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2,603 results for “Ecological data”
FIG. 7 in The genus Navicordulia Machado & Costa, 1995 (Insecta, Odonata, Corduliidae s.str.): new species, identification key for males and data on ecology and distribution
FIG. 7. — Rock-bottomed stream near locus typicus, Barruol Mounts. Photo by Stéphane Brûlé.
Data from: From environmental DNA sequences to ecological conclusions: how strong is the influence of methodological choices?
Aim: Environmental DNA (eDNA) is increasingly used for analysing and modelling all-inclusive biodiversity patterns. However, the reliability of eDNA-based diversity estimates is commonly compromised by arbitrary decisions for curating the data from molecular artefacts. Here, we test the sensitivity of common ecological analyses to these curation steps, and identify the crucial ones to draw sound ecological conclusions. Location : Valloire, French Alps. Taxon: Vascular plants and Fungi. Methods: Using soil eDNA metabarcoding data for plants and fungi from twenty plots sampled along a 1000-m elevation gradient, we tested how the conclusions from three types of ecological analyses: (i) the spatial partitioning of diversity, (ii) the diversity-environment relationship, and (iii) the distance-decay relationship, are robust to data curation steps. Since eDNA metabarcoding data also comprise erroneous sequences with low frequencies, diversity estimates were further calculated using abundance-based Hill numbers, which penalize rare sequences through a scaling parameter, namely the order of diversity q (Richness with q=0, Shannon diversity with q~1, Simpson diversity with q=2). Results: We showed that results from different ecological analyses had varying degrees of sensitivity to data curation strategies and that the use of Shannon and Simpson diversities led to more reliable results. We demonstrated that MOTU clustering, removal of PCR errors and of cross-sample contaminations had major impacts on ecological analyses. Main conclusions: In the Era of Big Data, eDNA metabarcoding is going to be one of the major tools to describe, model and predict biodiversity in space and time. However, ignoring crucial data curation steps will impede the robustness of several ecological conclusions. Here, we propose a roadmap of crucial curation steps for different types of ecological analyses.
Data from: Effects of livestock grazing on soil, plant functional diversity and ecological traits vary between regions with different climate in northeastern Iran
Understanding the responses of vegetation characteristics and soil properties to grazing in different precipitation regimes is useful for the management of rangelands, especially in the arid regions. In northeastern Iran, we studied the responses of vegetation to livestock grazing in three regions with different climate: arid, semi-arid and sub-humid. In each region, we selected 6-7 pairwise sampling areas of high versus low grazing intensity and six traits of the present species were recorded on 1 m2 plots - 5 grazed and 5 ungrazed in each area. The overall fertility was compared using the dissimilarity analysis, linear mixed-effect models were used to compare the individual fertility parameters, functional diversity indices and species traits between the plots with high and low grazing intensity and between the climatic regions. Both climate and grazing, as well as their interaction, affected fertility parameters, functional diversity indices and the representation of species traits. Grazing reduced functional evenness, height of the community, the representation of annuals, but increased the community leaf area. In the sub-humid region, grazing also reduced functional richness. Further, grazing decreased the share of annual species in the semi-arid region and seed mass in the arid region. Larger leaf area and seed mass, smaller height and lower share of annuals were associated with intensive grazing. Species with large LA and seed mass, lower height and perennials can be therefore presumed to tolerate trampling and benefit from high nutrient levels, associated with intensive grazing. By providing a detailed view on the impacts of overgrazing, this study highlights the importance of protection from grazing as an effective management tool for maintaining the pastoral ecosystems. In general, the composition of plant traits across the pastures of northeastern Iran was more affected by intensive grazing compared to climate.
Data from: Prey fractionation in the Archaeocyatha and its implication for the ecology of the first animal reef systems
Archaeocyaths are the most abundant sponges from the Cambrian period, forming the first animal reef communities over 500 million years ago. The Archaeocyatha are index fossils for correlating rocks of similar ages globally, because of their abundance, extensive geographic distribution, their detailed anatomy and well established taxonomy. Their ecological significance remains incompletely explored yet they are known to strongly competitively interact unlike modern sponges. This study examines the feeding ecology of the fossil remains of Siberian archaeocyath assemblages. As suspension feeders, archaeocyaths filtered plankton from the water column through pores in their outer wall. Here we outline a new method to estimate the limit on the upper size of plankton that could be consumed by an archaeocyath during life. The archaeocyaths examined were predominantly feeding on nanoplankton and microplankton such as phytoplankton and protozooplankton. Size-frequency distributions of pore sizes from six different Siberian archaeocyath assemblages, ranging from Tommotian to Botoman in age, reveal significantly different upper limits to the prey consumed at each locality. Some of the assemblages contain specimens that could have fed on larger organisms extending in to the mesoplankton including micro-invertebrates as a possible food resource. These results show that during the establishment of the first animal reef systems, prey partitioning was established as a way of reducing competition. This method has applicability for understanding the construction and the functioning of the first reef systems, as well as helping to understanding modern reef systems and their development though time and space.
Data from: Imbalance in individual researcher's peer review activities quantified for four British Ecological Society Journals, 2003-2010
Researchers contribute to the scientific peer review system by providing reviews, and "withdraw" from it by submitting manuscripts that are subsequently reviewed. So far as we are aware, there has been no quantification of the balance of individual's contributions and withdrawals. We compared the number of reviews provided by individual researchers (i.e., their contribution) to the number required by their submissions (i.e. their withdrawals) in a large and anonymised database provided by the British Ecological Society. The database covered the Journal of Ecology, Journal of Animal Ecology, Journal of Applied Ecology, and Functional Ecology from 2003–2010. The majority of researchers (64%) did not have balanced contributions and withdrawals. Depending on assumptions, 12% to 44% contributed more than twice as much as required; 20% to 52% contributed less than half as much as required. Balance, or lack thereof, varied little in relation to the number of years a researcher had been active (reviewing or submitting). Researchers who contributed less than required did not lack the opportunity to review. Researchers who submitted more were more likely to accept invitations to review. These finding suggest overall that peer review of the four analysed journals is not in crisis, but only due to the favourable balance of over- and under-contributing researchers. These findings are limited to the four journals analysed, and therefore cannot include researcher's other peer review activities, which if included might change the proportions reported. Relatively low effort was required to assemble, check, and analyse the data. Broader analyses of individual researcher's peer review activities would contribute to greater quality, efficiency, and fairness in the peer review system.
Data from: Genetic consequences of post-glacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus
How does range expansion affect genetic diversity in species with different ecologies, and do different types of genetic markers lead to different conclusions? We addressed these questions by assessing the genetic consequences of post-glacial range expansion using mitochondrial DNA (mtDNA) and nuclear restriction site associated DNA (RAD) sequencing in two congeneric and co-distributed rodents with different ecological characteristics: the desert kangaroo rat (Dipodomys deserti), a sand specialist, and the Merriam's kangaroo rat (D. merriami), a substrate generalist. For each species, we compared genetic variation between populations that retained stable distributions throughout glacial periods and those inferred to have expanded since the last glacial maximum. Our results suggest that expanded populations of both species experienced a loss of private mtDNA haplotypes and differentiation among populations, as well as a loss of nuclear SNP private alleles and polymorphism. However, only D. deserti experienced a loss of nucleotide diversity (both mtDNA and nuclear) and nuclear heterozygosity. For all indices of diversity and differentiation that showed reduced values in the expanded areas, D. deserti populations experienced a greater degree of loss than did D. merriami populations. Additionally, patterns of loss in genetic diversity in expanded populations were substantially less extreme (by two orders of magnitude in some cases) for nuclear SNPs in both species compared to that observed for mitochondrial data. Our results demonstrate that ecological characteristics may play a role in determining genetic variation associated with range expansions, yet mtDNA diversity loss is not necessarily accompanied by a matched magnitude of loss in nuclear diversity.
Data from: Characteristics of pneumonia deaths after earthquake and tsunami: an ecological study of 5.7 million subjects in 131 municipalities, Japan
Objective: On 11 March 2011, the Great East Japan Earthquake struck off Japan. Although some studies showed that the earthquake increased the risk of pneumonia death, no study reported whether and how much tsunami increased the risk. We examined the risk for pneumonia death after the earthquake/tsunami. Design: This is an ecological study. Setting: Data on population and pneumonia deaths obtained from the Vital Statistics 2010 and 2012, National Census 2010 and Basic Resident Register 2010 and 2012 in Japan. Participants: About 5.7 million subjects residing in Miyagi, Iwate and Fukushima Prefectures during 1 year after the disaster were targeted. All municipalities (n=131) were categorized into inland (n=93), that is, the earthquake-impacted area, and coastal types (n=38), that is, the earthquake- and tsunami-impacted area. Outcome measures: The number of pneumonia deaths per week was totaled from 12 March 2010 to 9 March 2012. The number of observed pneumonia deaths (O) and the sum of the sex- and age-classes in the observed population multiplied by the sex- and age-classes of expected pneumonia mortality (E) were calculated. Expected pneumonia mortality was the pneumonia mortality during the year before. Standardized mortality ratios (SMRs) were calculated for pneumonia deaths (O/E), adjusting for sex and age using the indirect method. SMRs were then calculated by coastal and inland municipalities. Results: Six thousand six hundred three subjects died of pneumonia during 1 year after the earthquake. SMRs significantly increased during the 1st to 12th week. In the 2nd week, SMRs in coastal and inland municipalities were 2.49 (95% CI 2.02 to 7.64) and 1.48 (95% CI 1.24 to 2.61), respectively. SMRs of coastal municipalities were higher than those of inland municipalities. Conclusions: Earthquake increased the risk of pneumonia death and tsunamis additionally increased the risk.
Data from: Daphnia galeata and D. dentifera are geographically and ecologically separated whereas their hybrids occur in intermediate habitats: a survey of 44 Chinese lakes
The idea that hybridization promotes range expansion has received recent attention, but support from field studies is limited. We hypothesized that in the cladoceran waterflea Daphnia, parental species are geographically and ecologically separated, whereas hybrids occupy intermediate or occasionally extreme environments, potentially facilitating range expansion of parental species. We assessed the distribution of Daphnia dentifera, D. galeata and their interspecific hybrids across 44 lakes in China (using mitochondrial and microsatellite markers), and related it to geographical and environmental lake descriptors. Parental species were geographically separated: D. dentifera occurred in western and central China, and D. galeata in eastern and central China, whereas hybrids were found in the western and central parts of country. However, after controlling for geographical differences, the effect of environment on species distribution was strong and significant. Specifically, D. dentifera was present in high-altitude oligotrophic lakes, D. galeata in low-altitude eutrophic lakes, and hybrids at intermediate to high altitudes, mainly in mesotrophic lakes. Microsatellite data indicated that hybrids were locally produced rather than having migrated from elsewhere; they probably resulted from encounters between expanding D. galeata and resident D. dentifera. The present study provides evidence that hybrids can survive in habitats that are otherwise suitable for only one of their parental species, emphasizing the importance of hybridization in expansion of species gene pools.
Data from: Phylogenomics supports incongruence between ecological specialization and taxonomy in a charismatic clade of buck moths
Local adaptation can be a fundamental component of speciation, but its dynamics in relation to gene flow are not necessarily straightforward. Herbivorous taxa with localized host plant or habitat specialization across their geographic range are ideal models for investigating the patterns and constraints of local adaptation and its impact on diversification. The charismatic, day-flying moths of the Hemileuca maia species complex (Lepidoptera: Saturniidae) are such taxa, as they are geographically-widespread, exhibit considerable ecological and morphological variability and host and habitat specificity, but apparently lack genetic differentiation across their range. Here, we use genome-wide single nucleotide polymorphisms to assess relationships and population structure of this group across North America, and investigate the scales where genomic divergence correlates with adaptive ecological characteristics. In contrast to previous genetic studies of the group, we find broad- and fine-scale genetic differentiation between lineages, which is at odds with various levels of taxonomic description and recognition of conservation units. Furthermore, ecological specialization only explains some fine-scale genetic differentiation, and across much of the group's range, local adaptation is apparently occurring in the face of strong gene flow. These results provide unprecedented insight into drivers of speciation in this group, the relationship between taxonomy and genomics-informed species boundaries, and conservation management of internationally-protected entities. Broadly, this system provides a model for understanding how local adaptation in an herbivore can arise and be maintained in the face of apparently strong gene flow, and the importance of geographic isolation in generating genomic divergence, despite a lack of ecological divergence.
Data from: Adjustable temperature array for characterising ecological and evolutionary effects on thermal physiology
1. To accurately characterise a species' thermal niche and aid in predicting effects of climate change we must not only include information on thermal tolerances and physiological responses to changing temperatures, but also incorporate ecological effects and evolutionary processes that may shape a species' niche. However, quickly and practically collecting data on key factors such as adaptation potential, behaviour, effects of species interactions, plasticity, and thermal tolerances is logistically challenging. 2. We have therefore created an adjustable temperature array (ATA) to assist with experimental ecology and evolution research. ATA's are a row of independent temperature points controlled and set by the user and made from commercially-available parts. This allows the user to create unique thermal landscapes relevant to their study organism(s) and question(s). Further, the option of using an enclosed cage allows the user to answer questions at the individual, population, or community level in the context of changing thermal environments. ATA's are able to be user-set to constant or dynamic temperature regimes and are designed for use on small animals (e.g., fruit flies, beetles, mosquitoes) or plants (e.g., germinating seeds). 3. We have tested and confirmed the accuracy of the ATA to several thermal landscapes that would be useful for experimental ecology and evolution, including: 1) coarse resolution of a broad thermal niche ranging from 12° to 42°C in 2°C intervals (R2= 0.998); 2) fine resolution of a narrow thermal niche ranging from 15° to 32°C in 1°C intervals (R2= 0.997); 3) a pyramid-shaped niche consisting of a gradient from 14° to 30°C in 2°C intervals (R2 = 0.997); and 4) a very narrow thermal niche with replicate thermal resources ranging from 26.5° to 34°C in 1.5°C. intervals (R2= 0.989). 4. The equipment described here is an important tool for thermal niche studies and will aid in gathering information on effects of ecological and evolutionary processes to create a comprehensive picture of species responses to climate change.
Data from: Sex ratio variation shapes the ecological effects of a globally introduced freshwater fish
Sex ratio and sexual dimorphism have long been of interest in population and evolutionary ecology, but consequences for communities and ecosystems remain untested. Sex ratio could influence ecological conditions whenever sexual dimorphism is associated with ecological dimorphism in species with strong ecological interactions. We tested for ecological implications of sex ratio variation in the sexually dimorphic western mosquitofish, Gambusia affinis. This species causes strong pelagic trophic cascades and exhibits substantial variation in adult sex ratios. We found that female-biased populations induced stronger pelagic trophic cascades compared with male-biased populations, causing larger changes to key community and ecosystem responses, including zooplankton abundance, phytoplankton abundance, productivity, pH and temperature. The magnitude of such effects indicates that sex ratio is important for mediating the ecological role of mosquitofish. Because both sex ratio variation and sexual dimorphism are common features of natural populations, our findings should encourage broader consideration of the ecological significance of sex ratio variation in nature, including the relative contributions of various sexually dimorphic traits to these effects.
Data from: Improved demethylation in ecological epigenetic experiments: testing a simple and harmless foliar demethylation application
1. Experimental demethylation of plant DNA enables testing for epigenetic effects in a simple and straightforward way without the use of expensive and laborious DNA sequencing. Plants are commonly demethylated during their germination with the application of agents such as 5-azacytidine (5-azaC). However, this approach can cause unwanted effects such as underdeveloped root systems and high mortality of treated plants, hindering a full comparison with untreated plants, and can be applied only on plant reproducing by seeds. Here we test a simple alternative method of plant demethylation, designed to overcome the shortcomings of the germinating method. 2. We compared a novel method of demethylating plants, based on periodical spraying of 5-azaC aqueous solution on established seedlings, with the previous method in which seeds were germinated directly in 5-azaC solution. We quantified the amount of methylated DNA and measured various aspects of plant performance. Also, we demonstrated its applicability in ecological epigenetic experiments, by testing transgenerational effects of plant-plant competition. 3. We found that the spray application had similar DNA-demethylating efficiency than the germination method, particularly in the earlier phases of plant development, but without unwanted effects. The spray application method did not reduce plant growth and performance compared to untreated plants, as opposed to the traditional method which showed reduced growth. Also, the spray application method equalized the epigenetically-modified plant features of seedlings coming from plants grown under competition and plants growing without competition, demonstrating its application in ecological epigenetic experiments. 4. We conclude that regular spraying of 5-azaC solution onto established seedlings surpassed the germination-in-solution method in terms of vigor and fitness of treated plants. This novel method could thus be better suited for experimental studies seeking valuable insights into ecological epigenetics. Furthermore, the spray method can be suitable for clonal species reproducing asexually, and, most importantly, it opens the possibility of community-level experimental demethylation of plants.
Data from: Cophylogenetic signal is detectable in pollination interactions across ecological scales
That evolutionary history can influence the way that species interact is a basic tenet of evolutionary ecology. However, when the role of evolution in determining ecological interactions is investigated, focus typically centers on just one side of the interaction. A cophylogenetic signal, the congruence of evolutionary history across both sides of an ecological interaction, extends these previous explorations and provides a more complete picture of how evolutionary patterns influence the way species interact. To date, cophylogenetic signal has most typically been studied in interactions that occur between fine taxonomic clades that show high intimacy. In this study, we took an alternative approach and made an exhaustive assessment of cophylogeny in pollination interactions. To do so, we assessed the strength of cophylogenetic signal at four distinct scales of pollination interaction: (1) across plant–pollinator associations globally, (2) in local pollination communities, (3) within the modular structure of those communities, and (4) in individual modules. We did so using a globally distributed dataset comprised of 54 pollination networks, over 4000 species, and over 12,000 interactions. Within these data, we detected cophylogenetic signal at all four scales. Cophylogenetic signal was found at the level of plant–pollinator interactions on a global scale and in the majority of pollination communities. At the scale defined by the modular structure within those communities, however, we observed a much weaker cophylogenetic signal. Cophylogenetic signal was detectable in a significant proportion of individual modules and most typically when within-module phylogenetic diversity was low. In sum, the detection of cophylogenetic signal in pollination interactions across scales provides a new dimension to the story of how past evolution shapes extant pollinator–angiosperm interactions.
Data from: A new specimen of large-bodied basal enantiornithine Bohaiornis from the early Cretaceous of China and the inference of feeding ecology in Mesozoic birds
A new specimen of Bohaiornis guoi from the Jiufotang Formation, comprising a nearly complete skeleton, sheds light on enantiornithine morphological variation and ecological specialization. The new specimen was collected from near Lamadong Village in Liaoning Province, which is the same area where the sub-adult holotype specimen was reported. It provides new information on the cranial and pectoral girdle anatomy of the species, e.g., broad nasal, strikingly robust acromion, medially curved acrocoracoid process. In contrast to the holotype, the newly referred specimen has small rounded stones in the thoracic region that in other extinct taxa has been interpreted as direct evidence of diet. Direct evidence of diet is so far unknown in other Enantiornithes. Specifically the lack of "stomach stones" or gastroliths in enantiornithines despite their excellent fossil record has been proposed to be related to their insectivorous diet as well as to their arboreal ecology. We hypothesize that cranial morphology as well as the number and shape of the preserved stones in Bohaiornis may be most consistent with a raptorial ecology previously unknown for Enantiornithes and considered rare for Avialae. While rostrum shape has a strong relationship to feeding ecology in living birds, in basal avialan birds most diversity is in dental morphology, number, and distribution of the teeth.
Data from: The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA (mtDNA) indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.
Data from: Testing and interpreting the shared space-environment fraction in variation partitioning analyses of ecological data
Variation partitioning analyses combined with spatial predictors (Moran's eigenvector maps, MEM) are commonly used in ecology to test the fractions of species abundance variation purely explained by environment and space. However, while these pure fractions can be tested using a classical residuals permutation procedure, no specific method has been developed to test the shared space-environment fraction (SSEF). Yet, the SSEF is expected to encompass a major driver of community assembly, that is, an induced spatial dependence effect (ISD; i.e. the reflection of a spatially structured habitat filter on a species distribution). A reliable test of this fraction is therefore crucial to properly test the presence of an ISD on ecological data. To bridge the gap, we propose to test the SSEF through spatially-constrained null models: torus-translations, and Moran spectral randomisations. We investigated the type I error rate and statistical power of our method based on two real environmental datasets and simulations of tree distributions. Ten types of tree distribution displaying contrasted aggregation properties were simulated, and their abundances were sampled in 153 regularly-distributed 20 × 20 m quadrats. The SSEF was tested for 1000 simulated tree distributions either unrelated to the environment, or filtered by environmental variables displaying contrasting spatial structures. The method proposed provided a correct type I error rate (< 0.05). The statistical power was high (> 0.9) when abundances were filtered by an environmental variable structured at broad scale. However, the spatial resolution allowed by the sampling design limited the power of the method when using a fine-scale filtering variable. This highlighted that an ISD can be properly detected providing that the spatial pattern of the filtering process is correctly captured by the sampling design of the study. An R function to apply the SSEF testing method is provided and detailed in a tutorial.
Data from: A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys
Premise of the Study: Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. Methods: Our study included most Tetragonostachys species, using plastid and nuclear sequences, fossil and herbarium records, and climate variables to describe the species diversity, phylogenetic relationships, divergence times, and climatic niche evolution in the subgenus. Key Results: We found that subgenus Tetragonostachys forms a monophyletic group sister to Selaginella lepidophylla and may have diverged from other Selaginella because of a Gondwanan–Laurasian vicariance event ca. 240 mya. The North American radiation of Tetragonostachys appears to be much more recent and to have occurred during the Early Cretaceous–late Paleocene interval. We identified two significant and nested ecological niche shifts during the evolution of Tetragonostachys associated with extreme drought tolerance and a more recent shift to cold climates. Our analyses suggest that drought tolerance evolved in the warm deserts of southwest North America and may have been advantageous for colonization of cold and dry boreal climates. Conclusions: Our investigation provides a foundation for future research addressing the genomics of ecological niche evolution and the potential role of reticulate evolution in Selaginella subgenus Tetragonostachys.
Data from: Forbidden fruit: human settlement and abundant fruit create an ecological trap for an apex omnivore
Habitat choice is an evolutionary product of animals experiencing increased fitness when preferentially occupying high-quality habitat. However, an ecological trap (ET) can occur when an animal is presented with novel conditions and the animal's assessment of habitat quality is poorly matched to its resulting fitness. We tested for an ET for grizzly (brown) bears using demographic and movement data collected in an area with rich food resources and concentrated human settlement. We derived measures of habitat attractiveness from occurrence models of bear food resources and estimated demographic parameters using DNA mark–recapture information collected over 8 years (2006–2013). We then paired this information with grizzly bear mortality records to investigate kill and movement rates. Our results demonstrate that a valley high in both berry resources and human density was more attractive than surrounding areas, and bears occupying this region faced 17% lower apparent survival. Despite lower fitness, we detected a net flow of bears into the ET, which contributed to a study-wide population decline. This work highlights the presence and pervasiveness of an ET for an apex omnivore that lacks the evolutionary cues, under human-induced rapid ecological change, to assess trade-offs between food resources and human-caused mortality, which results in maladaptive habitat selection.
Data from: Machine learning to classify animal species in camera trap images: applications in ecology
Motion‐activated cameras ("camera traps") are increasingly used in ecological and management studies for remotely observing wildlife and are amongst the most powerful tools for wildlife research. However, studies involving camera traps result in millions of images that need to be analysed, typically by visually observing each image, in order to extract data that can be used in ecological analyses. We trained machine learning models using convolutional neural networks with the ResNet‐18 architecture and 3,367,383 images to automatically classify wildlife species from camera trap images obtained from five states across the United States. We tested our model on an independent subset of images not seen during training from the United States and on an out‐of‐sample (or "out‐of‐distribution" in the machine learning literature) dataset of ungulate images from Canada. We also tested the ability of our model to distinguish empty images from those with animals in another out‐of‐sample dataset from Tanzania, containing a faunal community that was novel to the model. The trained model classified approximately 2,000 images per minute on a laptop computer with 16 gigabytes of RAM. The trained model achieved 98% accuracy at identifying species in the United States, the highest accuracy of such a model to date. Out‐of‐sample validation from Canada achieved 82% accuracy and correctly identified 94% of images containing an animal in the dataset from Tanzania. We provide an r package (Machine Learning for Wildlife Image Classification) that allows the users to (a) use the trained model presented here and (b) train their own model using classified images of wildlife from their studies. The use of machine learning to rapidly and accurately classify wildlife in camera trap images can facilitate non‐invasive sampling designs in ecological studies by reducing the burden of manually analysing images. Our r package makes these methods accessible to ecologists.
Data from: The role of recombination, niche-specific gene pools and flexible genomes in the ecological speciation of bacteria
Bacteria diversify into genetic clusters analogous to those observed in sexual eukaryotes, but the definition of bacterial species is an ongoing problem. Recent work has focused on adaptation to distinct ecological niches as the main driver of clustering, but there remains debate about the role of recombination in that process. One view is that homologous recombination occurs too rarely for gene flow to constrain divergent selection. Another view is that homologous recombination is frequent enough in many bacterial populations that barriers to gene flow are needed to permit divergence. Niche‐specific gene pools have been proposed as a general mechanism to limit gene flow. We use theoretical models to evaluate additional hypotheses that evolving genetic architecture, specifically the effect sizes of genes and gene gain and loss, can limit gene flow between diverging populations. Our model predicts that (a) in the presence of gene flow and recombination, ecological divergence is concentrated in few loci of large effect and (b) high rates of gene flow plus recombination promote gene loss and favor the evolution of niche‐specific genes. The results show that changing genetic architecture and gene loss can facilitate ecological divergence, even without niche‐specific gene pools. We discuss these results in the context of recent studies of sympatric divergence in microbes.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.