The mitochondrial genome is now widely used in the study of the phylogenetics and molecular evolution due to its maternal inheritance, fast evolutionary rate and highly conserved gene content. To explore the phylogenetic relationships of the tribe Aeromachini within the subfamily Hesperiinae at the mitochondrial genomics level, we sequenced and annotated the complete mitogenomes of 3 skippers: Amipittia virgata, Halpe nephele and Onryza maga. All of these mitogenomes are double-stranded and have circular molecules with a total length of 15,333 bp, 15,291 bp and 15,381 bp, respectively. The mitogenomes all contain 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and a non-coding AT-rich region, and are consistent with other lepidopterans in gene order and type. In addition, we reconstruted the phylogenetic trees of Hesperiinae using maximum likelihood (ML) and Bayesian inference (BI) methods based on mitogenomic data. Results show that the 3 Aeromachini species in this study robustly constitute a monophyletic group in the subfamily Hesperiinae, with the relationships Coeliadinae + (Euschemoninae + ((Pyrginae + (Eudaminae + Tagiadinae)) + (Heteropterinae + (Barcinae + Hesperiinae)))). Moreover, our study supports the view that Apostictopterus fuliginosus and Barca bicolor should be placed out of the subfamily Hesperiinae.
The spatial-temporal patterns of fish assemblages in lotic systems can provide useful information in developing effective conservation measures. This study aimed to explore the spatiotemporal changes in fish assemblage and their association with environmental factors in mountain streams of Ren River, southwest China. Filed investigations were conducted at 18 sites during rainy and dry season in 2017. A total of 21 species, belonged to 3 orders, 8 families and 19 genera, were collected. Analysis of similarities (ANOSIM) showed fish assemblages structure varied significantly at the spatial scale, but not at the temporal scale. In low order sites, fish assemblages were mainly dominated by cold water and rheophilic species (e.g. Rhynchocypris oxycephalus, Scaphesthes macrolepis, Metahomaloptera omeiensis and Gnathopogon herzensteini), while those in high order sites were predominated by warm water and eurytopicity or stagnophilic species (e.g. Squalidus argentatus, Hemiculter leucisculus and Zacco platypus). Canonical correspondence analysis (CCA) showed fish assemblages were structured by a combination of large-scale landscape factors (e.g. altitude and C-link) and small-scale habitat features (e.g. channel width, water temperature and depth). Among these factors, landscape factors had the greatest influence on fish assemblage, while local habitat measures played less important roles or just acted in certain season.
Global change alters ecological communities with consequences for ecosystem processes. Such processes and functions are a central aspect of ecological research and vital to understanding and mitigating the consequences of global change, but also those of other drivers of change in organism communities. In this context, the concept of energy flux through trophic networks integrates food-web theory and biodiversity-ecosystem functioning theory and connects biodiversity to multitrophic ecosystem functioning. As such, the energy flux approach is a strikingly effective tool to answer central questions in ecology and global-change research. This might seem straight forward, given that the theoretical background and software to efficiently calculate energy flux are readily available. However, the implementation of such calculations is not always straight forward, especially for those who are new to the topic and not familiar with concepts central to this line of research, such as food-web theory or metabolic theory. To facilitate wider use of energy flux in ecological research, we thus provide a guide to adopting energy-flux calculations for people new to the method, struggling with its implementation, or simply looking for background reading, important resources, and standard solutions to the problems everyone faces when starting to quantify energy fluxes for their community data. First, we introduce energy flux and its use in community and ecosystem ecology. Then, we provide a comprehensive explanation of the single steps towards calculating energy flux for community data. Finally, we discuss remaining challenges and exciting research frontiers for future energy-flux research.
Sexual size dimorphism (SSD) is caused by differences in selection pressures and life-history tradeoffs faced by males and females. Proximate causes of SSD may involve sex-specific mortality, energy acqui-sition, and energy expenditure for maintenance, reproductive tissues, and reproductive behavior. Using a quantitative, individual-based, eco-genetic model parameterized for North Sea plaice, we explore the importance of these mechanisms for female-biased SSD, under which males are smaller and reach sexual maturity earlier than females (common among fish, but also arising in arthropods and mammals). We consider two mechanisms potentially serving as ultimate causes: (1) male investments into male repro-ductive behavior might detract energy resources that would otherwise be available for somatic growth, and (2) diminishing returns on male reproductive investments might lead to reduced energy acquisition. In general, both of these can bring about smaller male body sizes. We report the following findings. First, higher investments into male reproductive behavior alone cannot explain the North Sea plaice SSD. This is because such higher reproductive investments require increased energy acquisition, which would cause a delay in maturation, leading to male-biased SSD contrary to observations. When account-ing for the observed differential (lower) male mortality, maturation is postponed even further, leading to even larger males. Second, diminishing returns on male reproductive investments alone can qualitative-ly account for the North Sea plaice SSD, even though the quantitative match is imperfect. Third, both mechanisms can be reconciled with, and thus provide a mechanistic basis for, the previously advanced Ghiselin-Reiss hypothesis, according to which smaller males will evolve if their reproductive success is dominated by scramble competition for fertilizing females, as males would consequently invest more into reproduction than growth, potentially implying lower survival rates relaxing male-male competition. Fourth, a good quantitative fit is achieved by combining both mechanisms while accounting for costs males incur during spawning.
The populations of the endemic gelada outside protected areas are less studied and population estimates are not available. As a result, a study was conducted to investigate population structure and distribution of geladas in Kotu forest and associated grasslands, in Northern Ethiopia. The study area was stratified into five habitats namely; grassland, wooded grassland, plantation forest, natural forest and bushland based on dominant vegetation type. Each habitat type was further divided into blocks and total counting technique was employed to count the individuals of geladas. The total mean number of gelada in the Kotu forest was 229 ± 6.11. The mean ratio of male to female was 1:1.178. Age composition of geladas comprised: 113 (49.34%) adults, 77 (33.62%) sub adults and 39 (17.03%) juveniles. The mean group size of gelada was 18± 2.0, out of which 2.5± 0.5 (13.89%) was all- male unit (AMU) and 15.5± 1.5 (86.11%) was one male unit (OMU) social system. The average band size was 45.0± 2.53. The highest number of geladas was recorded from grassland habitat 68 (29.87%) and the lowest from plantation forest habitat 34 (14.74%). Even though, the sex ratio was female biased, the proportion of juveniles to other age classes was very low, indicating negative consequences for the future viability of the gelada populations in the area. Geladas were widely distributed over open grassland habitat. For sustainable conservation of the geladas in the area there is a need for integrated management of the area with special attention on the conservation of the grassland habitat.
In many farming landscapes, aquatic features such as wetlands, creeks and dams provide water needed for stock and irrigation, while also acting as habitat for a range of plants and animals. Indeed, some species threatened by land use change may otherwise be considerably rarer – or even extinct – in the absence of these habitats. Therefore, a critical issue for the maintenance of biodiversity in agricultural landscapes is the extent to which the management of aquatic systems can help promote the integration of agricultural production and biodiversity conservation. We completed a snapshot cross-sectional study in southern New South Wales (south-eastern Australia) to quantify the efficacy of simple management practices – partial revegetation and stock reduction via fencing – for improving vegetation structure, water quality, and macroinvertebrate assemblages. We found that even short-term livestock exclusion resulted in increased vegetation cover. Relative to dams that were unfenced, those that had been partially or completely fenced for many years were characterized by reduced turbidity and nutrient levels and contained fewer thermotolerant (faecal) coliforms. They also supported increased richness and abundance of macroinvertebrates. In contrast, control (unfenced) dams tended to have high abundance of a few macroinvertebrate taxa. Notably, differences remained between the macroinvertebrate assemblages of fenced dams and nearby ‘natural’ waterbodies. Our results show how management interventions can improve water quality in farm dams and provide a valuable reference and baseline for longer term studies of farm dam improvement.
Cheating in microbial communities is often regarded as a precursor to a “tragedy of the commons”, ultimately leading to over-exploitation by a few species, and destabilisation of the community. However, this view does not explain the ubiquity of cheaters in nature. Indeed, existing evidence suggests that cheaters are not only evolutionarily and ecologically inevitable, but also play important roles in communities, like promoting cooperative behaviour. We developed a chemostat model with two microbial species and a single, complex nutrient substrate. One of the organisms, an enzyme producer, degrades the substrate, releasing an essential and limiting resource that it can use both to grow and produce more enzymes, but at a cost. The second organism, a cheater, does not produce the enzyme but benefits from the diffused resource produced by the other species, allowing it to benefit from the public good, without contributing to it. We investigated evolutionarily stable states of coexistence between the two organisms and described how enzyme production rates and resource diffusion influence organism abundances. We found that, in the long-term evolutionary scale, monocultures of the producer drive themselves extinct because selection always favours mutant invaders that invest less in enzyme production. However, the presence of a cheater buffers this runaway selection process, preventing extinction of the producer and allowing coexistence. Resource diffusion rate controls cheater growth, preventing it from outcompeting the producer. These results show that competition from cheaters can force producers to maintain adequate enzyme production to sustain both itself and the cheater. This is known in evolutionary game theory as a “snowdrift game” – a metaphor describing a snow shoveler and a cheater following in their clean tracks. We move further to show that cheating can stabilise communities and possibly be a precursor to cooperation, rather than extinction.
Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden, this decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after presumed illegal release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (as a proxy for fitness) of introgressed and non-introgressed populations, and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition. We observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency towards higher body weight, relative to regional non-introgressed populations. These differences were not observed among introgressed and non-introgressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than southern populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of struggling range margin populations without distortion of local adaptation.
Phytoplasmas (Mollicutes, Acholeplasmataceae), vector-borne obligate bacterial plant-parasites, infect nearly 1,000 plant species and unknown numbers of insects, mainly leafhoppers (Hemiptera, Deltocephalinae), which play a key role in transmission and epidemiology. Although the plant-phytoplasma-insect association has been evolving for >300 million years, nearly all known phytoplasmas have been discovered as a result of the damage inflicted by phytoplasma diseases on crops. Few efforts have been made to study phytoplasmas occurring in non-economically important plants in natural habitats. In this study, a sub-sample of leafhopper specimens preserved in a large museum biorepository was analyzed to unveil potential new associations. PCR screening for phytoplasmas performed on 227 phloem-feeding leafhoppers collected worldwide from natural habitats revealed the presence of 6 different previously unknown phytoplasma strains. This indicates that museum collections of herbivorous insects represent a rich and largely untapped resource for discovery of new plant pathogens, that natural areas worldwide harbor a diverse but largely undiscovered diversity of phytoplasmas and potential insect vectors, and that independent epidemiological cycles occur in such habitats, posing a potential threat of disease spillover into agricultural systems. Larger-scale future investigations will contribute to a better understanding of phytoplasma genetic diversity, insect host range, and insect-borne phytoplasma transmission and provide an early warning for the emergence of new phytoplasma diseases across global agroecosystems.
The coastal heathlands of North-west Europe are valuable cultural landscapes, created and maintained over millennia by a land-use regime involving burning and grazing. These heathlands are now critically threatened throughout their range by land-use change and, increasingly, climatic changes. The climatic change impacts are complex, as the coastal heathland regions are experiencing increased temperature and precipitation, but also increased frequency and severity of extreme events, such as drought. Previous studies reveal that established heathland vegetation, including Calluna, are vulnerable to drought, but also that these vulnerabilities vary throughout the range, and with successional stage after fire. Recruitment from seed is an important regeneration strategy for Calluna heathland vegetation after burning, and our study is the first to assess how the seed germination and early seedling growth of Calluna respond to drought. We will do this in a lab germination experiment, where we will expose Calluna seeds to five different drought treatments, from -0.25 MPa to -1.7 MPa, and measure germination, and record germination percentage, germination rates, and seedling growth, below-ground allocation, and functional traits (Specific Leaf Area, Specific Root Length). To allow assessment of variation in drought responses due to geographic origin, successional stage, and the maternal plants’ drought exposure, we will conduct this experiment on seeds from 540 Calluna plants sampled from across three drought treatments (control, 50%, and 90% coverage), in three successional stages after fire (pioneer, building, mature), in two regions (60N, 65N), using a factorial design.
Chimpanzees Pan troglodytes are the closest extant relative of modern humans, and are often used as a model organism to help understand prehistoric human behavior and ecology. Originally presumed herbivorous, chimpanzees have been observed hunting 24 species of birds, ungulates, rodents, monkeys, and other primates, using an array of techniques from tools to group cooperation. Using the literature on chimpanzee hunting behavior and diet from 13 studies, we aimed to determine the prey preferences of chimpanzees. We extracted data on prey-specific variables such as targeted species, their body weight, and their abundance within the prey community, and hunter-specific variables such as hunting method, and chimpanzee group size and sex ratio. We used these in a generalized linear model to determine what factors drive chimpanzee prey preference. We calculated a Jacobs’ Index value for each prey species killed at two sites in Uganda and two sites in Tanzania. Chimpanzees prefer prey with a body weight of 7.6 ± 0.4 kg or less, which corresponds to animals such as juvenile bushbuck Tragelaphus scriptus and guereza colobus monkeys Colobus guereza. Sex ratio in chimpanzee groups appears to drive chimpanzee prey preference, where chimpanzees increasingly prefer prey when in male-dominated groups. Prey preference information from chimpanzee research can assist conservation management programs by identifying key prey species to manage, as well as contribute to a better understanding of the evolution of human hunting behavior.
We sought to generate a preliminary demographic framework for Psammochloa villosa to support of future studies of this ecologically important desert grass species, its conservation, and sustainable utilization. Psammochloa villosa occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. Here, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1728 well-defined amplified bands from eight pairs of primers, of which 1654 bands (95.72%) were polymorphic.All these values indicate that there is abundant genetic diversity, but limited gene flow in P. villosa. However, an analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within 43 populations of the species (64.16%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in the species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last inter-glacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau, which can be used to design in-situ conservation actions and to prioritize sustainable utilization of germplasm resources.
Quarry operations can have a negative impact on invertebrate biodiversity and threaten local species through a variety of factors, such as habitat loss and pollution. Quarrying is a common practice in Ghana, but little is known about its effects on local insect diversity and abundance. In this study, the relationship between quarry operations and insect communities on an active quarry site, the Mowire quarry site in the Ashanti region of Ghana was assessed. Transect counts, aerial nets, pitfall traps, Flight interception traps (FIT) and fruit baiting (Charaxes) traps were employed to assess arthropod assemblage, specifically insects as a surrogate for arthropod communities. A total of 2,902 individual insects belonging to 56 families and eleven orders were recorded in all transect points across the three sampling zones. Quarry operations had little impact on the relative abundance (N = 974) of insects at Transect point (TP) 400m in the Eastern Zone (EZ), species richness (S = 49) and the highest abundance (N = 302) corresponding with high diversity of flowering plants at this site that are a food source for pollinators and herbivorous insects. Quarry operations negatively affected the relative abundance (N= 541) and richness (S = 37) of insects in the Western zone (WZ), significantly affecting TP 400m in the WZ, corresponding to the low abundance of food plant as well as volumes of dust that settle at the WZ after every blast, as dust travels in the direction of this zone. It is recommended that interventions to prevent biodiversity habitat loss in and around the quarry operational site should focus on policies that ensure and enforce the establishment of a dust control mechanism system in the extractive industry.
Amblypygids are an arachnid order possessing a unique pair of spined pedipalps: appendages that perform in prey capture, courtship and contest. Pedipalp length, hypothesised to be under sexual selection, varies markedly across amblypygid species, and pedipalp spination, thought to reflect selection for function in prey capture, also differs interspecifically. Differences in pedipalp shape between species may indicate that the relative strength of selection for prey capture and sexual selection vary across the group. However, interspecific differences in pedipalp shape have not been quantified, due to difficulties in identifying homologous features. For the first time, we quantify trends in amblypygid pedipalp shape complexity. We use elliptical Fourier analysis to quantify 2D complexity in pedipalp outlines across eleven species and six genera. We find that complexity significantly decreases as pedipalp length increases. This appears to be driven by relative spine length, suggesting that a trade-off exists between pedipalp length and spination. Furthermore, significant female-biased sexual dimorphism in shape complexity is present in the tibial segment of the amblypygid pedipalp. Our results provide novel insights into the drivers of amblypygid pedipalp evolution, and suggest that a functional trade-off between performance in prey capture and other functions under sexual selection exist in this enigmatic structure.
Phragmites australis is the dominant species in the Yellow River Delta and plays an important role in wetland ecosystems. Ecological responses of the P. australis community to soil properties were investigated in 96 areas along the coastal-inland regions in the Yellow River Delta of China. The aim was to evaluate the relationship between phenotypic variation and environmental factors, reveal which functional traits could well respond to changes in electrical conductivity and soil water content, and the ecological strategies of P. australis. Within the range of soil water content (9.39–36.92%) and electrical conductivity (0.14–13.29 ms/cm), the results showed that the effects of soil water content and salinity were not equally important for the characterization of the morphological and physiological variability, and that plant functional traits including leaf traits and stem traits responded more strongly to soil salinity than soil water content. Our results suggested that salinity leads to reduced average height, specific leaf area, leaf area, and base stem diameter, but increased leaf water content and leaf thickness. The relationships between functional traits and electrical conductivity were generally linear and logarithmic. The coefficients of variation of morphological traits showed more phenotypic plasticity than the physiological traits. Salinity also led to the stress tolerator/competitor-stress tolerator (S/CS) strategies of P. australis; with the decrease of environmental stress, the main strategy gradually moved to the competitor (C) strategy, making P. australis the dominant species in the Yellow River Delta. KEYWORDS: Soil water content, Electrical conductivity, Functional traits, Plasticity, Life strategies.
1. Metadata plays an essential role in the long term preservation, reuse, and interoperability of data. Nevertheless, creating useful metadata can be sufficiently difficult and weakly-enough incentivised that many datasets may be accompanied by little or no metadata. One key challenge is, therefore, how to make metadata creation easier and more valuable. We present a solution that involves creating domain specific metadata schemes that are as complex as necessary and as simple as possible. These goals are achieved by co-development between a metadata expert and the researchers (i.e. the data creators). The final product is a bespoke metadata scheme into which researchers can enter information (and validate it) via the simplest of interfaces: a web browser application and a spreadsheet. 2.We provide the R package [‘dmdScheme‘](https://CRAN.R-project.org/package=dmdScheme) [@Krug2019] for creating a template domain specific scheme. We describe how to create a domain specific scheme from this template, including the iterative co-development process, and the simple methods for using the scheme, and simple methods for quality assessment, improvement, and validation. 3.The process of developing a metadata scheme following the outlined approach was successful, resulting in a metadata scheme which is used for the data generated in our research group. The validation quickly identifies forgotten metadata, as well as inconsistent metadata, therefore improving the quality of the metadata. Multiple output formats are available, including XML. 4. Making the provision of metadata easier while also ensuring high quality must be a priority for data curation initiatives. We show how both objectives are achieved by very close collaboration between metadata experts and researchers to create domain specific schemes. A near-future priority is to provide methods to interface domain specific schemes with general metadata schemes, such as the Ecological Metadata Language, to increase interoperability.
Detectors for the passive acoustic monitoring (PAM) of bats have become invaluable research tools, especially for surveys, monitoring programs and environmental impact assessments. However, little is known about the small-scale (within-site) variability of PAM recordings and especially about the influence of detector identity and distance, and of microphone orientation on the statistical confidence of activity estimates and species detection probabilities. We recorded vocalizations in a homogeneous meadow with no trees, bushes or tall ground vegetation. Eight detector pairs were arranged in an octagon, the two detectors of a pair facing in opposite directions. The call sequences of eight species were analyzed. The deviations of individual detectors from the overall mean were generally small, but large outliers occurred both at the file (temporal resolution: five seconds) and the night (resolution: one night) scale. All devices detected the main temporal patterns of calling activity in the study period, but three devices deviated systematically from the others and the sensitivity of two devices deteriorated over time. Detector orientation and distance were significant, yet small, sources of variability. The probability of detecting the presence of species correlated with species’ activity and ranged on average from 100 % for bats in total to only 18.8 % for the least active Myotis myotis. The sample sizes necessary to achieve 90 % statistical confidence of activity estimates ranged from 7 to 16 detectors and from 5 to 12 nights, depending on taxon. Increasing the number of nights resulted in much higher confidence than increasing the number of detectors. We recommend PAM studies of bats to frequently calibrate detector sensitivity; deploying at least three detectors per study site; sampling longer periods instead of deploying more detectors; randomly assigning and swapping detectors among sites, treatments, strata, etc.; and statistically scrutinizing the sample data, especially for outliers.
1. Accurate biodiversity and population monitoring is a requirement for effective conservation decision-making. Survey method bias is therefore a concern, particularly when research programs face logistical and cost limitations. 2. We employed point counts (PCs) and autonomous recording units (ARUs) to survey avian biodiversity across elevational gradients in comparable temperate mountain habitats at opposite ends of the Americas (9 mountains in British Columbia (BC), Canada and 10 in southern Chile). We compared detected species richness against multi-year species inventories and examined differences in detection probability by family. By incorporating time costs, we assessed the performance and efficiency of single vs. combined methods. 3. ARUs were predicted to capture ~92% of species present in BC but only ~58% in Chile, despite Chilean mountain communities being less diverse. Community, rather than landscape composition, appears to be the driver of this dramatic difference. Chilean communities contain less-vocal species, which ARUs missed. Further, 6/14 families in BC were better detected by ARUs while 11/11 families in Chile were better detected by PCs. Where survey conditions differentially impacted methods, PC detection varied over the morning and with canopy cover in BC and ARU detection probability mostly varied seasonally in Chile. Within a single year of monitoring, neither method alone was predicted to capture the full avian community, with the exception of ARUs in the alpine and subalpine of BC. PCs contributed little to detected diversity in BC, but including this method resulted in negligible increases in total time costs. Combining PCs with ARUs in Chile significantly increased species detections, again, for little cost. 4. Combined methods were among the most efficient and accurate approaches to capturing diversity. We recommend conducting observer point counts, where possible, when ARUs are deployed and retrieved, in order to capture additional diversity and flag methodology biases with minimal additional effort.