Showing papers in "Ecology and Evolution in 2019"

Animal movement tools (amt): R package for managing tracking data and conducting habitat selection analyses.

Abstract: Advances in tracking technology have led to an exponential increase in animal location data, greatly enhancing our ability to address interesting questions in movement ecology, but also presenting new challenges related to data management and analysis. Step-selection functions (SSFs) are commonly used to link environmental covariates to animal location data collected at fine temporal resolution. SSFs are estimated by comparing observed steps connecting successive animal locations to random steps, using a likelihood equivalent of a Cox proportional hazards model. By using common statistical distributions to model step length and turn angle distributions, and including habitat- and movement-related covariates (functions of distances between points, angular deviations), it is possible to make inference regarding habitat selection and movement processes or to control one process while investigating the other. The fitted model can also be used to estimate utilization distributions and mechanistic home ranges. Here, we present the R package amt (animal movement tools) that allows users to fit SSFs to data and to simulate space use of animals from fitted models. The amt package also provides tools for managing telemetry data. Using fisher (Pekania pennanti) data as a case study, we illustrate a four-step approach to the analysis of animal movement data, consisting of data management, exploratory data analysis, fitting of models, and simulating from fitted models.

EasyCodeML: A visual tool for analysis of selection using CodeML.

Abstract: The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here, we present a wrapper tool named EasyCodeML that provides a user-friendly graphical interface for using CodeML. EasyCodeML has a custom running mode in which parameters can be adjusted to meet different requirements. It also offers a preset running mode in which an evolutionary analysis pipeline and publication-quality tables can be exported by a single click. EasyCodeML allows visualized, interactive tree labelling, which greatly simplifies the use of the branch, branch-site, and clade models of selection. The program allows comparison of major codon-based models for analyses of selection. EasyCodeML is a stand-alone package that is supported in Windows, Mac, and Linux operating systems, and is freely available at https://github.com/BioEasy/EasyCodeML.

Collinearity in ecological niche modeling: Confusions and challenges

Abstract: University of Arizona Office of Research, Discovery, and Innovation; Oklahoma State University [NSF-OCI 1126330]; University of Tennessee

Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution.

Abstract: Environmental DNA (eDNA) analysis has successfully detected organisms in various aquatic environments. However, there is little basic information on eDNA, including the eDNA shedding and degradation processes. This study focused on water temperature and fish biomass and showed that eDNA shedding, degradation, and size distribution varied depending on water temperature and fish biomass. The tank experiments consisted of four temperature levels and three fish biomass levels. The total eDNA and size-fractioned eDNA from Japanese Jack Mackerels (Trachurus japonicus) were quantified before and after removing the fish. The results showed that the eDNA shedding rate increased at higher water temperature and larger fish biomass, and the eDNA decay rate also increased at higher temperature and fish biomass. In addition, the small-sized eDNA fractions were proportionally larger at higher temperatures, and these proportions varied among fish biomass. After removing the fish from the tanks, the percentage of eDNA temporally decreased when the eDNA size fraction was >10 µm, while the smaller size fractions increased. These results have the potential to make the use of eDNA analysis more widespread in the future.

A temporal beta-diversity index to identify sites that have changed in exceptional ways in space–time surveys

Abstract: Aim This paper presents the statistical bases for temporal beta-diversity analysis, a method to study changes in community composition through time from repeated surveys at several sites. Surveys of that type are presently done by ecologists around the world. A temporal beta-diversity Index (TBI) is computed for each site, measuring the change in species composition between the first (T1) and second surveys (T2). TBI indices can be decomposed into losses and gains; they can also be tested for significance, allowing one to identify the sites that have changed in composition in exceptional ways. This method will be of value to identify exceptional sites in space-time surveys carried out to study anthropogenic impacts, including climate change. Innovation The null hypothesis of the TBI test is that a species assemblage is not exceptionally different between T1 and T2, compared to assemblages that could have been observed at this site at T1 and T2 under conditions corresponding to H0. Tests of significance of coefficients in a dissimilarity matrix are usually not possible because the values in the matrix are interrelated. Here, however, the dissimilarity between T1 and T2 for a site is computed with different data from the dissimilarities used for the T1-T2 comparison at other sites. It is thus possible to compute a valid test of significance in that case. In addition, the paper shows how TBI dissimilarities can be decomposed into loss and gain components (of species, or abundances-per-species) and how a B-C plot can be produced from these components, which informs users about the processes of biodiversity losses and gains through time in space-time survey data. Main conclusion Three applications of the method to different ecological communities are presented. This method is applicable worldwide to all types of communities, marine, and terrestrial. R software is available implementing the method.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation.

Abstract: The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as FST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

Microbial functional diversity: From concepts to applications.

Abstract: Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods.

Abstract: Terrestrial arthropods comprise the most species-rich communities on Earth, and grassland flowers provide resources for hundreds of thousands of arthropod species. Diverse grassland ecosystems worldwide are threatened by various types of environmental change, which has led to decline in arthropod diversity. At the same time, monitoring grassland arthropod diversity is time-consuming and strictly dependent on declining taxonomic expertise. Environmental DNA (eDNA) metabarcoding of complex samples has demonstrated that information on species compositions can be efficiently and non-invasively obtained. Here, we test the potential of wild flowers as a novel source of arthropod eDNA. We performed eDNA metabarcoding of flowers from several different plant species using two sets of generic primers, targeting the mitochondrial genes 16S rRNA and COI. Our results show that terrestrial arthropod species leave traces of DNA on the flowers that they interact with. We obtained eDNA from at least 135 arthropod species in 67 families and 14 orders, together representing diverse ecological groups including pollinators, parasitoids, gall inducers, predators, and phytophagous species. Arthropod communities clustered together according to plant species. Our data also indicate that this experiment was not exhaustive, and that an even higher arthropod richness could be obtained using this eDNA approach. Overall, our results demonstrate that it is possible to obtain information on diverse communities of insects and other terrestrial arthropods from eDNA metabarcoding of wild flowers. This novel source of eDNA represents a vast potential for addressing fundamental research questions in ecology, obtaining data on cryptic and unknown species of plant-associated arthropods, as well as applied research on pest management or conservation of endangered species such as wild pollinators.

Gender differences in peer review outcomes and manuscript impact at six journals of ecology and evolution.

Abstract: The productivity and performance of men is generally rated more highly than that of women in controlled experiments, suggesting conscious or unconscious gender biases in assessment. The degree to which editors and reviewers of scholarly journals exhibit gender biases that influence outcomes of the peer-review process remains uncertain due to substantial variation among studies. We test whether gender predicts the outcomes of editorial and peer review for >23,000 research manuscripts submitted to six journals in ecology and evolution from 2010 to 2015. Papers with female and male first authors were equally likely to be sent for peer review. However, papers with female first authors obtained, on average, slightly worse peer-review scores and were more likely to be rejected after peer review, though the difference varied among journals. These gender differences appear to be partly due to differences in authorial roles. Papers for the which the first author deferred corresponding authorship to a coauthor (which women do more often than men) obtained significantly worse peer-review scores and were less likely to get positive editorial decisions. Gender differences in corresponding authorship explained some of the gender differences in peer-review scores and positive editorial decisions. In contrast to these observations on submitted manuscripts, gender differences in peer-review outcomes were observed in a survey of >12,000 published manuscripts; women reported similar rates of rejection (from a prior journal) before eventual publication. After publication, papers with female authors were cited less often than those with male authors, though the differences are very small (~2%). Our data do not allow us to test hypotheses about mechanisms underlying the gender discrepancies we observed, but strongly support the conclusion that papers authored by women have lower acceptance rates and are less well cited than are papers authored by men in ecology.

When water interacts with temperature: Ecological and evolutionary implications of thermo-hydroregulation in terrestrial ectotherms

Abstract: The regulation of body temperature (thermoregulation) and of water balance (defined here as hydroregulation) are key processes underlying ecological and evolutionary responses to climate fluctuations in wild animal populations. In terrestrial (or semiterrestrial) ectotherms, thermoregulation and hydroregulation closely interact and combined temperature and water constraints should directly influence individual performances. Although comparative physiologists traditionally investigate jointly water and temperature regulation, the ecological and evolutionary implications of these coupled processes have so far mostly been studied independently. Here, we revisit the concept of thermo‐hydroregulation to address the functional integration of body temperature and water balance regulation in terrestrial ectotherms. We demonstrate how thermo‐hydroregulation provides a framework to investigate functional adaptations to joint environmental variation in temperature and water availability, and potential physiological and/or behavioral conflicts between thermoregulation and hydroregulation. We extend the classical cost–benefit model of thermoregulation in ectotherms to highlight the adaptive evolution of optimal thermo‐hydroregulation strategies. Critical gaps in the parameterization of this conceptual optimality model and guidelines for future empirical research are discussed. We show that studies of thermo‐hydroregulation refine our mechanistic understanding of physiological and behavioral plasticity, and of the fundamental niche of the species. This is illustrated with relevant and recent examples of space use and dispersal, resource‐based trade‐offs, and life‐history tactics in insects, amphibians, and nonavian reptiles.

Rapid loss of an ecosystem engineer: Sphagnum decline in an experimentally warmed bog.

Abstract: Sphagnum mosses are keystone components of peatland ecosystems. They facilitate the accumulation of carbon in peat deposits, but climate change is predicted to expose peatland ecosystem to sustained and unprecedented warming leading to a significant release of carbon to the atmosphere. Sphagnum responses to climate change, and their interaction with other components of the ecosystem, will determine the future trajectory of carbon fluxes in peatlands. We measured the growth and productivity of Sphagnum in an ombrotrophic bog in northern Minnesota, where ten 12.8-m-diameter plots were exposed to a range of whole-ecosystem (air and soil) warming treatments (+0 to +9°C) in ambient or elevated (+500 ppm) CO2. The experiment is unique in its spatial and temporal scale, a focus on response surface analysis encompassing the range of elevated temperature predicted to occur this century, and consideration of an effect of co-occurring CO2 altering the temperature response surface. In the second year of warming, dry matter increment of Sphagnum increased with modest warming to a maximum at 5°C above ambient and decreased with additional warming. Sphagnum cover declined from close to 100% of the ground area to <50% in the warmest enclosures. After three years of warming, annual Sphagnum productivity declined linearly with increasing temperature (13-29 g C/m2 per °C warming) due to widespread desiccation and loss of Sphagnum. Productivity was less in elevated CO2 enclosures, which we attribute to increased shading by shrubs. Sphagnum desiccation and growth responses were associated with the effects of warming on hydrology. The rapid decline of the Sphagnum community with sustained warming, which appears to be irreversible, can be expected to have many follow-on consequences to the structure and function of this and similar ecosystems, with significant feedbacks to the global carbon cycle and climate change.

Maxent modeling for predicting the spatial distribution of three raptors in the Sanjiangyuan National Park, China

Abstract: Upland buzzard (Buteo hemilasius), Saker falcon (Falco cherrug), and Himalayan vulture (Gyps himalayensis) are three common large raptors in the Sanjiangyuan National Park (SNP), China's first national park. Among them, Upland buzzard and Saker falcon play a significant role in controlling plateau rodent populations and reducing the transmission of pathogens carried by rodents. The Himalayan vulture can provide services for the redistribution and recycling of nutrients in the ecosystem, and play an irreplaceable role in the celestial burial culture of Tibetans in China. Exploring their habitat suitability is important for the protection of the three raptors. Our research was based on the current distribution of Upland buzzard, Saker falcon, and Himalayan vulture that we had extensively surveyed in the Sanjiangyuan National Park from 2016 to 2017. Combined with the correlation analysis of environmental variables, we utilized maximum entropy model (MaxEnt) to evaluate and compare the habitat suitability of the three species in the Sanjiangyuan National Park. Elevation, climate, and human disturbance factors, which had direct or indirect effects on species survival and reproduction, were all included in the model. Among them, elevation was the most important environmental variables affecting the suitability of habitats of three species. Temperature-related factor was another important predictor. The high (>60%) suitable habitat areas for Upland buzzard, Saker falcon, and Himalayan vulture were 73,017.63, 40,732.78, and 61,654.33 km(2), respectively, accounted for 59.32%, 33.09%, and 50.08% of the Sanjiangyuan National Park and their total suitable area (i.e., the sum area of high and moderate habitats) reached 96.07%, 60.59%, and 93.70%, respectively. Besides, the three species have overlapping areas for the suitable habitats, which means that overlapping areas should be highly valued and protected. Therefore, understanding the distribution of suitable habitats of the three raptors can provide useful information and reasonable reference for us to put forward suggestions for their protection and regional management.

The past, present, and future of coral heat stress studies.

Abstract: The global loss and degradation of coral reefs, as a result of intensified frequency and severity of bleaching events, is a major concern. Evidence of heat stress affecting corals through loss of symbionts and consequent coral bleaching was first reported in the 1930s. However, it was not until the 1998 major global bleaching event that the urgency for heat stress studies became internationally recognized. Current efforts focus not only on examining the consequences of heat stress on corals but also on finding strategies to potentially improve thermal tolerance and aid coral reefs survival in future climate scenarios. Although initial studies were limited in comparison with modern technological tools, they provided the foundation for many of today's research methods and hypotheses. Technological advancements are providing new research prospects at a rapid pace. Understanding how coral heat stress studies have evolved is important for the critical assessment of their progress. This review summarizes the development of the field to date and assesses avenues for future research.

Worldwide insect declines: An important message, but interpret with caution

Abstract: A recent paper claiming evidence of global insect declines achieved huge media attention, including claims of “insectaggedon” and a “collapse of nature.” Here, we argue that while many insects are declining in many places around the world, the study has important limitations that should be highlighted. We emphasise the robust evidence of large and rapid insect declines present in the literature, while also highlighting the limitations of the original study.

Parallel declines in abundance of insects and insectivorous birds in Denmark over 22 years.

Abstract: 1. Farmers in most western countries have increased use of fertilizer and pesticides with impact on wild animals and plants, including the abundance of insects and their predators. 2. I used 1,375 surveys of insects killed on car windscreens as a measure of insect abundance during 1997-2017 at two transects in Denmark. I cross-validated this method against three other methods for sampling insect abundance, and I investigated the effects of this measure of insect abundance on the abundance of breeding insectivorous birds. 3. The abundance of flying insects was quantified using a windscreen resulting in reductions of 80% and 97% at two transects of 1.2 km and 25 km, respectively, according to general additive mixed model. Insect abundance increased with time of day, temperature, and June date, but decreased with wind resulting in a reduction by 54%. The abundance of insects killed on a car windscreen was strongly positively correlated with the abundance of insects caught in sweep nets and on sticky plates in the same study areas and at the same time as when insects were sampled using windscreens. The decline in abundance of insects on windscreens predicted the rate at which barn swallows Hirundo rustica fed their nestlings, even when controlling statistically for time of day, weather, and age and number of nestlings. The abundance of breeding pairs of three species of aerially insectivorous birds was positively correlated with the abundance of insects killed on windscreens at the same time in the same study area. This suggests a link between two trophic levels as affected by the temporal reduction in the abundance of flying insects. 4. These findings are consistent with recent dramatic declines in insect abundance in Europe and North America with consequences for the rate of food provisioning of barn swallow offspring, the abundance of aerially insectivorous birds and bottom up trophic cascades.

Highly flexible infection programs in a specialized wheat pathogen.

Abstract: Many filamentous plant pathogens exhibit high levels of genomic variability, yet the impact of this variation on host-pathogen interactions is largely unknown. We have addressed host specialization in the wheat pathogen Zymoseptoria tritici. Our study builds on comparative analyses of infection and gene expression phenotypes of three isolates and reveals the extent to which genomic variation translates into phenotypic variation. The isolates exhibit genetic and genomic variation but are similarly virulent. By combining confocal microscopy, disease monitoring, staining of ROS, and comparative transcriptome analyses, we conducted a detailed comparison of the infection processes of these isolates in a susceptible wheat cultivar. We characterized four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction that are shared by the three isolates. However, we demonstrate differentiated temporal and spatial infection development and significant differences in the expression profiles of the three isolates during the infection stages. More than 20% of the genes were differentially expressed and these genes were located significantly closer to transposable elements, suggesting an impact of epigenetic regulation. Further, differentially expressed genes were enriched in effector candidates suggesting that isolate-specific strategies for manipulating host defenses are present in Z. tritici. We demonstrate that individuals of a host-specialized pathogen have highly differentiated infection programs characterized by flexible infection development and functional redundancy. This illustrates how high genetic diversity in pathogen populations results in highly differentiated infection phenotypes, which fact needs to be acknowledged to understand host-pathogen interactions and pathogen evolution.

Incomplete estimates of genetic diversity within species: Implications for DNA barcoding.

Abstract: DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present levels of haplotype diversity, as well as patterning of standing genetic variation that exists within and between species. Typical sample sizes for molecular biodiversity assessment using DNA barcodes range from 5 to 10 individuals per species. However, required levels that are necessary to fully gauge haplotype variation at the species level are presumed to be strongly taxon-specific. Importantly, little attention has been paid to determining appropriate specimen sample sizes that are necessary to reveal the majority of intraspecific haplotype variation within any one species. In this paper, we present a brief outline of the current literature and methods on intraspecific sample size estimation for the assessment of COI DNA barcode haplotype sampling completeness. The importance of adequate sample sizes for studies of molecular biodiversity is stressed, with application to a variety of metazoan taxa, through reviewing foundational statistical and population genetic models, with specific application to ray-finned fishes (Chordata: Actinopterygii). Finally, promising avenues for further research in this area are highlighted.

Strong patterns of intraspecific variation and local adaptation in Great Basin plants revealed through a review of 75 years of experiments.

Abstract: Variation in natural selection across heterogeneous landscapes often produces (a) among-population differences in phenotypic traits, (b) trait-by-environment associations, and (c) higher fitness of local populations. Using a broad literature review of common garden studies published between 1941 and 2017, we documented the commonness of these three signatures in plants native to North America's Great Basin, an area of extensive restoration and revegetation efforts, and asked which traits and environmental variables were involved. We also asked, independent of geographic distance, whether populations from more similar environments had more similar traits. From 327 experiments testing 121 taxa in 170 studies, we found 95.1% of 305 experiments reported among-population differences, and 81.4% of 161 experiments reported trait-by-environment associations. Locals showed greater survival in 67% of 24 reciprocal experiments that reported survival, and higher fitness in 90% of 10 reciprocal experiments that reported reproductive output. A meta-analysis on a subset of studies found that variation in eight commonly measured traits was associated with mean annual precipitation and mean annual temperature at the source location, with notably strong relationships for flowering phenology, leaf size, and survival, among others. Although the Great Basin is sometimes perceived as a region of homogeneous ecosystems, our results demonstrate widespread habitat-related population differentiation and local adaptation. Locally sourced plants likely harbor adaptations at rates and magnitudes that are immediately relevant to restoration success, and our results suggest that certain key traits and environmental variables should be prioritized in future assessments of plants in this region.

Framing pictures: A conceptual framework to identify and correct for biases in detection probability of camera traps enabling multi-species comparison

Abstract: Obtaining reliable species observations is of great importance in animal ecology and wildlife conservation. An increasing number of studies use camera traps (CTs) to study wildlife communities, and an increasing effort is made to make better use and reuse of the large amounts of data that are produced. It is in these circumstances that it becomes paramount to correct for the species- and study-specific variation in imperfect detection within CTs. We reviewed the literature and used our own experience to compile a list of factors that affect CT detection of animals. We did this within a conceptual framework of six distinct scales separating out the influences of (a) animal characteristics, (b) CT specifications, (c) CT set-up protocols, and (d) environmental variables. We identified 40 factors that can potentially influence the detection of animals by CTs at these six scales. Many of these factors were related to only a few overarching parameters. Most of the animal characteristics scale with body mass and diet type, and most environmental characteristics differ with season or latitude such that remote sensing products like NDVI could be used as a proxy index to capture this variation. Factors that influence detection at the microsite and camera scales are probably the most important in determining CT detection of animals. The type of study and specific research question will determine which factors should be corrected. Corrections can be done by directly adjusting the CT metric of interest or by using covariates in a statistical framework. Our conceptual framework can be used to design better CT studies and help when analyzing CT data. Furthermore, it provides an overview of which factors should be reported in CT studies to make them repeatable, comparable, and their data reusable. This should greatly improve the possibilities for global scale analyses of (reused) CT data.

The active spread of adaptive variation for reef resilience.

Abstract: The speed at which species adapt depends partly on the rates of beneficial adaptation generation and how quickly they spread within and among populations. Natural rates of adaptation of corals may not be able to keep pace with climate warming. Several interventions have been proposed to fast-track thermal adaptation, including the intentional translocation of warm-adapted adults or their offspring (assisted gene flow, AGF) and the ex situ crossing of warm-adapted corals with conspecifics from cooler reefs (hybridization or selective breeding) and field deployment of those offspring. The introgression of temperature tolerance loci into the genomic background of cooler-environment corals aims to facilitate adaptation to warming while maintaining fitness under local conditions. Here we use research on selective sweeps and connectivity to understand the spread of adaptive variants as it applies to AGF on the Great Barrier Reef (GBR), focusing on the genus Acropora. Using larval biophysical dispersal modeling, we estimate levels of natural connectivity in warm-adapted northern corals. We then model the spread of adaptive variants from single and multiple reefs and assess if the natural and assisted spread of adaptive variants will occur fast enough to prepare receiving central and southern populations given current rates of warming. We also estimate fixation rates and spatial extent of fixation under multiple release scenarios to inform intervention design. Our results suggest that thermal tolerance is unlikely to spread beyond northern reefs to the central and southern GBR without intervention, and if it does, 30+ generations are needed for adaptive gene variants to reach fixation even under multiple release scenarios. We argue that if translocation, breeding, and reseeding risks are managed, AGF using multiple release reefs can be beneficial for the restoration of coral populations. These interventions should be considered in addition to conventional management and accompanied by strong mitigation of CO2 emissions.

From feces to data : A metabarcoding method for analyzing consumed and available prey in a bird-insect food web

Abstract: Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.

Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization

Abstract: DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding-based biodiversity studies is gaining popularity as a noninvasive, time-efficient, and cost-effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under-surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA-related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species-level assignment) and universal (broad taxonomic group with genus/family-level assignment) approaches obtained from replicates treated with the optimal and a low-performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false-negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol-chloroform-isoamyl for successful implementation of eDNA multi-marker metabarcoding surveys.

Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments

Abstract: High-throughput sequencing has the potential to describe biological communities with high efficiency yet comprehensive assessment of diversity with species-level resolution remains one of the most challenging aspects of metabarcoding studies. We investigated the utility of curated ribosomal and mitochondrial nematode reference sequence databases for determining phylum-specific species-level clustering thresholds. We compiled 438 ribosomal and 290 mitochondrial sequences which identified 99% and 94% as the species delineation clustering threshold, respectively. These thresholds were evaluated in HTS data from mock communities containing 39 nematode species as well as environmental samples from Vietnam. We compared the taxonomic description of the mocks generated by two read-merging and two clustering algorithms and the cluster-free Dada2 pipeline. Taxonomic assignment with the RDP classifier was assessed under different training sets. Our results showed that 36/39 mock nematode species were identified across the molecular markers (18S: 32, JB2: 19, JB3: 21) in UClust_ref OTUs at their respective clustering thresholds, outperforming UParse_denovo and the commonly used 97% similarity. Dada2 generated the most realistic number of ASVs (18S: 83, JB2: 75, JB3: 82), collectively identifying 30/39 mock species. The ribosomal marker outperformed the mitochondrial markers in terms of species and genus-level detections for both OTUs and ASVs. The number of taxonomic assignments of OTUs/ASVs was highest when the smallest reference database containing only nematode sequences was used and when sequences were truncated to the respective amplicon length. Overall, OTUs generated more species-level detections, which were, however, associated with higher error rates compared to ASVs. Genus-level assignments using ASVs exhibited higher accuracy and lower error rates compared to species-level assignments, suggesting that this is the most reliable pipeline for rapid assessment of alpha diversity from environmental samples.

Evidence of region-wide bat population decline from long-term monitoring and Bayesian occupancy models with empirically informed priors.

Abstract: Strategic conservation efforts for cryptic species, especially bats, are hindered by limited understanding of distribution and population trends. Integrating long-term encounter surveys with multi-season occupancy models provides a solution whereby inferences about changing occupancy probabilities and latent changes in abundance can be supported. When harnessed to a Bayesian inferential paradigm, this modeling framework offers flexibility for conservation programs that need to update prior model-based understanding about at-risk species with new data. This scenario is exemplified by a bat monitoring program in the Pacific Northwestern United States in which results from 8 years of surveys from 2003 to 2010 require updating with new data from 2016 to 2018. The new data were collected after the arrival of bat white-nose syndrome and expansion of wind power generation, stressors expected to cause population declines in at least two vulnerable species, little brown bat (Myotis lucifugus) and the hoary bat (Lasiurus cinereus). We used multi-season occupancy models with empirically informed prior distributions drawn from previous occupancy results (2003-2010) to assess evidence of contemporary decline in these two species. Empirically informed priors provided the bridge across the two monitoring periods and increased precision of parameter posterior distributions, but did not alter inferences relative to use of vague priors. We found evidence of region-wide summertime decline for the hoary bat ( λ ^ = 0.86 ± 0.10) since 2010, but no evidence of decline for the little brown bat ( λ ^ = 1.1 ± 0.10). White-nose syndrome was documented in the region in 2016 and may not yet have caused regional impact to the little brown bat. However, our discovery of hoary bat decline is consistent with the hypothesis that the longer duration and greater geographic extent of the wind energy stressor (collision and barotrauma) have impacted the species. These hypotheses can be evaluated and updated over time within our framework of pre-post impact monitoring and modeling. Our approach provides the foundation for a strategic evidence-based conservation system and contributes to a growing preponderance of evidence from multiple lines of inquiry that bat species are declining.

Pollinator size and its consequences: Robust estimates of body size in pollinating insects

Abstract: Body size is an integral functional trait that underlies pollination-related ecological processes, yet it is often impractical to measure directly. Allometric scaling laws have been used to overcome this problem. However, most existing models rely upon small sample sizes, geographically restricted sampling and have limited applicability for non-bee taxa. Allometric models that consider biogeography, phylogenetic relatedness, and intraspecific variation are urgently required to ensure greater accuracy. We measured body size as dry weight and intertegular distance (ITD) of 391 bee species (4,035 specimens) and 103 hoverfly species (399 specimens) across four biogeographic regions: Australia, Europe, North America, and South America. We updated existing models within a Bayesian mixed-model framework to test the power of ITD to predict interspecific variation in pollinator dry weight in interaction with different co-variates: phylogeny or taxonomy, sexual dimorphism, and biogeographic region. In addition, we used ordinary least squares regression to assess intraspecific dry weight ~ ITD relationships for ten bees and five hoverfly species. Including co-variates led to more robust interspecific body size predictions for both bees and hoverflies relative to models with the ITD alone. In contrast, at the intraspecific level, our results demonstrate that the ITD is an inconsistent predictor of body size for bees and hoverflies. The use of allometric scaling laws to estimate body size is more suitable for interspecific comparative analyses than assessing intraspecific variation. Collectively, these models form the basis of the dynamic R package, "pollimetry," which provides a comprehensive resource for allometric pollination research worldwide.

Performances of machine learning algorithms for mapping fractional cover of an invasive plant species in a dryland ecosystem.

Abstract: In recent years, an increasing number of distribution maps of invasive alien plant species (IAPS) have been published using different machine learning algorithms (MLAs). However, for designing spatially explicit management strategies, distribution maps should include information on the local cover/abundance of the IAPS. This study compares the performances of five MLAs: gradient boosting machine in two different implementations, random forest, support vector machine and deep learning neural network, one ensemble model and a generalized linear model; thereby identifying the best-performing ones in mapping the fractional cover/abundance and distribution of IPAS, in this case called Prosopis juliflora (SW. DC.). Field level Prosopis cover and spatial datasets of seventeen biophysical and anthropogenic variables were collected, processed, and used to train and validate the algorithms so as to generate fractional cover maps of Prosopis in the dryland ecosystem of the Afar Region, Ethiopia. Out of the seven tested algorithms, random forest performed the best with an accuracy of 92% and sensitivity and specificity >0.89. The next best-performing algorithms were the ensemble model and gradient boosting machine with an accuracy of 89% and 88%, respectively. The other tested algorithms achieved comparably low performances. The strong explanatory variables for Prosopis distributions in all models were NDVI, elevation, distance to villages and distance to rivers; rainfall, temperature, near-infrared and red reflectance, whereas topographic variables, except for elevation, did not contribute much to the current distribution of Prosopis. According to the random forest model, a total of 1.173 million ha (12.33% of the study region) was found to be invaded by Prosopis to varying degrees of cover. Our findings demonstrate that MLAs can be successfully used to develop fractional cover maps of plant species, particularly IAPS so as to design targeted and spatially explicit management strategies.

Animal Scanner: Software for classifying humans, animals, and empty frames in camera trap images

Abstract: Camera traps are a popular tool to sample animal populations because they are noninvasive, detect a variety of species, and can record many thousands of animal detections per deployment. Cameras are typically set to take bursts of multiple photographs for each detection and are deployed in arrays of dozens or hundreds of sites, often resulting in millions of photographs per study. The task of converting photographs to animal detection records from such large image collections is daunting, and made worse by situations that generate copious empty pictures from false triggers (e.g., camera malfunction or moving vegetation) or pictures of humans. We developed computer vision algorithms to detect and classify moving objects to aid the first step of camera trap image filtering-separating the animal detections from the empty frames and pictures of humans. Our new work couples foreground object segmentation through background subtraction with deep learning classification to provide a fast and accurate scheme for human-animal detection. We provide these programs as both Matlab GUI and command prompt developed with C++. The software reads folders of camera trap images and outputs images annotated with bounding boxes around moving objects and a text file summary of results. This software maintains high accuracy while reducing the execution time by 14 times. It takes about 6 seconds to process a sequence of ten frames (on a 2.6 GHZ CPU computer). For those cameras with excessive empty frames due to camera malfunction or blowing vegetation automatically removes 54% of the false-triggers sequences without influencing the human/animal sequences. We achieve 99.58% on image-level empty versus object classification of Serengeti dataset. We offer the first computer vision tool for processing camera trap images providing substantial time savings for processing large image datasets, thus improving our ability to monitor wildlife across large scales with camera traps.

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats.

Abstract: Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free-ranging animals. Rapid land-use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land-use change on wildlife microbiotas, we analyzed long-term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross-species pathogen transmission.

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

Abstract: We wish to extend our greatest thanks to the Seychelles National Parks Authority (SNPA) for unparalleled support across all years in generation of the annual ecological assessments, and sample collection in 2016. Also, we are indebted to the Seychelles Ministry for Environment, Energy and Climate for permitting non-commercial transfer of genetic material of analysis or this publication. We also thank Craig Michell for sequencing library preparation and the KAUST Bioscience Core Lab (BCL) for sequencing. Data collection, analysis and write up was supported by The Earthwatch Institute and the Mitsubishi Corporation (DJSm), an Endeavour Fellowship (EFC), an ARC Discovery Grant (DJSu; DP160100271) as well as a KAUST baseline research funds to CRV

Drought-response strategies of savanna herbivores.

Abstract: Climate models predict increases in drought frequency and severity worldwide, with potential impacts on diverse systems, including African savannas. These droughts pose a concern for the conservation of savanna mammal communities, such that understanding how different species respond to drought is vital.Because grass decreases so consistently during droughts, we predict that grass-dependent species (grazers and mixed feeders) will respond strongly to drought, whether by changing diets, seeking drought refugia, or suffering mortality.A recent severe but heterogeneous drought in Kruger National Park, South Africa, afforded a rare opportunity to test these hypotheses in situ-crucial, given the central role of landscape-scale movement as a potential herbivore strategy. We used herbivore dung as a proxy, integrating spatial distributions (dung counts) with diet composition (carbon isotope analysis of dung).As predicted, browsers showed little response to drought. However, mixed feeders switched their diets to incorporate more C3 trees/forbs, but did not move. Meanwhile, grazers and megaherbivores instead moved toward drought refugia. Synthesis and applications: The responses we observed by savanna herbivores are largely amplifications of typical dry season strategies and reflect constraints imposed by body size and feeding ecology. Grazers may be at particular risk from increased drought frequency and spatial extent if drought refugia become decreasingly available. Conservation strategies should recognize these constraints and work to facilitate the diverse responses of herbivores to drought.