could extract more soil water than the other (i.e., unique hydrological niches of 4 to 13 mm water). 4. The effect of rooting distributions has long been inferred. By quantifying the depth and timing of water uptake, this research demonstrated that even though rooting distributions appeared similar, they provided trees and grasses with more total water, access to a unique hydrologic niche, or both. This approach demonstrated how even small differences in rooting distributions can provide plants with resource niches that can contribute to species coexistence.